{
"@id": "./",
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"identifier": "2025_IronAndHemeRegulatoryNetworks",
"title": "Genome-wide analysis of DtxR and HrrA regulons reveals novel targets and a high level of interconnectivity between iron and heme regulatory networks in Corynebacterium glutamicum ",
"description": "Iron is vital for most organisms, serving as cofactor in enzymes, regulatory proteins, and respiratory cytochromes. In Corynebacterium glutamicum, iron and heme homeostasis are tightly interconnected and controlled by the global regulators DtxR and HrrA. While DtxR senses intracellular Fe2+, HrrSA is activated by heme. This study provides the first genome-wide analysis of DtxR and HrrA binding dynamics under varying iron and heme conditions using chromatin affinity purification and sequencing (ChAP-seq). We revealed 25 novel DtxR targets and 210 previously unrecognized HrrA targets. Among these, metH, encoding homocysteine methyltransferase, and xerC, encoding a tyrosine recombinase, were bound by DtxR exclusively under heme conditions, underscoring condition-dependent variation. Activation of metH by DtxR links iron metabolism to methionine synthesis, potentially relevant for the mitigation of oxidative stress. Beyond novel targets, 16 shared targets between DtxR and HrrA, some with overlapping operator sequences, highlight their interconnected regulons. Strikingly, we demonstrate the significance of weak ChAP-Seq peaks that are often disregarded in global approaches, but feature an impact of the regulator on differential gene expression. These findings emphasize the importance of genome-wide profiling under different conditions to uncover novel targets and shed light on the complexity and dynamic nature of bacterial regulatory networks. ",
"submissionDate": "2025-01-16T00:09",
"publications": [
{
"doi": "https://doi.org/10.1111/mmi.15376",
"authorList": "Aileen Kr\u00fcger, Ulrike Weber, Julia Frunzke",
"title": "Genome-wide analysis of DtxR and HrrA regulons reveals novel targets and a high level of interconnectivity between iron and heme regulatory networks in Corynebacterium glutamicum ",
"status": {
"annotationValue": "Accepted in Mol Microbio"
},
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"firstName": "Aileen",
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"affiliation": "IBG-1: Institute of Bio- and Geosciences, Forschungszentrum J\u00fclich GmbH",
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"@id": "0000-0001-6209-7950",
"firstName": "Julia",
"lastName": "Frunzke",
"email": "j.frunzke@fz-juelich.de",
"affiliation": "IBG-1: Institute of Bio- and Geosciences, Forschungszentrum J\u00fclich GmbH",
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{
"@id": "ul.weber@fz-juelich.de",
"firstName": "Ulrike",
"lastName": "Weber",
"email": "ul.weber@fz-juelich.de",
"affiliation": "IBG-1: Institute of Bio- and Geosciences, Forschungszentrum J\u00fclich GmbH"
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},
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{
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{
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"@id": "#UserTerm_20.95%",
"annotationValue": "20.95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
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"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_68,55538_h",
"annotationValue": "68,55538 h"
}
}
],
"inputs": [
{
"@id": "#Material_Strain=C._glutamicum_WT",
"name": "Strain=C. glutamicum WT"
},
{
"@id": "#Sample_Strain=C._glutamicum_WT",
"name": "Strain=C. glutamicum WT",
"characteristics": [
{
"@id": "#MaterialAttributeValue/sample name=WT_standard_3",
"category": {
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"characteristicType": {
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"annotationValue": "sample name",
"termSource": "MS",
"termAccession": "MS:1000002"
}
},
"value": {
"@id": "#UserTerm_WT_standard_3",
"annotationValue": "WT_standard_3"
}
},
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum ATCC13032 WT",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
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"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
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},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032_WT",
"annotationValue": "C. glutamicum ATCC13032 WT"
}
}
]
}
],
"outputs": [
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
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},
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-taggedVariants_3",
"name": "Biolector-taggedVariants_3",
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{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
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"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D5",
"annotationValue": "D5"
}
},
{
"category": {
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"parameterName": {
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"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_",
"annotationValue": "CGXII + 2% glucose "
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_iron_concentration_(FeSO4)",
"parameterName": {
"@id": "#UserTerm_iron_concentration_(FeSO4)",
"annotationValue": "iron concentration (FeSO4)"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M",
"annotationValue": "100 \u00b5M"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_1",
"annotationValue": "1"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(EX:620_nm,_gain:_20)",
"annotationValue": "backscatter (EX:620 nm, gain: 20)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20.95%",
"annotationValue": "20.95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
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"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
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"@id": "#UserTerm_shaker_frequency",
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}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
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},
{
"category": {
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},
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"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
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"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
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"annotationValue": "68,55538 h"
}
}
],
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{
"@id": "#Material_Strain=C._glutamicum_WT",
"name": "Strain=C. glutamicum WT"
},
{
"@id": "#Sample_Strain=C._glutamicum_WT",
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{
"@id": "#MaterialAttributeValue/sample name=WT_ironExcess_1",
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"termAccession": "MS:1000002"
}
},
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}
},
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum ATCC13032 WT",
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},
"value": {
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}
}
]
}
],
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{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
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{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
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}
]
},
{
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{
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},
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},
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},
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},
{
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},
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},
{
"category": {
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},
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},
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}
},
{
"category": {
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},
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},
{
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},
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},
{
"category": {
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},
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},
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},
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},
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},
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},
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},
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}
},
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},
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{
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},
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},
{
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},
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]
},
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},
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},
{
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},
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},
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},
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},
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},
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},
{
"category": {
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},
{
"category": {
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},
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},
{
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},
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},
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},
{
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},
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},
{
"category": {
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},
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}
},
{
"category": {
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},
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}
},
{
"category": {
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}
},
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},
{
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"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_68,55538_h",
"annotationValue": "68,55538 h"
}
}
],
"inputs": [
{
"@id": "#Material_Strain=C._glutamicum_WT",
"name": "Strain=C. glutamicum WT"
},
{
"@id": "#Sample_Strain=C._glutamicum_WT",
"name": "Strain=C. glutamicum WT",
"characteristics": [
{
"@id": "#MaterialAttributeValue/sample name=WT_ironExcess_3",
"category": {
"@id": "#MaterialAttribute/MS:1000002",
"characteristicType": {
"@id": "MS:1000002",
"annotationValue": "sample name",
"termSource": "MS",
"termAccession": "MS:1000002"
}
},
"value": {
"@id": "#UserTerm_WT_ironExcess_3",
"annotationValue": "WT_ironExcess_3"
}
},
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum ATCC13032 WT",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032_WT",
"annotationValue": "C. glutamicum ATCC13032 WT"
}
}
]
}
],
"outputs": [
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
},
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-taggedVariants_6",
"name": "Biolector-taggedVariants_6",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A6",
"annotationValue": "A6"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_",
"annotationValue": "CGXII + 2% glucose "
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_iron_concentration_(FeSO4)",
"parameterName": {
"@id": "#UserTerm_iron_concentration_(FeSO4)",
"annotationValue": "iron concentration (FeSO4)"
}
},
"value": {
"@id": "#UserTerm_36_\u00b5M",
"annotationValue": "36 \u00b5M"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_1",
"annotationValue": "1"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(EX:620_nm,_gain:_20)",
"annotationValue": "backscatter (EX:620 nm, gain: 20)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20.95%",
"annotationValue": "20.95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_68,55538_h",
"annotationValue": "68,55538 h"
}
}
],
"inputs": [
{
"@id": "#Material_Strain=C._glutamicum::dtxR-His-Cterm-2link",
"name": "Strain=C. glutamicum::dtxR-His-Cterm-2link"
},
{
"@id": "#Sample_Strain=C._glutamicum::dtxR-His-Cterm-2link",
"name": "Strain=C. glutamicum::dtxR-His-Cterm-2link",
"characteristics": [
{
"@id": "#MaterialAttributeValue/sample name=DtxR-His-C-2link_standard_1",
"category": {
"@id": "#MaterialAttribute/MS:1000002",
"characteristicType": {
"@id": "MS:1000002",
"annotationValue": "sample name",
"termSource": "MS",
"termAccession": "MS:1000002"
}
},
"value": {
"@id": "#UserTerm_DtxR-His-C-2link_standard_1",
"annotationValue": "DtxR-His-C-2link_standard_1"
}
},
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum ATCC13032::dtxR-His-Cterm-2link",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032::dtxR-His-Cterm-2link",
"annotationValue": "C. glutamicum ATCC13032::dtxR-His-Cterm-2link"
}
}
]
}
],
"outputs": [
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
},
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-taggedVariants_7",
"name": "Biolector-taggedVariants_7",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B6",
"annotationValue": "B6"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
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"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_",
"annotationValue": "CGXII + 2% glucose "
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_iron_concentration_(FeSO4)",
"parameterName": {
"@id": "#UserTerm_iron_concentration_(FeSO4)",
"annotationValue": "iron concentration (FeSO4)"
}
},
"value": {
"@id": "#UserTerm_36_\u00b5M",
"annotationValue": "36 \u00b5M"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
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"parameterName": {
"@id": "DPBO:0000101",
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"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_1",
"annotationValue": "1"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
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"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
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"parameterName": {
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"annotationValue": "filterset"
}
},
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"annotationValue": "backscatter (EX:620 nm, gain: 20)"
}
},
{
"category": {
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"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
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"parameterName": {
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"annotationValue": "humidity",
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"termAccession": "PATO:0015009"
}
},
"value": {
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"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
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}
},
"value": {
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}
},
{
"category": {
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"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
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"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
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}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
"@id": "#UserTerm_30_min",
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}
},
{
"category": {
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}
},
"value": {
"@id": "#UserTerm_68,55538_h",
"annotationValue": "68,55538 h"
}
}
],
"inputs": [
{
"@id": "#Material_Strain=C._glutamicum::dtxR-His-Cterm-2link",
"name": "Strain=C. glutamicum::dtxR-His-Cterm-2link"
},
{
"@id": "#Sample_Strain=C._glutamicum::dtxR-His-Cterm-2link",
"name": "Strain=C. glutamicum::dtxR-His-Cterm-2link",
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{
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},
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},
{
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}
},
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}
]
}
],
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{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
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{
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}
]
},
{
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},
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"annotationValue": "C6"
}
},
{
"category": {
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}
},
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},
{
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}
},
"value": {
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"annotationValue": "36 \u00b5M"
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},
{
"category": {
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}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
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},
{
"category": {
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},
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
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}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
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},
{
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}
},
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},
{
"category": {
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"termAccession": "PATO:0015009"
}
},
"value": {
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}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
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}
},
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}
},
{
"category": {
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"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
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},
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}
},
{
"category": {
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}
},
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},
{
"category": {
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}
},
"value": {
"@id": "#UserTerm_30_min",
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}
},
{
"category": {
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},
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}
],
"inputs": [
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"name": "Strain=C. glutamicum::dtxR-His-Cterm-2link"
},
{
"@id": "#Sample_Strain=C._glutamicum::dtxR-His-Cterm-2link",
"name": "Strain=C. glutamicum::dtxR-His-Cterm-2link",
"characteristics": [
{
"@id": "#MaterialAttributeValue/sample name=DtxR-His-C-2link_standard_3",
"category": {
"@id": "#MaterialAttribute/MS:1000002",
"characteristicType": {
"@id": "MS:1000002",
"annotationValue": "sample name",
"termSource": "MS",
"termAccession": "MS:1000002"
}
},
"value": {
"@id": "#UserTerm_DtxR-His-C-2link_standard_3",
"annotationValue": "DtxR-His-C-2link_standard_3"
}
},
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum ATCC13032::dtxR-His-Cterm-2link",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032::dtxR-His-Cterm-2link",
"annotationValue": "C. glutamicum ATCC13032::dtxR-His-Cterm-2link"
}
}
]
}
],
"outputs": [
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
},
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-taggedVariants_9",
"name": "Biolector-taggedVariants_9",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D6",
"annotationValue": "D6"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_",
"annotationValue": "CGXII + 2% glucose "
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_iron_concentration_(FeSO4)",
"parameterName": {
"@id": "#UserTerm_iron_concentration_(FeSO4)",
"annotationValue": "iron concentration (FeSO4)"
}
},
"value": {
"@id": "#UserTerm_36_\u00b5M",
"annotationValue": "36 \u00b5M"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_1",
"annotationValue": "1"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(EX:620_nm,_gain:_20)",
"annotationValue": "backscatter (EX:620 nm, gain: 20)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20.95%",
"annotationValue": "20.95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_68,55538_h",
"annotationValue": "68,55538 h"
}
}
],
"inputs": [
{
"@id": "#Material_Strain=C._glutamicum::dtxR-Strep-Nterm-2link",
"name": "Strain=C. glutamicum::dtxR-Strep-Nterm-2link"
},
{
"@id": "#Sample_Strain=C._glutamicum::dtxR-Strep-Nterm-2link",
"name": "Strain=C. glutamicum::dtxR-Strep-Nterm-2link",
"characteristics": [
{
"@id": "#MaterialAttributeValue/sample name=DtxR-Strep-C-2link_standard_1",
"category": {
"@id": "#MaterialAttribute/MS:1000002",
"characteristicType": {
"@id": "MS:1000002",
"annotationValue": "sample name",
"termSource": "MS",
"termAccession": "MS:1000002"
}
},
"value": {
"@id": "#UserTerm_DtxR-Strep-C-2link_standard_1",
"annotationValue": "DtxR-Strep-C-2link_standard_1"
}
},
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum ATCC13032::dtxR-Strep-Nterm-2link",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032::dtxR-Strep-Nterm-2link",
"annotationValue": "C. glutamicum ATCC13032::dtxR-Strep-Nterm-2link"
}
}
]
}
],
"outputs": [
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
},
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-taggedVariants_10",
"name": "Biolector-taggedVariants_10",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E6",
"annotationValue": "E6"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_",
"annotationValue": "CGXII + 2% glucose "
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_iron_concentration_(FeSO4)",
"parameterName": {
"@id": "#UserTerm_iron_concentration_(FeSO4)",
"annotationValue": "iron concentration (FeSO4)"
}
},
"value": {
"@id": "#UserTerm_36_\u00b5M",
"annotationValue": "36 \u00b5M"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_1",
"annotationValue": "1"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(EX:620_nm,_gain:_20)",
"annotationValue": "backscatter (EX:620 nm, gain: 20)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
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"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20.95%",
"annotationValue": "20.95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
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"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
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"annotationValue": "shaker frequency"
}
},
"value": {
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"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_68,55538_h",
"annotationValue": "68,55538 h"
}
}
],
"inputs": [
{
"@id": "#Material_Strain=C._glutamicum::dtxR-Strep-Nterm-2link",
"name": "Strain=C. glutamicum::dtxR-Strep-Nterm-2link"
},
{
"@id": "#Sample_Strain=C._glutamicum::dtxR-Strep-Nterm-2link",
"name": "Strain=C. glutamicum::dtxR-Strep-Nterm-2link",
"characteristics": [
{
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}
},
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"annotationValue": "DtxR-Strep-C-2link_standard_2"
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},
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum ATCC13032::dtxR-Strep-Nterm-2link",
"category": {
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"characteristicType": {
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"termSource": "MIAPPE",
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}
},
"value": {
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}
}
]
}
],
"outputs": [
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
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},
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
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"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-taggedVariants_11",
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"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
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"annotationValue": "F6"
}
},
{
"category": {
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"termAccession": "NCIT:C85504"
}
},
"value": {
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},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
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},
{
"category": {
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"termAccession": "DPBO:0000101"
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},
"value": {
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"annotationValue": "1"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
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"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
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},
{
"category": {
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"parameterName": {
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}
},
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},
{
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},
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},
{
"category": {
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"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
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},
"value": {
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}
},
{
"category": {
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"parameterName": {
"@id": "NCIT:C65288",
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"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
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"parameterName": {
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}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
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},
{
"category": {
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}
},
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}
},
{
"category": {
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}
},
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}
],
"inputs": [
{
"@id": "#Material_Strain=C._glutamicum::dtxR-Strep-Nterm-2link",
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},
{
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"characteristics": [
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"characteristicType": {
"@id": "MS:1000002",
"annotationValue": "sample name",
"termSource": "MS",
"termAccession": "MS:1000002"
}
},
"value": {
"@id": "#UserTerm_DtxR-Strep-C-2link_standard_3",
"annotationValue": "DtxR-Strep-C-2link_standard_3"
}
},
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum ATCC13032::dtxR-Strep-Nterm-2link",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032::dtxR-Strep-Nterm-2link",
"annotationValue": "C. glutamicum ATCC13032::dtxR-Strep-Nterm-2link"
}
}
]
}
],
"outputs": [
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
},
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-taggedVariants_12",
"name": "Biolector-taggedVariants_12",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A7",
"annotationValue": "A7"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_",
"annotationValue": "CGXII + 2% glucose "
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_iron_concentration_(FeSO4)",
"parameterName": {
"@id": "#UserTerm_iron_concentration_(FeSO4)",
"annotationValue": "iron concentration (FeSO4)"
}
},
"value": {
"@id": "#UserTerm_36_\u00b5M",
"annotationValue": "36 \u00b5M"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_1",
"annotationValue": "1"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(EX:620_nm,_gain:_20)",
"annotationValue": "backscatter (EX:620 nm, gain: 20)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20.95%",
"annotationValue": "20.95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_68,55538_h",
"annotationValue": "68,55538 h"
}
}
],
"inputs": [
{
"@id": "#Material_Strain=C._glutamicum::dtxR-Strep-Nterm-4link",
"name": "Strain=C. glutamicum::dtxR-Strep-Nterm-4link"
},
{
"@id": "#Sample_Strain=C._glutamicum::dtxR-Strep-Nterm-4link",
"name": "Strain=C. glutamicum::dtxR-Strep-Nterm-4link",
"characteristics": [
{
"@id": "#MaterialAttributeValue/sample name=DtxR-Strep-C-4link_standard_1",
"category": {
"@id": "#MaterialAttribute/MS:1000002",
"characteristicType": {
"@id": "MS:1000002",
"annotationValue": "sample name",
"termSource": "MS",
"termAccession": "MS:1000002"
}
},
"value": {
"@id": "#UserTerm_DtxR-Strep-C-4link_standard_1",
"annotationValue": "DtxR-Strep-C-4link_standard_1"
}
},
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum ATCC13032::dtxR-Strep-Nterm-4link",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032::dtxR-Strep-Nterm-4link",
"annotationValue": "C. glutamicum ATCC13032::dtxR-Strep-Nterm-4link"
}
}
]
}
],
"outputs": [
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
},
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-taggedVariants_13",
"name": "Biolector-taggedVariants_13",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B7",
"annotationValue": "B7"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
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"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_",
"annotationValue": "CGXII + 2% glucose "
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_iron_concentration_(FeSO4)",
"parameterName": {
"@id": "#UserTerm_iron_concentration_(FeSO4)",
"annotationValue": "iron concentration (FeSO4)"
}
},
"value": {
"@id": "#UserTerm_36_\u00b5M",
"annotationValue": "36 \u00b5M"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_1",
"annotationValue": "1"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
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}
},
{
"category": {
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"parameterName": {
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"annotationValue": "filterset"
}
},
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}
},
{
"category": {
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"parameterName": {
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"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
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"parameterName": {
"@id": "PATO:0015009",
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"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
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"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
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}
},
"value": {
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}
},
{
"category": {
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"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
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"termSource": "UO",
"termAccession": "UO:0000196"
}
},
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}
},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
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},
{
"category": {
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}
},
"value": {
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"annotationValue": "68,55538 h"
}
}
],
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{
"@id": "#Material_Strain=C._glutamicum::dtxR-Strep-Nterm-4link",
"name": "Strain=C. glutamicum::dtxR-Strep-Nterm-4link"
},
{
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},
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},
{
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},
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}
]
}
],
"outputs": [
{
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"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
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{
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"type": "Raw Data File"
}
]
},
{
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},
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}
},
{
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},
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},
{
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},
"value": {
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},
{
"category": {
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},
"value": {
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},
{
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},
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
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"annotationValue": "cultivation device"
}
},
"value": {
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}
},
{
"category": {
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},
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},
{
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}
},
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},
{
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},
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}
},
{
"category": {
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},
{
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}
},
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}
},
{
"category": {
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},
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}
},
{
"category": {
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},
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},
{
"category": {
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}
},
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},
{
"category": {
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},
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}
],
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{
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"value": {
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"annotationValue": "DtxR-Strep-C-4link_standard_3"
}
},
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum ATCC13032::dtxR-Strep-Nterm-4link",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032::dtxR-Strep-Nterm-4link",
"annotationValue": "C. glutamicum ATCC13032::dtxR-Strep-Nterm-4link"
}
}
]
}
],
"outputs": [
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
},
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-taggedVariants_15",
"name": "Biolector-taggedVariants_15",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D7",
"annotationValue": "D7"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_",
"annotationValue": "CGXII + 2% glucose "
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_iron_concentration_(FeSO4)",
"parameterName": {
"@id": "#UserTerm_iron_concentration_(FeSO4)",
"annotationValue": "iron concentration (FeSO4)"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M",
"annotationValue": "100 \u00b5M"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_1",
"annotationValue": "1"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(EX:620_nm,_gain:_20)",
"annotationValue": "backscatter (EX:620 nm, gain: 20)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20.95%",
"annotationValue": "20.95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_68,55538_h",
"annotationValue": "68,55538 h"
}
}
],
"inputs": [
{
"@id": "#Material_Strain=C._glutamicum::dtxR-His-Cterm-2link",
"name": "Strain=C. glutamicum::dtxR-His-Cterm-2link"
},
{
"@id": "#Sample_Strain=C._glutamicum::dtxR-His-Cterm-2link",
"name": "Strain=C. glutamicum::dtxR-His-Cterm-2link",
"characteristics": [
{
"@id": "#MaterialAttributeValue/sample name=DtxR-His-C-2link_ironExcess_1",
"category": {
"@id": "#MaterialAttribute/MS:1000002",
"characteristicType": {
"@id": "MS:1000002",
"annotationValue": "sample name",
"termSource": "MS",
"termAccession": "MS:1000002"
}
},
"value": {
"@id": "#UserTerm_DtxR-His-C-2link_ironExcess_1",
"annotationValue": "DtxR-His-C-2link_ironExcess_1"
}
},
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum ATCC13032::dtxR-His-Cterm-2link",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032::dtxR-His-Cterm-2link",
"annotationValue": "C. glutamicum ATCC13032::dtxR-His-Cterm-2link"
}
}
]
}
],
"outputs": [
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
},
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-taggedVariants_16",
"name": "Biolector-taggedVariants_16",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E7",
"annotationValue": "E7"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_",
"annotationValue": "CGXII + 2% glucose "
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_iron_concentration_(FeSO4)",
"parameterName": {
"@id": "#UserTerm_iron_concentration_(FeSO4)",
"annotationValue": "iron concentration (FeSO4)"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M",
"annotationValue": "100 \u00b5M"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
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"parameterName": {
"@id": "DPBO:0000101",
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"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_1",
"annotationValue": "1"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
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"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
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}
},
{
"category": {
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"parameterName": {
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"annotationValue": "filterset"
}
},
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"annotationValue": "backscatter (EX:620 nm, gain: 20)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
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"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
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"@id": "PATO:0015009",
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"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
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}
},
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}
},
{
"category": {
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"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
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"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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"parameterName": {
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}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
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}
}
],
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{
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"name": "Strain=C. glutamicum::dtxR-His-Cterm-2link"
},
{
"@id": "#Sample_Strain=C._glutamicum::dtxR-His-Cterm-2link",
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},
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},
{
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},
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}
]
}
],
"outputs": [
{
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{
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}
]
},
{
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},
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}
},
{
"category": {
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},
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},
{
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}
},
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},
{
"category": {
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},
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},
{
"category": {
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},
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
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}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
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},
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},
{
"category": {
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}
},
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},
{
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},
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},
{
"category": {
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"termAccession": "PATO:0015009"
}
},
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}
},
{
"category": {
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},
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}
},
{
"category": {
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},
"value": {
"@id": "#UserTerm_0%",
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}
},
{
"category": {
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},
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}
},
{
"category": {
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},
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},
{
"category": {
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}
},
"value": {
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},
{
"category": {
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},
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}
],
"inputs": [
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},
{
"@id": "#Sample_Strain=C._glutamicum::dtxR-His-Cterm-2link",
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},
{
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"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032::dtxR-His-Cterm-2link",
"annotationValue": "C. glutamicum ATCC13032::dtxR-His-Cterm-2link"
}
}
]
}
],
"outputs": [
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
},
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-taggedVariants_18",
"name": "Biolector-taggedVariants_18",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A8",
"annotationValue": "A8"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_",
"annotationValue": "CGXII + 2% glucose "
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_iron_concentration_(FeSO4)",
"parameterName": {
"@id": "#UserTerm_iron_concentration_(FeSO4)",
"annotationValue": "iron concentration (FeSO4)"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M",
"annotationValue": "100 \u00b5M"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_1",
"annotationValue": "1"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(EX:620_nm,_gain:_20)",
"annotationValue": "backscatter (EX:620 nm, gain: 20)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20.95%",
"annotationValue": "20.95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_68,55538_h",
"annotationValue": "68,55538 h"
}
}
],
"inputs": [
{
"@id": "#Material_Strain=C._glutamicum::dtxR-Strep-Nterm-2link",
"name": "Strain=C. glutamicum::dtxR-Strep-Nterm-2link"
},
{
"@id": "#Sample_Strain=C._glutamicum::dtxR-Strep-Nterm-2link",
"name": "Strain=C. glutamicum::dtxR-Strep-Nterm-2link",
"characteristics": [
{
"@id": "#MaterialAttributeValue/sample name=DtxR-Strep-C-2link_ironExcess_1",
"category": {
"@id": "#MaterialAttribute/MS:1000002",
"characteristicType": {
"@id": "MS:1000002",
"annotationValue": "sample name",
"termSource": "MS",
"termAccession": "MS:1000002"
}
},
"value": {
"@id": "#UserTerm_DtxR-Strep-C-2link_ironExcess_1",
"annotationValue": "DtxR-Strep-C-2link_ironExcess_1"
}
},
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum ATCC13032::dtxR-Strep-Nterm-2link",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032::dtxR-Strep-Nterm-2link",
"annotationValue": "C. glutamicum ATCC13032::dtxR-Strep-Nterm-2link"
}
}
]
}
],
"outputs": [
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
},
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-taggedVariants_19",
"name": "Biolector-taggedVariants_19",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B8",
"annotationValue": "B8"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_",
"annotationValue": "CGXII + 2% glucose "
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_iron_concentration_(FeSO4)",
"parameterName": {
"@id": "#UserTerm_iron_concentration_(FeSO4)",
"annotationValue": "iron concentration (FeSO4)"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M",
"annotationValue": "100 \u00b5M"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_1",
"annotationValue": "1"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
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"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(EX:620_nm,_gain:_20)",
"annotationValue": "backscatter (EX:620 nm, gain: 20)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
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"termAccession": "NCIT:C722"
}
},
"value": {
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"annotationValue": "20.95%"
}
},
{
"category": {
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"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
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"annotationValue": "not applicable"
}
},
{
"category": {
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"parameterName": {
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}
},
"value": {
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"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
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"annotationValue": "30 min"
}
},
{
"category": {
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"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_68,55538_h",
"annotationValue": "68,55538 h"
}
}
],
"inputs": [
{
"@id": "#Material_Strain=C._glutamicum::dtxR-Strep-Nterm-2link",
"name": "Strain=C. glutamicum::dtxR-Strep-Nterm-2link"
},
{
"@id": "#Sample_Strain=C._glutamicum::dtxR-Strep-Nterm-2link",
"name": "Strain=C. glutamicum::dtxR-Strep-Nterm-2link",
"characteristics": [
{
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"characteristicType": {
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},
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},
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum ATCC13032::dtxR-Strep-Nterm-2link",
"category": {
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"@id": "MIAPPE:0041",
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},
"value": {
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}
]
}
],
"outputs": [
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
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{
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"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-taggedVariants_20",
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}
},
"value": {
"@id": "#UserTerm_C8",
"annotationValue": "C8"
}
},
{
"category": {
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"termAccession": "NCIT:C85504"
}
},
"value": {
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},
{
"category": {
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}
},
"value": {
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},
{
"category": {
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}
},
"value": {
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},
{
"category": {
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},
"value": {
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"annotationValue": "1"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
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"@id": "MS:1001938",
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}
},
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},
{
"category": {
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}
},
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},
{
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},
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},
{
"category": {
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"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
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"annotationValue": "85%"
}
},
{
"category": {
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}
},
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}
},
{
"category": {
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"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
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"termAccession": "UO:0000196"
}
},
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}
},
{
"category": {
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}
},
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}
},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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}
},
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}
],
"inputs": [
{
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},
{
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},
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},
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum ATCC13032::dtxR-Strep-Nterm-2link",
"category": {
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"characteristicType": {
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},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032::dtxR-Strep-Nterm-2link",
"annotationValue": "C. glutamicum ATCC13032::dtxR-Strep-Nterm-2link"
}
}
]
}
],
"outputs": [
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
},
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-taggedVariants_21",
"name": "Biolector-taggedVariants_21",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D8",
"annotationValue": "D8"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_",
"annotationValue": "CGXII + 2% glucose "
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_iron_concentration_(FeSO4)",
"parameterName": {
"@id": "#UserTerm_iron_concentration_(FeSO4)",
"annotationValue": "iron concentration (FeSO4)"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M",
"annotationValue": "100 \u00b5M"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_1",
"annotationValue": "1"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(EX:620_nm,_gain:_20)",
"annotationValue": "backscatter (EX:620 nm, gain: 20)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20.95%",
"annotationValue": "20.95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_68,55538_h",
"annotationValue": "68,55538 h"
}
}
],
"inputs": [
{
"@id": "#Material_Strain=C._glutamicum::dtxR-Strep-Nterm-4link",
"name": "Strain=C. glutamicum::dtxR-Strep-Nterm-4link"
},
{
"@id": "#Sample_Strain=C._glutamicum::dtxR-Strep-Nterm-4link",
"name": "Strain=C. glutamicum::dtxR-Strep-Nterm-4link",
"characteristics": [
{
"@id": "#MaterialAttributeValue/sample name=DtxR-Strep-C-4link_ironExcess_1",
"category": {
"@id": "#MaterialAttribute/MS:1000002",
"characteristicType": {
"@id": "MS:1000002",
"annotationValue": "sample name",
"termSource": "MS",
"termAccession": "MS:1000002"
}
},
"value": {
"@id": "#UserTerm_DtxR-Strep-C-4link_ironExcess_1",
"annotationValue": "DtxR-Strep-C-4link_ironExcess_1"
}
},
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum ATCC13032::dtxR-Strep-Nterm-4link",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032::dtxR-Strep-Nterm-4link",
"annotationValue": "C. glutamicum ATCC13032::dtxR-Strep-Nterm-4link"
}
}
]
}
],
"outputs": [
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
},
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-taggedVariants_22",
"name": "Biolector-taggedVariants_22",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E8",
"annotationValue": "E8"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_",
"annotationValue": "CGXII + 2% glucose "
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_iron_concentration_(FeSO4)",
"parameterName": {
"@id": "#UserTerm_iron_concentration_(FeSO4)",
"annotationValue": "iron concentration (FeSO4)"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M",
"annotationValue": "100 \u00b5M"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_1",
"annotationValue": "1"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
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"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(EX:620_nm,_gain:_20)",
"annotationValue": "backscatter (EX:620 nm, gain: 20)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
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"parameterName": {
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"termAccession": "NCIT:C722"
}
},
"value": {
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"annotationValue": "20.95%"
}
},
{
"category": {
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"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
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"annotationValue": "not applicable"
}
},
{
"category": {
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"parameterName": {
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}
},
"value": {
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"annotationValue": "1200 rpm"
}
},
{
"category": {
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"parameterName": {
"@id": "#UserTerm_cycle_time",
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}
},
"value": {
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"annotationValue": "30 min"
}
},
{
"category": {
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"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_68,55538_h",
"annotationValue": "68,55538 h"
}
}
],
"inputs": [
{
"@id": "#Material_Strain=C._glutamicum::dtxR-Strep-Nterm-4link",
"name": "Strain=C. glutamicum::dtxR-Strep-Nterm-4link"
},
{
"@id": "#Sample_Strain=C._glutamicum::dtxR-Strep-Nterm-4link",
"name": "Strain=C. glutamicum::dtxR-Strep-Nterm-4link",
"characteristics": [
{
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"category": {
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"characteristicType": {
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}
},
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}
},
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum ATCC13032::dtxR-Strep-Nterm-4link",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
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}
},
"value": {
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}
]
}
],
"outputs": [
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
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},
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-taggedVariants_23",
"name": "Biolector-taggedVariants_23",
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{
"category": {
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"parameterName": {
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"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F8",
"annotationValue": "F8"
}
},
{
"category": {
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"parameterName": {
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"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
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},
{
"category": {
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}
},
"value": {
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"annotationValue": "100 \u00b5M"
}
},
{
"category": {
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"parameterName": {
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"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
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},
{
"category": {
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"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
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"annotationValue": "1"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
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"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
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},
{
"category": {
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"parameterName": {
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}
},
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},
{
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}
},
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},
{
"category": {
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"parameterName": {
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"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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"parameterName": {
"@id": "NCIT:C65288",
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"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
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"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
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"parameterName": {
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}
},
"value": {
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"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
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"@id": "#UserTerm_experiment_time",
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}
},
"value": {
"@id": "#UserTerm_68,55538_h",
"annotationValue": "68,55538 h"
}
}
],
"inputs": [
{
"@id": "#Material_Strain=C._glutamicum::dtxR-Strep-Nterm-4link",
"name": "Strain=C. glutamicum::dtxR-Strep-Nterm-4link"
},
{
"@id": "#Sample_Strain=C._glutamicum::dtxR-Strep-Nterm-4link",
"name": "Strain=C. glutamicum::dtxR-Strep-Nterm-4link",
"characteristics": [
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},
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},
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum ATCC13032::dtxR-Strep-Nterm-4link",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
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}
}
]
}
],
"outputs": [
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
},
{
"@id": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"name": "assays/1-1_GrowthMonitoring-taggedVariants/dataset/20210218_BiolectorAK59_raw.csv",
"type": "Raw Data File"
}
]
}
]
}
],
"characteristicCategories": [
{
"@id": "#MaterialAttribute/#UserTerm_parental_strain",
"characteristicType": {
"@id": "#UserTerm_parental_strain",
"annotationValue": "parental strain"
}
},
{
"@id": "#MaterialAttribute/#UserTerm_integration_plasmid",
"characteristicType": {
"@id": "#UserTerm_integration_plasmid",
"annotationValue": "integration plasmid"
}
},
{
"@id": "#MaterialAttribute/#UserTerm_Tag",
"characteristicType": {
"@id": "#UserTerm_Tag",
"annotationValue": "Tag"
}
},
{
"@id": "#MaterialAttribute/#UserTerm_linker",
"characteristicType": {
"@id": "#UserTerm_linker",
"annotationValue": "linker"
}
},
{
"@id": "#MaterialAttribute/#UserTerm_terminus_of_tag",
"characteristicType": {
"@id": "#UserTerm_terminus_of_tag",
"annotationValue": "terminus of tag"
}
}
]
},
{
"@id": "studies/2_ChAP-Seq/",
"filename": "studies/2_ChAP-Seq/isa.study.xlsx",
"identifier": "2_ChAP-Seq",
"title": "Genome-wideBindingProfiling",
"description": "In order to evaluate on the genome-wide binding of DtxR and HrrA, chromatin-affinity purification coupled to sequencing (ChAP-seq) was performed.",
"people": [
{
"@id": "0000-0002-4172-2398",
"firstName": "Aileen",
"lastName": "Kr\u00fcger",
"email": "ai.krueger@fz-juelich.de",
"affiliation": "IBG-1: Institute of Bio- and Geosciences, Forschungszentrum J\u00fclich GmbH",
"comments": [
{
"name": "ORCID",
"value": "0000-0002-4172-2398"
}
]
},
{
"@id": "ul.weber@fz-juelich.de",
"firstName": "Ulrike",
"lastName": "Weber",
"email": "ul.weber@fz-juelich.de",
"affiliation": "IBG-1: Institute of Bio- and Geosciences, Forschungszentrum J\u00fclich GmbH"
},
{
"@id": "0000-0001-6209-7950",
"firstName": "Julia",
"lastName": "Frunzke",
"email": "j.frunzke@fz-juelich.de",
"affiliation": "IBG-1: Institute of Bio- and Geosciences, Forschungszentrum J\u00fclich GmbH",
"comments": [
{
"name": "ORCID",
"value": "0000-0001-6209-7950"
}
]
},
{
"@id": "ul.weber@fz-juelich.de",
"firstName": "Ulrike",
"lastName": "Weber",
"email": "ul.weber@fz-juelich.de",
"affiliation": "IBG-1: Institute of Bio- and Geosciences, Forschungszentrum J\u00fclich GmbH",
"comments": [
{
"name": "performer (ARC:00000168) 2-1_Sequencing and Analysis",
"value": "2-1_Sequencing and Analysis"
}
]
},
{
"@id": "ai.krueger@fz-juelich.de",
"firstName": "Aileen",
"lastName": "Kr\u00fcger",
"email": "ai.krueger@fz-juelich.de",
"affiliation": "Forschungszentrum J\u00fclich GmbH",
"comments": [
{
"name": "performer (ARC:00000168) 2-1_Sequencing and Analysis",
"value": "2-1_Sequencing and Analysis"
}
]
}
],
"materials": {
"samples": [
{
"@id": "#Sample_DtxR_iron1",
"name": "DtxR_iron1"
},
{
"@id": "#Sample_DtxR_iron1_culture",
"name": "DtxR_iron1_culture"
},
{
"@id": "#Sample_DtxR_iron2",
"name": "DtxR_iron2"
},
{
"@id": "#Sample_DtxR_iron2_culture",
"name": "DtxR_iron2_culture"
},
{
"@id": "#Sample_DtxR_iron3",
"name": "DtxR_iron3"
},
{
"@id": "#Sample_DtxR_iron3_culture",
"name": "DtxR_iron3_culture"
},
{
"@id": "#Sample_HrrA_iron1",
"name": "HrrA_iron1"
},
{
"@id": "#Sample_HrrA_iron1_culture",
"name": "HrrA_iron1_culture"
},
{
"@id": "#Sample_HrrA_iron2",
"name": "HrrA_iron2"
},
{
"@id": "#Sample_HrrA_iron2_culture",
"name": "HrrA_iron2_culture"
},
{
"@id": "#Sample_HrrA_iron3",
"name": "HrrA_iron3"
},
{
"@id": "#Sample_HrrA_iron3_culture",
"name": "HrrA_iron3_culture"
},
{
"@id": "#Sample_DtxR_heme1",
"name": "DtxR_heme1"
},
{
"@id": "#Sample_DtxR_heme1_culture",
"name": "DtxR_heme1_culture"
},
{
"@id": "#Sample_DtxR_heme2",
"name": "DtxR_heme2"
},
{
"@id": "#Sample_DtxR_heme2_culture",
"name": "DtxR_heme2_culture"
},
{
"@id": "#Sample_DtxR_heme3",
"name": "DtxR_heme3"
},
{
"@id": "#Sample_DtxR_heme3_culture",
"name": "DtxR_heme3_culture"
},
{
"@id": "#Sample_HrrA_heme1",
"name": "HrrA_heme1"
},
{
"@id": "#Sample_HrrA_heme1_culture",
"name": "HrrA_heme1_culture"
},
{
"@id": "#Sample_HrrA_heme2",
"name": "HrrA_heme2"
},
{
"@id": "#Sample_HrrA_heme2_culture",
"name": "HrrA_heme2_culture"
},
{
"@id": "#Sample_HrrA_heme3",
"name": "HrrA_heme3"
},
{
"@id": "#Sample_HrrA_heme3_culture",
"name": "HrrA_heme3_culture"
},
{
"@id": "#Sample_DtxR_starvation1",
"name": "DtxR_starvation1"
},
{
"@id": "#Sample_DtxR_starvation1_culture",
"name": "DtxR_starvation1_culture"
},
{
"@id": "#Sample_DtxR_starvation2",
"name": "DtxR_starvation2"
},
{
"@id": "#Sample_DtxR_starvation2_culture",
"name": "DtxR_starvation2_culture"
},
{
"@id": "#Sample_DtxR_starvation3",
"name": "DtxR_starvation3"
},
{
"@id": "#Sample_DtxR_starvation3_culture",
"name": "DtxR_starvation3_culture"
},
{
"@id": "#Sample_HrrA_starvation1",
"name": "HrrA_starvation1"
},
{
"@id": "#Sample_HrrA_starvation1_culture",
"name": "HrrA_starvation1_culture"
},
{
"@id": "#Sample_HrrA_starvation2",
"name": "HrrA_starvation2"
},
{
"@id": "#Sample_HrrA_starvation2_culture",
"name": "HrrA_starvation2_culture"
},
{
"@id": "#Sample_HrrA_starvation3",
"name": "HrrA_starvation3"
},
{
"@id": "#Sample_HrrA_starvation3_culture",
"name": "HrrA_starvation3_culture"
},
{
"@id": "#Sample_His_background1",
"name": "His_background1"
},
{
"@id": "#Sample_His_background1_culture",
"name": "His_background1_culture"
},
{
"@id": "#Sample_His_background2",
"name": "His_background2"
},
{
"@id": "#Sample_His_background2_culture",
"name": "His_background2_culture"
},
{
"@id": "#Sample_His_background3",
"name": "His_background3"
},
{
"@id": "#Sample_His_background3_culture",
"name": "His_background3_culture"
},
{
"@id": "#Sample_Strep_background1",
"name": "Strep_background1"
},
{
"@id": "#Sample_Strep_background1_culture",
"name": "Strep_background1_culture"
},
{
"@id": "#Sample_Strep_background2",
"name": "Strep_background2"
},
{
"@id": "#Sample_Strep_background2_culture",
"name": "Strep_background2_culture"
},
{
"@id": "#Sample_Strep_background3",
"name": "Strep_background3"
},
{
"@id": "#Sample_Strep_background3_culture",
"name": "Strep_background3_culture"
}
]
},
"processSequence": [
{
"@id": "#Process_Sample_preparation_0",
"name": "Sample preparation_0",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C14250",
"parameterName": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITaxon_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITaxon",
"termAccession": "http://purl.obolibrary.org/obo/NCBITaxon_196627"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C95501",
"parameterName": {
"@id": "NCIT:C95501",
"annotationValue": "Strain",
"termSource": "NCIT",
"termAccession": "NCIT:C95501"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032::dtxR-C-linker-His",
"annotationValue": "C. glutamicum ATCC13032::dtxR-C-linker-His"
}
},
{
"category": {
"@id": "#ProtocolParameter/MI:0507",
"parameterName": {
"@id": "MI:0507",
"annotationValue": "tag",
"termSource": "MI",
"termAccession": "MI:0507"
}
},
"value": {
"@id": "#UserTerm_DtxR,_C-terminal_His_Tag,_including_linker_(2x_GGGS)",
"annotationValue": "DtxR, C-terminal His Tag, including linker (2x GGGS)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Main_cultivation_condition",
"parameterName": {
"@id": "#UserTerm_Main_cultivation_condition",
"annotationValue": "Main cultivation condition"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%(w/v)_glucose_+_MgSO4_+_CaCl2_+_Biotin_+_PCA_+_trace_elements_with_100_\u00b5M_FeSO4",
"annotationValue": "CGXII + 2%(w/v) glucose + MgSO4 + CaCl2 + Biotin + PCA + trace elements with 100 \u00b5M FeSO4"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_iron_source",
"parameterName": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Cultivation_volume",
"parameterName": {
"@id": "#UserTerm_Cultivation_volume",
"annotationValue": "Cultivation volume"
}
},
"value": 5.0,
"unit": {
"@id": "https://bioregistry.io/UO:0000099",
"annotationValue": "liter",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000099"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_end_OD600",
"parameterName": {
"@id": "#UserTerm_end_OD600",
"annotationValue": "end OD600"
}
},
"value": {
"@id": "#UserTerm_7.24",
"annotationValue": "7.24"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Timepoint_Harvesting",
"parameterName": {
"@id": "#UserTerm_Timepoint_Harvesting",
"annotationValue": "Timepoint Harvesting"
}
},
"value": 2,
"unit": {
"@id": "#UserTerm_hours",
"annotationValue": "hours"
}
}
],
"inputs": [
{
"@id": "#Sample_DtxR_iron1",
"name": "DtxR_iron1"
}
],
"outputs": [
{
"@id": "#Sample_DtxR_iron1_culture",
"name": "DtxR_iron1_culture"
}
]
},
{
"@id": "#Process_Sample_preparation_1",
"name": "Sample preparation_1",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C14250",
"parameterName": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITaxon_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITaxon",
"termAccession": "http://purl.obolibrary.org/obo/NCBITaxon_196627"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C95501",
"parameterName": {
"@id": "NCIT:C95501",
"annotationValue": "Strain",
"termSource": "NCIT",
"termAccession": "NCIT:C95501"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032::dtxR-C-linker-His",
"annotationValue": "C. glutamicum ATCC13032::dtxR-C-linker-His"
}
},
{
"category": {
"@id": "#ProtocolParameter/MI:0507",
"parameterName": {
"@id": "MI:0507",
"annotationValue": "tag",
"termSource": "MI",
"termAccession": "MI:0507"
}
},
"value": {
"@id": "#UserTerm_DtxR,_C-terminal_His_Tag,_including_linker_(2x_GGGS)",
"annotationValue": "DtxR, C-terminal His Tag, including linker (2x GGGS)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Main_cultivation_condition",
"parameterName": {
"@id": "#UserTerm_Main_cultivation_condition",
"annotationValue": "Main cultivation condition"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%(w/v)_glucose_+_MgSO4_+_CaCl2_+_Biotin_+_PCA_+_trace_elements_with_100_\u00b5M_FeSO4",
"annotationValue": "CGXII + 2%(w/v) glucose + MgSO4 + CaCl2 + Biotin + PCA + trace elements with 100 \u00b5M FeSO4"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_iron_source",
"parameterName": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Cultivation_volume",
"parameterName": {
"@id": "#UserTerm_Cultivation_volume",
"annotationValue": "Cultivation volume"
}
},
"value": 5.0,
"unit": {
"@id": "https://bioregistry.io/UO:0000099",
"annotationValue": "liter",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000099"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_end_OD600",
"parameterName": {
"@id": "#UserTerm_end_OD600",
"annotationValue": "end OD600"
}
},
"value": {
"@id": "#UserTerm_7.42",
"annotationValue": "7.42"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Timepoint_Harvesting",
"parameterName": {
"@id": "#UserTerm_Timepoint_Harvesting",
"annotationValue": "Timepoint Harvesting"
}
},
"value": 2,
"unit": {
"@id": "#UserTerm_hours",
"annotationValue": "hours"
}
}
],
"inputs": [
{
"@id": "#Sample_DtxR_iron2",
"name": "DtxR_iron2"
}
],
"outputs": [
{
"@id": "#Sample_DtxR_iron2_culture",
"name": "DtxR_iron2_culture"
}
]
},
{
"@id": "#Process_Sample_preparation_2",
"name": "Sample preparation_2",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C14250",
"parameterName": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITaxon_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITaxon",
"termAccession": "http://purl.obolibrary.org/obo/NCBITaxon_196627"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C95501",
"parameterName": {
"@id": "NCIT:C95501",
"annotationValue": "Strain",
"termSource": "NCIT",
"termAccession": "NCIT:C95501"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032::dtxR-C-linker-His",
"annotationValue": "C. glutamicum ATCC13032::dtxR-C-linker-His"
}
},
{
"category": {
"@id": "#ProtocolParameter/MI:0507",
"parameterName": {
"@id": "MI:0507",
"annotationValue": "tag",
"termSource": "MI",
"termAccession": "MI:0507"
}
},
"value": {
"@id": "#UserTerm_DtxR,_C-terminal_His_Tag,_including_linker_(2x_GGGS)",
"annotationValue": "DtxR, C-terminal His Tag, including linker (2x GGGS)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Main_cultivation_condition",
"parameterName": {
"@id": "#UserTerm_Main_cultivation_condition",
"annotationValue": "Main cultivation condition"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%(w/v)_glucose_+_MgSO4_+_CaCl2_+_Biotin_+_PCA_+_trace_elements_with_100_\u00b5M_FeSO4",
"annotationValue": "CGXII + 2%(w/v) glucose + MgSO4 + CaCl2 + Biotin + PCA + trace elements with 100 \u00b5M FeSO4"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_iron_source",
"parameterName": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Cultivation_volume",
"parameterName": {
"@id": "#UserTerm_Cultivation_volume",
"annotationValue": "Cultivation volume"
}
},
"value": 5.0,
"unit": {
"@id": "https://bioregistry.io/UO:0000099",
"annotationValue": "liter",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000099"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_end_OD600",
"parameterName": {
"@id": "#UserTerm_end_OD600",
"annotationValue": "end OD600"
}
},
"value": {
"@id": "#UserTerm_5.98",
"annotationValue": "5.98"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Timepoint_Harvesting",
"parameterName": {
"@id": "#UserTerm_Timepoint_Harvesting",
"annotationValue": "Timepoint Harvesting"
}
},
"value": 2,
"unit": {
"@id": "#UserTerm_hours",
"annotationValue": "hours"
}
}
],
"inputs": [
{
"@id": "#Sample_DtxR_iron3",
"name": "DtxR_iron3"
}
],
"outputs": [
{
"@id": "#Sample_DtxR_iron3_culture",
"name": "DtxR_iron3_culture"
}
]
},
{
"@id": "#Process_Sample_preparation_3",
"name": "Sample preparation_3",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C14250",
"parameterName": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITaxon_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITaxon",
"termAccession": "http://purl.obolibrary.org/obo/NCBITaxon_196627"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C95501",
"parameterName": {
"@id": "NCIT:C95501",
"annotationValue": "Strain",
"termSource": "NCIT",
"termAccession": "NCIT:C95501"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032::hrrA-C-twinstrep",
"annotationValue": "C. glutamicum ATCC13032::hrrA-C-twinstrep"
}
},
{
"category": {
"@id": "#ProtocolParameter/MI:0507",
"parameterName": {
"@id": "MI:0507",
"annotationValue": "tag",
"termSource": "MI",
"termAccession": "MI:0507"
}
},
"value": {
"@id": "#UserTerm_HrrA,_C-terminal_Twinstrep_Tag",
"annotationValue": "HrrA, C-terminal Twinstrep Tag"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Main_cultivation_condition",
"parameterName": {
"@id": "#UserTerm_Main_cultivation_condition",
"annotationValue": "Main cultivation condition"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%(w/v)_glucose_+_MgSO4_+_CaCl2_+_Biotin_+_PCA_+_trace_elements_with_100_\u00b5M_FeSO4",
"annotationValue": "CGXII + 2%(w/v) glucose + MgSO4 + CaCl2 + Biotin + PCA + trace elements with 100 \u00b5M FeSO4"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_iron_source",
"parameterName": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
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},
{
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},
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},
{
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},
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},
{
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},
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},
{
"category": {
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},
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"annotationValue": "hours"
}
}
],
"inputs": [
{
"@id": "#Sample_HrrA_iron1",
"name": "HrrA_iron1"
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],
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{
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}
]
},
{
"@id": "#Process_Sample_preparation_4",
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},
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},
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},
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},
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},
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{
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},
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},
{
"category": {
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},
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"annotationValue": "hours"
}
}
],
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{
"@id": "#Sample_HrrA_iron2",
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},
{
"@id": "#Process_Sample_preparation_5",
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},
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},
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},
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},
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},
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{
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}
},
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}
},
{
"category": {
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"parameterName": {
"@id": "#UserTerm_Main_cultivation_condition",
"annotationValue": "Main cultivation condition"
}
},
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},
{
"category": {
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},
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},
{
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}
},
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},
{
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},
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}
},
{
"category": {
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},
"value": {
"@id": "#UserTerm_5.92",
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}
},
{
"category": {
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},
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}
}
],
"inputs": [
{
"@id": "#Sample_HrrA_heme1",
"name": "HrrA_heme1"
}
],
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{
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"name": "HrrA_heme1_culture"
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]
},
{
"@id": "#Process_Sample_preparation_10",
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{
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},
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},
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},
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},
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},
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},
{
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},
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},
{
"category": {
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},
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},
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},
{
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},
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},
{
"category": {
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}
},
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}
}
],
"inputs": [
{
"@id": "#Sample_HrrA_heme2",
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],
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]
},
{
"@id": "#Process_Sample_preparation_11",
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},
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},
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},
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},
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},
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},
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},
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},
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},
{
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},
{
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}
],
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],
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},
{
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],
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],
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},
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],
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],
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},
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},
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},
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},
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},
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}
],
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],
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},
{
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},
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{
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"name": "assays/2-1_Sequencing and Analysis/dataset/1_RawReads/Starvation/DtxR_Starvation.7z",
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{
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{
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{
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{
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{
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{
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},
{
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{
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},
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"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITaxon",
"termAccession": "http://purl.obolibrary.org/obo/NCBITaxon_196627"
}
},
{
"@id": "#MaterialAttributeValue/strain=C. glutamicum ATCC13032 (WT)",
"category": {
"@id": "#MaterialAttribute/EFO:0005135",
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"annotationValue": "strain",
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_ATCC13032_(WT)",
"annotationValue": "C. glutamicum ATCC13032 (WT)"
}
},
{
"@id": "#MaterialAttributeValue/next generation sequencing instrument model=Illumina MiSeq",
"category": {
"@id": "#MaterialAttribute/DPBO:0000040",
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}
},
"value": {
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}
}
]
},
{
"@id": "#Source_Strep_background3_culture",
"name": "Strep_background3_culture",
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{
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"category": {
"@id": "#MaterialAttribute/NCIT:C14250",
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}
},
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"termAccession": "http://purl.obolibrary.org/obo/NCBITaxon_196627"
}
},
{
"@id": "#MaterialAttributeValue/strain=C. glutamicum ATCC13032 (WT)",
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}
},
"value": {
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}
},
{
"@id": "#MaterialAttributeValue/next generation sequencing instrument model=Illumina MiSeq",
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}
},
"value": {
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}
]
}
],
"outputs": [
{
"@id": "assays/2-1_Sequencing_and_Analysis/dataset/1_RawReads/Background/Strep-Background.7z",
"name": "assays/2-1_Sequencing and Analysis/dataset/1_RawReads/Background/Strep-Background.7z",
"type": "Raw Data File"
},
{
"@id": "assays/2-1_Sequencing_and_Analysis/dataset/1_RawReads/Background/Strep-Background.7z",
"name": "assays/2-1_Sequencing and Analysis/dataset/1_RawReads/Background/Strep-Background.7z",
"type": "Raw Data File"
},
{
"@id": "assays/2-1_Sequencing_and_Analysis/dataset/1_RawReads/Background/Strep-Background.7z",
"name": "assays/2-1_Sequencing and Analysis/dataset/1_RawReads/Background/Strep-Background.7z",
"type": "Raw Data File"
}
]
}
]
}
],
"unitCategories": [
{
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"annotationValue": "liter",
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"termAccession": "https://bioregistry.io/UO:0000099"
},
{
"@id": "#UserTerm_hours",
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}
]
},
{
"@id": "studies/3_ReporterStrainGeneration/",
"filename": "studies/3_ReporterStrainGeneration/isa.study.xlsx",
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"title": "Reporter Assay Strain Generation",
"description": "In order to evaluate on ChAP-Seq targets, it is required to couple it to expression data. To investigate on the influence of DtxR on the respective new targets (where expression data for these targets was not evaluable from former microarrays (Wennerhold et al. 2006, Brune et al. 2006) as well as being able to check this at different conditions and deletion mutants, we want to perform reporter assays on selected genes. The overall idea about choosing genes was to choose each strong, middle and weak binding peaks for each the iron excess condition and the heme condition.",
"people": [
{
"@id": "ul.weber@fz-juelich.de",
"firstName": "Ulrike",
"lastName": "Weber",
"email": "ul.weber@fz-juelich.de",
"affiliation": "Forschungszentrum J\u00fclich GmbH"
},
{
"@id": "0000-0001-7060-4879",
"firstName": "Aileen",
"lastName": "Kr\u00fcger",
"email": "ai.krueger@fz-juelich.de",
"affiliation": "Forschungszentrum J\u00fclich GmbH",
"comments": [
{
"name": "ORCID",
"value": "0000-0001-7060-4879"
}
]
}
],
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{
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},
{
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},
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},
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},
{
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},
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},
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},
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},
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},
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},
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}
},
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},
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},
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}
},
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},
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}
},
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},
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},
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}
},
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}
},
{
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},
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},
{
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}
},
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},
{
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}
},
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{
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}
},
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}
},
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},
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{
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},
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}
},
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}
},
{
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}
},
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}
},
{
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}
},
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}
},
{
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]
},
{
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}
},
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}
},
{
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}
},
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},
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}
},
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}
},
{
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}
},
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},
{
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},
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},
{
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},
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}
},
{
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"category": {
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}
},
"value": {
"@id": "#UserTerm_ATGATATCTCCTTCTTAAAGTTCATGTTGAGCCTTGCGGAGTGG",
"annotationValue": "ATGATATCTCCTTCTTAAAGTTCATGTTGAGCCTTGCGGAGTGG"
}
},
{
"@id": "#MaterialAttributeValue/primer forward_venus insert=TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_forward_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_forward_venus_insert",
"annotationValue": "primer forward_venus insert"
}
},
"value": {
"@id": "#UserTerm_TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
"annotationValue": "TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA"
}
},
{
"@id": "#MaterialAttributeValue/primer reverse_venus insert=AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_reverse_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_reverse_venus_insert",
"annotationValue": "primer reverse_venus insert"
}
},
"value": {
"@id": "#UserTerm_AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
"annotationValue": "AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC"
}
},
{
"@id": "#MaterialAttributeValue/Template=Corynebacterium glutamicum ATCC 13032",
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"@id": "#MaterialAttribute/NCIT:C45677",
"characteristicType": {
"@id": "NCIT:C45677",
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}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
}
]
},
{
"@id": "#Source_ReporterPlasmidCloning_Input_7",
"name": "ReporterPlasmidCloning_Input_7",
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{
"@id": "#MaterialAttributeValue/primer forward=AGCGACGCCGCAGGGGGATCCTATCCAAACTCATCCGCTGCAGTTT",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_forward",
"characteristicType": {
"@id": "#UserTerm_primer_forward",
"annotationValue": "primer forward"
}
},
"value": {
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"annotationValue": "AGCGACGCCGCAGGGGGATCCTATCCAAACTCATCCGCTGCAGTTT"
}
},
{
"@id": "#MaterialAttributeValue/primer reverse=ATGATATCTCCTTCTTAAAGTTCAACGGGCGGCGTCAGTTAAC",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_reverse",
"characteristicType": {
"@id": "#UserTerm_primer_reverse",
"annotationValue": "primer reverse"
}
},
"value": {
"@id": "#UserTerm_ATGATATCTCCTTCTTAAAGTTCAACGGGCGGCGTCAGTTAAC",
"annotationValue": "ATGATATCTCCTTCTTAAAGTTCAACGGGCGGCGTCAGTTAAC"
}
},
{
"@id": "#MaterialAttributeValue/primer forward_venus insert=TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_forward_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_forward_venus_insert",
"annotationValue": "primer forward_venus insert"
}
},
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"@id": "#UserTerm_TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
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}
},
{
"@id": "#MaterialAttributeValue/primer reverse_venus insert=AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
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"@id": "#UserTerm_primer_reverse_venus_insert",
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}
},
"value": {
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}
},
{
"@id": "#MaterialAttributeValue/Template=Corynebacterium glutamicum ATCC 13032",
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},
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}
}
]
},
{
"@id": "#Source_ReporterPlasmidCloning_Input_8",
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{
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}
},
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}
},
{
"@id": "#MaterialAttributeValue/primer reverse=ATGATATCTCCTTCTTAAAGTTCAATCGTGGAGTCTTCTAAATTTTCGAGT",
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"@id": "#UserTerm_primer_reverse",
"annotationValue": "primer reverse"
}
},
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}
},
{
"@id": "#MaterialAttributeValue/primer forward_venus insert=TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
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}
},
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}
},
{
"@id": "#MaterialAttributeValue/primer reverse_venus insert=AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
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}
},
"value": {
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}
},
{
"@id": "#MaterialAttributeValue/Template=Corynebacterium glutamicum ATCC 13032",
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}
},
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}
}
]
},
{
"@id": "#Source_ReporterPlasmidCloning_Input_9",
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}
},
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}
},
{
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}
},
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}
},
{
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},
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}
},
{
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}
},
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}
},
{
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}
]
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{
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}
},
{
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},
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}
},
{
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}
},
{
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},
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}
},
{
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"name": "pJC1-PNCgl1781-venus"
},
{
"@id": "#Sample_pJC1-PxerC-venus",
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{
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},
{
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},
{
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},
{
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},
{
"@id": "#Sample_pJC1-PNCgl1451-venus",
"name": "pJC1-PNCgl1451-venus"
},
{
"@id": "#Sample_pJC1-PNCgl0176-venus",
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},
{
"@id": "#Sample_pJC1-PNCgl0177-venus",
"name": "pJC1-PNCgl0177-venus"
},
{
"@id": "#Sample_pJC1-PgyrB-venus",
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},
{
"@id": "#Sample_pJC1-Pwzy-venus",
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},
{
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}
},
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}
},
{
"@id": "#MaterialAttributeValue/Parental strain=WT",
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"annotationValue": "Parental strain"
}
},
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}
}
]
},
{
"@id": "#Sample_pJC1-PNCgl1781-venus",
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}
},
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}
},
{
"@id": "#MaterialAttributeValue/Parental strain=DdtxR",
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"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
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}
},
"value": {
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}
}
]
},
{
"@id": "#Sample_pJC1-PxerC-venus",
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}
},
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}
},
{
"@id": "#MaterialAttributeValue/Parental strain=WT",
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}
},
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}
}
]
},
{
"@id": "#Sample_pJC1-PxerC-venus",
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{
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}
},
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}
},
{
"@id": "#MaterialAttributeValue/Parental strain=DdtxR",
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}
},
"value": {
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}
}
]
},
{
"@id": "#Sample_pJC1-Pqor3-venus",
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{
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}
},
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}
},
{
"@id": "#MaterialAttributeValue/Parental strain=WT",
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}
},
"value": {
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}
}
]
},
{
"@id": "#Sample_pJC1-Pqor3-venus",
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{
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}
},
"value": {
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}
},
{
"@id": "#MaterialAttributeValue/Parental strain=DdtxR",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
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}
}
]
},
{
"@id": "#Sample_pJC1-PcepA-venus",
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{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
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"characteristicType": {
"@id": "NCIT:C14250",
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}
},
"value": {
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"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
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}
},
{
"@id": "#MaterialAttributeValue/Parental strain=WT",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
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}
}
]
},
{
"@id": "#Sample_pJC1-PcepA-venus",
"name": "pJC1-PcepA-venus",
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{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
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}
},
"value": {
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"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=DdtxR",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
"@id": "#UserTerm_DdtxR",
"annotationValue": "DdtxR"
}
}
]
},
{
"@id": "#Sample_pJC1-PNCgl2766-venus",
"name": "pJC1-PNCgl2766-venus",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=WT",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
"@id": "#UserTerm_WT",
"annotationValue": "WT"
}
}
]
},
{
"@id": "#Sample_pJC1-PNCgl2766-venus",
"name": "pJC1-PNCgl2766-venus",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=DdtxR",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
"@id": "#UserTerm_DdtxR",
"annotationValue": "DdtxR"
}
}
]
},
{
"@id": "#Sample_pJC1-PmetH-venus",
"name": "pJC1-PmetH-venus",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=WT",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
"@id": "#UserTerm_WT",
"annotationValue": "WT"
}
}
]
},
{
"@id": "#Sample_pJC1-PmetH-venus",
"name": "pJC1-PmetH-venus",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=DdtxR",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
"@id": "#UserTerm_DdtxR",
"annotationValue": "DdtxR"
}
}
]
},
{
"@id": "#Sample_pJC1-PNCgl1451-venus",
"name": "pJC1-PNCgl1451-venus",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=WT",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
"@id": "#UserTerm_WT",
"annotationValue": "WT"
}
}
]
},
{
"@id": "#Sample_pJC1-PNCgl1451-venus",
"name": "pJC1-PNCgl1451-venus",
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{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=DdtxR",
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"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
"@id": "#UserTerm_DdtxR",
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}
}
]
},
{
"@id": "#Sample_pJC1-PNCgl0176-venus",
"name": "pJC1-PNCgl0176-venus",
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{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
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"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
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"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=WT",
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"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
"@id": "#UserTerm_WT",
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}
}
]
},
{
"@id": "#Sample_pJC1-PNCgl0176-venus",
"name": "pJC1-PNCgl0176-venus",
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{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
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"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
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}
},
{
"@id": "#MaterialAttributeValue/Parental strain=DdtxR",
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"@id": "#UserTerm_Parental_strain",
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}
},
"value": {
"@id": "#UserTerm_DdtxR",
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}
}
]
},
{
"@id": "#Sample_pJC1-PNCgl0177-venus",
"name": "pJC1-PNCgl0177-venus",
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{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
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"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
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}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
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}
},
{
"@id": "#MaterialAttributeValue/Parental strain=WT",
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}
},
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}
}
]
},
{
"@id": "#Sample_pJC1-PNCgl0177-venus",
"name": "pJC1-PNCgl0177-venus",
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{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
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"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
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}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=DdtxR",
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"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
"@id": "#UserTerm_DdtxR",
"annotationValue": "DdtxR"
}
}
]
},
{
"@id": "#Sample_pJC1-PgyrB-venus",
"name": "pJC1-PgyrB-venus",
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{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
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"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
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}
},
{
"@id": "#MaterialAttributeValue/Parental strain=WT",
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"@id": "#UserTerm_Parental_strain",
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}
},
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}
}
]
},
{
"@id": "#Sample_pJC1-PgyrB-venus",
"name": "pJC1-PgyrB-venus",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
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}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=DdtxR",
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}
},
"value": {
"@id": "#UserTerm_DdtxR",
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}
}
]
},
{
"@id": "#Sample_pJC1-Pwzy-venus",
"name": "pJC1-Pwzy-venus",
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{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=WT",
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"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
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}
},
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}
}
]
},
{
"@id": "#Sample_pJC1-Pwzy-venus",
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{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
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"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
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"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
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}
},
{
"@id": "#MaterialAttributeValue/Parental strain=DdtxR",
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}
},
"value": {
"@id": "#UserTerm_DdtxR",
"annotationValue": "DdtxR"
}
}
]
},
{
"@id": "#Sample_WT-NCgl1781",
"name": "WT-NCgl1781"
},
{
"@id": "#Sample_DdtxR-NCgl1781",
"name": "DdtxR-NCgl1781"
},
{
"@id": "#Sample_WT-xerC",
"name": "WT-xerC"
},
{
"@id": "#Sample_DdtxR-xerC",
"name": "DdtxR-xerC"
},
{
"@id": "#Sample_WT-qor3",
"name": "WT-qor3"
},
{
"@id": "#Sample_DdtxR-qor3",
"name": "DdtxR-qor3"
},
{
"@id": "#Sample_WT-cepA",
"name": "WT-cepA"
},
{
"@id": "#Sample_DdtxR-cepA",
"name": "DdtxR-cepA"
},
{
"@id": "#Sample_WT-NCgl2766",
"name": "WT-NCgl2766"
},
{
"@id": "#Sample_DdtxR-NCgl2766",
"name": "DdtxR-NCgl2766"
},
{
"@id": "#Sample_WT-metH",
"name": "WT-metH"
},
{
"@id": "#Sample_DdtxR-metH",
"name": "DdtxR-metH"
},
{
"@id": "#Sample_WT-NCgl1451",
"name": "WT-NCgl1451"
},
{
"@id": "#Sample_DdtxR-NCgl1451",
"name": "DdtxR-NCgl1451"
},
{
"@id": "#Sample_WT-NCgl0176",
"name": "WT-NCgl0176"
},
{
"@id": "#Sample_DdtxR-NCgl0176",
"name": "DdtxR-NCgl0176"
},
{
"@id": "#Sample_WT-NCgl0177",
"name": "WT-NCgl0177"
},
{
"@id": "#Sample_DdtxR-NCgl0177",
"name": "DdtxR-NCgl0177"
},
{
"@id": "#Sample_WT-gyrB",
"name": "WT-gyrB"
},
{
"@id": "#Sample_DdtxR-gyrB",
"name": "DdtxR-gyrB"
},
{
"@id": "#Sample_WT-wzy",
"name": "WT-wzy"
},
{
"@id": "#Sample_DdtxR-wzy",
"name": "DdtxR-wzy"
}
]
},
"processSequence": [
{
"@id": "#Process_ReporterPlasmidCloning_0",
"name": "ReporterPlasmidCloning_0",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Gene_of_interest",
"parameterName": {
"@id": "#UserTerm_Gene_of_interest",
"annotationValue": "Gene of interest"
}
},
"value": {
"@id": "#UserTerm_NCgl1781",
"annotationValue": "NCgl1781"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Plasmid_backbone",
"parameterName": {
"@id": "#UserTerm_Plasmid_backbone",
"annotationValue": "Plasmid backbone"
}
},
"value": {
"@id": "#UserTerm_pJC1-venus-term-BS",
"annotationValue": "pJC1-venus-term-BS"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Backbone_restriction",
"parameterName": {
"@id": "#UserTerm_Backbone_restriction",
"annotationValue": "Backbone restriction"
}
},
"value": {
"@id": "#UserTerm_BamHI/BcuI",
"annotationValue": "BamHI/BcuI"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Insert_Amplification",
"parameterName": {
"@id": "#UserTerm_Insert_Amplification",
"annotationValue": "Insert Amplification"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_34079",
"annotationValue": "PCR",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Strategy",
"parameterName": {
"@id": "#UserTerm_Strategy",
"annotationValue": "Strategy"
}
},
"value": {
"@id": "#UserTerm_Gibson_Assembly",
"annotationValue": "Gibson Assembly"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Amplification_of_plasmid",
"parameterName": {
"@id": "#UserTerm_Amplification_of_plasmid",
"annotationValue": "Amplification of plasmid"
}
},
"value": {
"@id": "#UserTerm_Transformation_of_E._coli_DH5a_via_heat_shock",
"annotationValue": "Transformation of E. coli DH5a via heat shock"
}
}
],
"inputs": [
{
"@id": "#Source_ReporterPlasmidCloning_Input_0",
"name": "ReporterPlasmidCloning_Input_0",
"characteristics": [
{
"@id": "#MaterialAttributeValue/primer forward=AGCGACGCCGCAGGGGGATCCTCCAATACAAGCGCTGCTACC",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_forward",
"characteristicType": {
"@id": "#UserTerm_primer_forward",
"annotationValue": "primer forward"
}
},
"value": {
"@id": "#UserTerm_AGCGACGCCGCAGGGGGATCCTCCAATACAAGCGCTGCTACC",
"annotationValue": "AGCGACGCCGCAGGGGGATCCTCCAATACAAGCGCTGCTACC"
}
},
{
"@id": "#MaterialAttributeValue/primer reverse=ATGATATCTCCTTCTTAAAGTTCATGCAGGGGCTGGGGTATCAG",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_reverse",
"characteristicType": {
"@id": "#UserTerm_primer_reverse",
"annotationValue": "primer reverse"
}
},
"value": {
"@id": "#UserTerm_ATGATATCTCCTTCTTAAAGTTCATGCAGGGGCTGGGGTATCAG",
"annotationValue": "ATGATATCTCCTTCTTAAAGTTCATGCAGGGGCTGGGGTATCAG"
}
},
{
"@id": "#MaterialAttributeValue/primer forward_venus insert=TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_forward_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_forward_venus_insert",
"annotationValue": "primer forward_venus insert"
}
},
"value": {
"@id": "#UserTerm_TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
"annotationValue": "TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA"
}
},
{
"@id": "#MaterialAttributeValue/primer reverse_venus insert=AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_reverse_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_reverse_venus_insert",
"annotationValue": "primer reverse_venus insert"
}
},
"value": {
"@id": "#UserTerm_AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
"annotationValue": "AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC"
}
},
{
"@id": "#MaterialAttributeValue/Template=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C45677",
"characteristicType": {
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"annotationValue": "Template",
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}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_pJC1-PNCgl1781-venus",
"name": "pJC1-PNCgl1781-venus"
}
]
},
{
"@id": "#Process_ReporterPlasmidCloning_1",
"name": "ReporterPlasmidCloning_1",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Gene_of_interest",
"parameterName": {
"@id": "#UserTerm_Gene_of_interest",
"annotationValue": "Gene of interest"
}
},
"value": {
"@id": "#UserTerm_xerC",
"annotationValue": "xerC"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Plasmid_backbone",
"parameterName": {
"@id": "#UserTerm_Plasmid_backbone",
"annotationValue": "Plasmid backbone"
}
},
"value": {
"@id": "#UserTerm_pJC1-venus-term-BS",
"annotationValue": "pJC1-venus-term-BS"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Backbone_restriction",
"parameterName": {
"@id": "#UserTerm_Backbone_restriction",
"annotationValue": "Backbone restriction"
}
},
"value": {
"@id": "#UserTerm_BamHI/BcuI",
"annotationValue": "BamHI/BcuI"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Insert_Amplification",
"parameterName": {
"@id": "#UserTerm_Insert_Amplification",
"annotationValue": "Insert Amplification"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_34079",
"annotationValue": "PCR",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Strategy",
"parameterName": {
"@id": "#UserTerm_Strategy",
"annotationValue": "Strategy"
}
},
"value": {
"@id": "#UserTerm_Gibson_Assembly",
"annotationValue": "Gibson Assembly"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Amplification_of_plasmid",
"parameterName": {
"@id": "#UserTerm_Amplification_of_plasmid",
"annotationValue": "Amplification of plasmid"
}
},
"value": {
"@id": "#UserTerm_Transformation_of_E._coli_DH5a_via_heat_shock",
"annotationValue": "Transformation of E. coli DH5a via heat shock"
}
}
],
"inputs": [
{
"@id": "#Source_ReporterPlasmidCloning_Input_1",
"name": "ReporterPlasmidCloning_Input_1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/primer forward=AGCGACGCCGCAGGGGGATCGAGTATCGCTACCGAAGCCG",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_forward",
"characteristicType": {
"@id": "#UserTerm_primer_forward",
"annotationValue": "primer forward"
}
},
"value": {
"@id": "#UserTerm_AGCGACGCCGCAGGGGGATCGAGTATCGCTACCGAAGCCG",
"annotationValue": "AGCGACGCCGCAGGGGGATCGAGTATCGCTACCGAAGCCG"
}
},
{
"@id": "#MaterialAttributeValue/primer reverse=ATGATATCTCCTTCTTAAAGTTCAACGCGCCACCTTCTTTTTTGACTC",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_reverse",
"characteristicType": {
"@id": "#UserTerm_primer_reverse",
"annotationValue": "primer reverse"
}
},
"value": {
"@id": "#UserTerm_ATGATATCTCCTTCTTAAAGTTCAACGCGCCACCTTCTTTTTTGACTC",
"annotationValue": "ATGATATCTCCTTCTTAAAGTTCAACGCGCCACCTTCTTTTTTGACTC"
}
},
{
"@id": "#MaterialAttributeValue/primer forward_venus insert=TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_forward_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_forward_venus_insert",
"annotationValue": "primer forward_venus insert"
}
},
"value": {
"@id": "#UserTerm_TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
"annotationValue": "TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA"
}
},
{
"@id": "#MaterialAttributeValue/primer reverse_venus insert=AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_reverse_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_reverse_venus_insert",
"annotationValue": "primer reverse_venus insert"
}
},
"value": {
"@id": "#UserTerm_AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
"annotationValue": "AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC"
}
},
{
"@id": "#MaterialAttributeValue/Template=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C45677",
"characteristicType": {
"@id": "NCIT:C45677",
"annotationValue": "Template",
"termSource": "NCIT",
"termAccession": "NCIT:C45677"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_pJC1-PxerC-venus",
"name": "pJC1-PxerC-venus"
}
]
},
{
"@id": "#Process_ReporterPlasmidCloning_2",
"name": "ReporterPlasmidCloning_2",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Gene_of_interest",
"parameterName": {
"@id": "#UserTerm_Gene_of_interest",
"annotationValue": "Gene of interest"
}
},
"value": {
"@id": "#UserTerm_qor3",
"annotationValue": "qor3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Plasmid_backbone",
"parameterName": {
"@id": "#UserTerm_Plasmid_backbone",
"annotationValue": "Plasmid backbone"
}
},
"value": {
"@id": "#UserTerm_pJC1-venus-term-BS",
"annotationValue": "pJC1-venus-term-BS"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Backbone_restriction",
"parameterName": {
"@id": "#UserTerm_Backbone_restriction",
"annotationValue": "Backbone restriction"
}
},
"value": {
"@id": "#UserTerm_BamHI/BcuI",
"annotationValue": "BamHI/BcuI"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Insert_Amplification",
"parameterName": {
"@id": "#UserTerm_Insert_Amplification",
"annotationValue": "Insert Amplification"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_34079",
"annotationValue": "PCR",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Strategy",
"parameterName": {
"@id": "#UserTerm_Strategy",
"annotationValue": "Strategy"
}
},
"value": {
"@id": "#UserTerm_Gibson_Assembly",
"annotationValue": "Gibson Assembly"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Amplification_of_plasmid",
"parameterName": {
"@id": "#UserTerm_Amplification_of_plasmid",
"annotationValue": "Amplification of plasmid"
}
},
"value": {
"@id": "#UserTerm_Transformation_of_E._coli_DH5a_via_heat_shock",
"annotationValue": "Transformation of E. coli DH5a via heat shock"
}
}
],
"inputs": [
{
"@id": "#Source_ReporterPlasmidCloning_Input_2",
"name": "ReporterPlasmidCloning_Input_2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/primer forward=AGCGACGCCGCAGGGGGATCCTATGTGCCTGCGCCACATTCTG",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_forward",
"characteristicType": {
"@id": "#UserTerm_primer_forward",
"annotationValue": "primer forward"
}
},
"value": {
"@id": "#UserTerm_AGCGACGCCGCAGGGGGATCCTATGTGCCTGCGCCACATTCTG",
"annotationValue": "AGCGACGCCGCAGGGGGATCCTATGTGCCTGCGCCACATTCTG"
}
},
{
"@id": "#MaterialAttributeValue/primer reverse=ATGATATCTCCTTCTTAAAGTTCAGGGATCAGGGGTATCCATTTGC",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_reverse",
"characteristicType": {
"@id": "#UserTerm_primer_reverse",
"annotationValue": "primer reverse"
}
},
"value": {
"@id": "#UserTerm_ATGATATCTCCTTCTTAAAGTTCAGGGATCAGGGGTATCCATTTGC",
"annotationValue": "ATGATATCTCCTTCTTAAAGTTCAGGGATCAGGGGTATCCATTTGC"
}
},
{
"@id": "#MaterialAttributeValue/primer forward_venus insert=TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_forward_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_forward_venus_insert",
"annotationValue": "primer forward_venus insert"
}
},
"value": {
"@id": "#UserTerm_TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
"annotationValue": "TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA"
}
},
{
"@id": "#MaterialAttributeValue/primer reverse_venus insert=AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_reverse_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_reverse_venus_insert",
"annotationValue": "primer reverse_venus insert"
}
},
"value": {
"@id": "#UserTerm_AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
"annotationValue": "AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC"
}
},
{
"@id": "#MaterialAttributeValue/Template=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C45677",
"characteristicType": {
"@id": "NCIT:C45677",
"annotationValue": "Template",
"termSource": "NCIT",
"termAccession": "NCIT:C45677"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_pJC1-Pqor3-venus",
"name": "pJC1-Pqor3-venus"
}
]
},
{
"@id": "#Process_ReporterPlasmidCloning_3",
"name": "ReporterPlasmidCloning_3",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Gene_of_interest",
"parameterName": {
"@id": "#UserTerm_Gene_of_interest",
"annotationValue": "Gene of interest"
}
},
"value": {
"@id": "#UserTerm_cepA",
"annotationValue": "cepA"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Plasmid_backbone",
"parameterName": {
"@id": "#UserTerm_Plasmid_backbone",
"annotationValue": "Plasmid backbone"
}
},
"value": {
"@id": "#UserTerm_pJC1-venus-term-BS",
"annotationValue": "pJC1-venus-term-BS"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Backbone_restriction",
"parameterName": {
"@id": "#UserTerm_Backbone_restriction",
"annotationValue": "Backbone restriction"
}
},
"value": {
"@id": "#UserTerm_BamHI/BcuI",
"annotationValue": "BamHI/BcuI"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Insert_Amplification",
"parameterName": {
"@id": "#UserTerm_Insert_Amplification",
"annotationValue": "Insert Amplification"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_34079",
"annotationValue": "PCR",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Strategy",
"parameterName": {
"@id": "#UserTerm_Strategy",
"annotationValue": "Strategy"
}
},
"value": {
"@id": "#UserTerm_Gibson_Assembly",
"annotationValue": "Gibson Assembly"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Amplification_of_plasmid",
"parameterName": {
"@id": "#UserTerm_Amplification_of_plasmid",
"annotationValue": "Amplification of plasmid"
}
},
"value": {
"@id": "#UserTerm_Transformation_of_E._coli_DH5a_via_heat_shock",
"annotationValue": "Transformation of E. coli DH5a via heat shock"
}
}
],
"inputs": [
{
"@id": "#Source_ReporterPlasmidCloning_Input_3",
"name": "ReporterPlasmidCloning_Input_3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/primer forward=AGCGACGCCGCAGGGGGATCGGCTACCAGCTGAGTTAGATTGATAAC",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_forward",
"characteristicType": {
"@id": "#UserTerm_primer_forward",
"annotationValue": "primer forward"
}
},
"value": {
"@id": "#UserTerm_AGCGACGCCGCAGGGGGATCGGCTACCAGCTGAGTTAGATTGATAAC",
"annotationValue": "AGCGACGCCGCAGGGGGATCGGCTACCAGCTGAGTTAGATTGATAAC"
}
},
{
"@id": "#MaterialAttributeValue/primer reverse=ATGATATCTCCTTCTTAAAGTTCACCGTGCTTCGGGCGCGGT",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_reverse",
"characteristicType": {
"@id": "#UserTerm_primer_reverse",
"annotationValue": "primer reverse"
}
},
"value": {
"@id": "#UserTerm_ATGATATCTCCTTCTTAAAGTTCACCGTGCTTCGGGCGCGGT",
"annotationValue": "ATGATATCTCCTTCTTAAAGTTCACCGTGCTTCGGGCGCGGT"
}
},
{
"@id": "#MaterialAttributeValue/primer forward_venus insert=TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_forward_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_forward_venus_insert",
"annotationValue": "primer forward_venus insert"
}
},
"value": {
"@id": "#UserTerm_TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
"annotationValue": "TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA"
}
},
{
"@id": "#MaterialAttributeValue/primer reverse_venus insert=AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_reverse_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_reverse_venus_insert",
"annotationValue": "primer reverse_venus insert"
}
},
"value": {
"@id": "#UserTerm_AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
"annotationValue": "AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC"
}
},
{
"@id": "#MaterialAttributeValue/Template=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C45677",
"characteristicType": {
"@id": "NCIT:C45677",
"annotationValue": "Template",
"termSource": "NCIT",
"termAccession": "NCIT:C45677"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_pJC1-PcepA-venus",
"name": "pJC1-PcepA-venus"
}
]
},
{
"@id": "#Process_ReporterPlasmidCloning_4",
"name": "ReporterPlasmidCloning_4",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Gene_of_interest",
"parameterName": {
"@id": "#UserTerm_Gene_of_interest",
"annotationValue": "Gene of interest"
}
},
"value": {
"@id": "#UserTerm_NCgl2766",
"annotationValue": "NCgl2766"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Plasmid_backbone",
"parameterName": {
"@id": "#UserTerm_Plasmid_backbone",
"annotationValue": "Plasmid backbone"
}
},
"value": {
"@id": "#UserTerm_pJC1-venus-term-BS",
"annotationValue": "pJC1-venus-term-BS"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Backbone_restriction",
"parameterName": {
"@id": "#UserTerm_Backbone_restriction",
"annotationValue": "Backbone restriction"
}
},
"value": {
"@id": "#UserTerm_BamHI/BcuI",
"annotationValue": "BamHI/BcuI"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Insert_Amplification",
"parameterName": {
"@id": "#UserTerm_Insert_Amplification",
"annotationValue": "Insert Amplification"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_34079",
"annotationValue": "PCR",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Strategy",
"parameterName": {
"@id": "#UserTerm_Strategy",
"annotationValue": "Strategy"
}
},
"value": {
"@id": "#UserTerm_Gibson_Assembly",
"annotationValue": "Gibson Assembly"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Amplification_of_plasmid",
"parameterName": {
"@id": "#UserTerm_Amplification_of_plasmid",
"annotationValue": "Amplification of plasmid"
}
},
"value": {
"@id": "#UserTerm_Transformation_of_E._coli_DH5a_via_heat_shock",
"annotationValue": "Transformation of E. coli DH5a via heat shock"
}
}
],
"inputs": [
{
"@id": "#Source_ReporterPlasmidCloning_Input_4",
"name": "ReporterPlasmidCloning_Input_4",
"characteristics": [
{
"@id": "#MaterialAttributeValue/primer forward=AGCGACGCCGCAGGGGGATCCACATCCCCACGTTACCCCA",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_forward",
"characteristicType": {
"@id": "#UserTerm_primer_forward",
"annotationValue": "primer forward"
}
},
"value": {
"@id": "#UserTerm_AGCGACGCCGCAGGGGGATCCACATCCCCACGTTACCCCA",
"annotationValue": "AGCGACGCCGCAGGGGGATCCACATCCCCACGTTACCCCA"
}
},
{
"@id": "#MaterialAttributeValue/primer reverse=ATGATATCTCCTTCTTAAAGTTCATTTGGTCGAAGAAGGAGTGGGC",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_reverse",
"characteristicType": {
"@id": "#UserTerm_primer_reverse",
"annotationValue": "primer reverse"
}
},
"value": {
"@id": "#UserTerm_ATGATATCTCCTTCTTAAAGTTCATTTGGTCGAAGAAGGAGTGGGC",
"annotationValue": "ATGATATCTCCTTCTTAAAGTTCATTTGGTCGAAGAAGGAGTGGGC"
}
},
{
"@id": "#MaterialAttributeValue/primer forward_venus insert=TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_forward_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_forward_venus_insert",
"annotationValue": "primer forward_venus insert"
}
},
"value": {
"@id": "#UserTerm_TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
"annotationValue": "TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA"
}
},
{
"@id": "#MaterialAttributeValue/primer reverse_venus insert=AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_reverse_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_reverse_venus_insert",
"annotationValue": "primer reverse_venus insert"
}
},
"value": {
"@id": "#UserTerm_AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
"annotationValue": "AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC"
}
},
{
"@id": "#MaterialAttributeValue/Template=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C45677",
"characteristicType": {
"@id": "NCIT:C45677",
"annotationValue": "Template",
"termSource": "NCIT",
"termAccession": "NCIT:C45677"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_pJC1-PNCgl2766-venus",
"name": "pJC1-PNCgl2766-venus"
}
]
},
{
"@id": "#Process_ReporterPlasmidCloning_5",
"name": "ReporterPlasmidCloning_5",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Gene_of_interest",
"parameterName": {
"@id": "#UserTerm_Gene_of_interest",
"annotationValue": "Gene of interest"
}
},
"value": {
"@id": "#UserTerm_metH",
"annotationValue": "metH"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Plasmid_backbone",
"parameterName": {
"@id": "#UserTerm_Plasmid_backbone",
"annotationValue": "Plasmid backbone"
}
},
"value": {
"@id": "#UserTerm_pJC1-venus-term-BS",
"annotationValue": "pJC1-venus-term-BS"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Backbone_restriction",
"parameterName": {
"@id": "#UserTerm_Backbone_restriction",
"annotationValue": "Backbone restriction"
}
},
"value": {
"@id": "#UserTerm_BamHI/BcuI",
"annotationValue": "BamHI/BcuI"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Insert_Amplification",
"parameterName": {
"@id": "#UserTerm_Insert_Amplification",
"annotationValue": "Insert Amplification"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_34079",
"annotationValue": "PCR",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Strategy",
"parameterName": {
"@id": "#UserTerm_Strategy",
"annotationValue": "Strategy"
}
},
"value": {
"@id": "#UserTerm_Gibson_Assembly",
"annotationValue": "Gibson Assembly"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Amplification_of_plasmid",
"parameterName": {
"@id": "#UserTerm_Amplification_of_plasmid",
"annotationValue": "Amplification of plasmid"
}
},
"value": {
"@id": "#UserTerm_Transformation_of_E._coli_DH5a_via_heat_shock",
"annotationValue": "Transformation of E. coli DH5a via heat shock"
}
}
],
"inputs": [
{
"@id": "#Source_ReporterPlasmidCloning_Input_5",
"name": "ReporterPlasmidCloning_Input_5",
"characteristics": [
{
"@id": "#MaterialAttributeValue/primer forward=AGCGACGCCGCAGGGGGATCCTAAGAGGTGGCTTTTACGTCGTCAAG",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_forward",
"characteristicType": {
"@id": "#UserTerm_primer_forward",
"annotationValue": "primer forward"
}
},
"value": {
"@id": "#UserTerm_AGCGACGCCGCAGGGGGATCCTAAGAGGTGGCTTTTACGTCGTCAAG",
"annotationValue": "AGCGACGCCGCAGGGGGATCCTAAGAGGTGGCTTTTACGTCGTCAAG"
}
},
{
"@id": "#MaterialAttributeValue/primer reverse=ATGATATCTCCTTCTTAAAGTTCAGGTGCCCATGGCGCCGTC",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_reverse",
"characteristicType": {
"@id": "#UserTerm_primer_reverse",
"annotationValue": "primer reverse"
}
},
"value": {
"@id": "#UserTerm_ATGATATCTCCTTCTTAAAGTTCAGGTGCCCATGGCGCCGTC",
"annotationValue": "ATGATATCTCCTTCTTAAAGTTCAGGTGCCCATGGCGCCGTC"
}
},
{
"@id": "#MaterialAttributeValue/primer forward_venus insert=TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_forward_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_forward_venus_insert",
"annotationValue": "primer forward_venus insert"
}
},
"value": {
"@id": "#UserTerm_TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
"annotationValue": "TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA"
}
},
{
"@id": "#MaterialAttributeValue/primer reverse_venus insert=AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_reverse_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_reverse_venus_insert",
"annotationValue": "primer reverse_venus insert"
}
},
"value": {
"@id": "#UserTerm_AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
"annotationValue": "AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC"
}
},
{
"@id": "#MaterialAttributeValue/Template=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C45677",
"characteristicType": {
"@id": "NCIT:C45677",
"annotationValue": "Template",
"termSource": "NCIT",
"termAccession": "NCIT:C45677"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_pJC1-PmetH-venus",
"name": "pJC1-PmetH-venus"
}
]
},
{
"@id": "#Process_ReporterPlasmidCloning_6",
"name": "ReporterPlasmidCloning_6",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Gene_of_interest",
"parameterName": {
"@id": "#UserTerm_Gene_of_interest",
"annotationValue": "Gene of interest"
}
},
"value": {
"@id": "#UserTerm_NCgl1451",
"annotationValue": "NCgl1451"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Plasmid_backbone",
"parameterName": {
"@id": "#UserTerm_Plasmid_backbone",
"annotationValue": "Plasmid backbone"
}
},
"value": {
"@id": "#UserTerm_pJC1-venus-term-BS",
"annotationValue": "pJC1-venus-term-BS"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Backbone_restriction",
"parameterName": {
"@id": "#UserTerm_Backbone_restriction",
"annotationValue": "Backbone restriction"
}
},
"value": {
"@id": "#UserTerm_BamHI/BcuI",
"annotationValue": "BamHI/BcuI"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Insert_Amplification",
"parameterName": {
"@id": "#UserTerm_Insert_Amplification",
"annotationValue": "Insert Amplification"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_34079",
"annotationValue": "PCR",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Strategy",
"parameterName": {
"@id": "#UserTerm_Strategy",
"annotationValue": "Strategy"
}
},
"value": {
"@id": "#UserTerm_Gibson_Assembly",
"annotationValue": "Gibson Assembly"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Amplification_of_plasmid",
"parameterName": {
"@id": "#UserTerm_Amplification_of_plasmid",
"annotationValue": "Amplification of plasmid"
}
},
"value": {
"@id": "#UserTerm_Transformation_of_E._coli_DH5a_via_heat_shock",
"annotationValue": "Transformation of E. coli DH5a via heat shock"
}
}
],
"inputs": [
{
"@id": "#Source_ReporterPlasmidCloning_Input_6",
"name": "ReporterPlasmidCloning_Input_6",
"characteristics": [
{
"@id": "#MaterialAttributeValue/primer forward=AGCGACGCCGCAGGGGGATCCTACATCAGGGCGGGTGTCGTTG",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_forward",
"characteristicType": {
"@id": "#UserTerm_primer_forward",
"annotationValue": "primer forward"
}
},
"value": {
"@id": "#UserTerm_AGCGACGCCGCAGGGGGATCCTACATCAGGGCGGGTGTCGTTG",
"annotationValue": "AGCGACGCCGCAGGGGGATCCTACATCAGGGCGGGTGTCGTTG"
}
},
{
"@id": "#MaterialAttributeValue/primer reverse=ATGATATCTCCTTCTTAAAGTTCATGTTGAGCCTTGCGGAGTGG",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_reverse",
"characteristicType": {
"@id": "#UserTerm_primer_reverse",
"annotationValue": "primer reverse"
}
},
"value": {
"@id": "#UserTerm_ATGATATCTCCTTCTTAAAGTTCATGTTGAGCCTTGCGGAGTGG",
"annotationValue": "ATGATATCTCCTTCTTAAAGTTCATGTTGAGCCTTGCGGAGTGG"
}
},
{
"@id": "#MaterialAttributeValue/primer forward_venus insert=TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_forward_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_forward_venus_insert",
"annotationValue": "primer forward_venus insert"
}
},
"value": {
"@id": "#UserTerm_TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
"annotationValue": "TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA"
}
},
{
"@id": "#MaterialAttributeValue/primer reverse_venus insert=AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_reverse_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_reverse_venus_insert",
"annotationValue": "primer reverse_venus insert"
}
},
"value": {
"@id": "#UserTerm_AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
"annotationValue": "AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC"
}
},
{
"@id": "#MaterialAttributeValue/Template=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C45677",
"characteristicType": {
"@id": "NCIT:C45677",
"annotationValue": "Template",
"termSource": "NCIT",
"termAccession": "NCIT:C45677"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_pJC1-PNCgl1451-venus",
"name": "pJC1-PNCgl1451-venus"
}
]
},
{
"@id": "#Process_ReporterPlasmidCloning_7",
"name": "ReporterPlasmidCloning_7",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Gene_of_interest",
"parameterName": {
"@id": "#UserTerm_Gene_of_interest",
"annotationValue": "Gene of interest"
}
},
"value": {
"@id": "#UserTerm_NCgl0176",
"annotationValue": "NCgl0176"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Plasmid_backbone",
"parameterName": {
"@id": "#UserTerm_Plasmid_backbone",
"annotationValue": "Plasmid backbone"
}
},
"value": {
"@id": "#UserTerm_pJC1-venus-term-BS",
"annotationValue": "pJC1-venus-term-BS"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Backbone_restriction",
"parameterName": {
"@id": "#UserTerm_Backbone_restriction",
"annotationValue": "Backbone restriction"
}
},
"value": {
"@id": "#UserTerm_BamHI/BcuI",
"annotationValue": "BamHI/BcuI"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Insert_Amplification",
"parameterName": {
"@id": "#UserTerm_Insert_Amplification",
"annotationValue": "Insert Amplification"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_34079",
"annotationValue": "PCR",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Strategy",
"parameterName": {
"@id": "#UserTerm_Strategy",
"annotationValue": "Strategy"
}
},
"value": {
"@id": "#UserTerm_Gibson_Assembly",
"annotationValue": "Gibson Assembly"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Amplification_of_plasmid",
"parameterName": {
"@id": "#UserTerm_Amplification_of_plasmid",
"annotationValue": "Amplification of plasmid"
}
},
"value": {
"@id": "#UserTerm_Transformation_of_E._coli_DH5a_via_heat_shock",
"annotationValue": "Transformation of E. coli DH5a via heat shock"
}
}
],
"inputs": [
{
"@id": "#Source_ReporterPlasmidCloning_Input_7",
"name": "ReporterPlasmidCloning_Input_7",
"characteristics": [
{
"@id": "#MaterialAttributeValue/primer forward=AGCGACGCCGCAGGGGGATCCTATCCAAACTCATCCGCTGCAGTTT",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_forward",
"characteristicType": {
"@id": "#UserTerm_primer_forward",
"annotationValue": "primer forward"
}
},
"value": {
"@id": "#UserTerm_AGCGACGCCGCAGGGGGATCCTATCCAAACTCATCCGCTGCAGTTT",
"annotationValue": "AGCGACGCCGCAGGGGGATCCTATCCAAACTCATCCGCTGCAGTTT"
}
},
{
"@id": "#MaterialAttributeValue/primer reverse=ATGATATCTCCTTCTTAAAGTTCAACGGGCGGCGTCAGTTAAC",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_reverse",
"characteristicType": {
"@id": "#UserTerm_primer_reverse",
"annotationValue": "primer reverse"
}
},
"value": {
"@id": "#UserTerm_ATGATATCTCCTTCTTAAAGTTCAACGGGCGGCGTCAGTTAAC",
"annotationValue": "ATGATATCTCCTTCTTAAAGTTCAACGGGCGGCGTCAGTTAAC"
}
},
{
"@id": "#MaterialAttributeValue/primer forward_venus insert=TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_forward_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_forward_venus_insert",
"annotationValue": "primer forward_venus insert"
}
},
"value": {
"@id": "#UserTerm_TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
"annotationValue": "TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA"
}
},
{
"@id": "#MaterialAttributeValue/primer reverse_venus insert=AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_reverse_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_reverse_venus_insert",
"annotationValue": "primer reverse_venus insert"
}
},
"value": {
"@id": "#UserTerm_AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
"annotationValue": "AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC"
}
},
{
"@id": "#MaterialAttributeValue/Template=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C45677",
"characteristicType": {
"@id": "NCIT:C45677",
"annotationValue": "Template",
"termSource": "NCIT",
"termAccession": "NCIT:C45677"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_pJC1-PNCgl0176-venus",
"name": "pJC1-PNCgl0176-venus"
}
]
},
{
"@id": "#Process_ReporterPlasmidCloning_8",
"name": "ReporterPlasmidCloning_8",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Gene_of_interest",
"parameterName": {
"@id": "#UserTerm_Gene_of_interest",
"annotationValue": "Gene of interest"
}
},
"value": {
"@id": "#UserTerm_NCgl0177",
"annotationValue": "NCgl0177"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Plasmid_backbone",
"parameterName": {
"@id": "#UserTerm_Plasmid_backbone",
"annotationValue": "Plasmid backbone"
}
},
"value": {
"@id": "#UserTerm_pJC1-venus-term-BS",
"annotationValue": "pJC1-venus-term-BS"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Backbone_restriction",
"parameterName": {
"@id": "#UserTerm_Backbone_restriction",
"annotationValue": "Backbone restriction"
}
},
"value": {
"@id": "#UserTerm_BamHI/BcuI",
"annotationValue": "BamHI/BcuI"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Insert_Amplification",
"parameterName": {
"@id": "#UserTerm_Insert_Amplification",
"annotationValue": "Insert Amplification"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_34079",
"annotationValue": "PCR",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Strategy",
"parameterName": {
"@id": "#UserTerm_Strategy",
"annotationValue": "Strategy"
}
},
"value": {
"@id": "#UserTerm_Gibson_Assembly",
"annotationValue": "Gibson Assembly"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Amplification_of_plasmid",
"parameterName": {
"@id": "#UserTerm_Amplification_of_plasmid",
"annotationValue": "Amplification of plasmid"
}
},
"value": {
"@id": "#UserTerm_Transformation_of_E._coli_DH5a_via_heat_shock",
"annotationValue": "Transformation of E. coli DH5a via heat shock"
}
}
],
"inputs": [
{
"@id": "#Source_ReporterPlasmidCloning_Input_8",
"name": "ReporterPlasmidCloning_Input_8",
"characteristics": [
{
"@id": "#MaterialAttributeValue/primer forward=AGCGACGCCGCAGGGGGATCCTAGGCGAGTACTTTGTCACGGG",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_forward",
"characteristicType": {
"@id": "#UserTerm_primer_forward",
"annotationValue": "primer forward"
}
},
"value": {
"@id": "#UserTerm_AGCGACGCCGCAGGGGGATCCTAGGCGAGTACTTTGTCACGGG",
"annotationValue": "AGCGACGCCGCAGGGGGATCCTAGGCGAGTACTTTGTCACGGG"
}
},
{
"@id": "#MaterialAttributeValue/primer reverse=ATGATATCTCCTTCTTAAAGTTCAATCGTGGAGTCTTCTAAATTTTCGAGT",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_reverse",
"characteristicType": {
"@id": "#UserTerm_primer_reverse",
"annotationValue": "primer reverse"
}
},
"value": {
"@id": "#UserTerm_ATGATATCTCCTTCTTAAAGTTCAATCGTGGAGTCTTCTAAATTTTCGAGT",
"annotationValue": "ATGATATCTCCTTCTTAAAGTTCAATCGTGGAGTCTTCTAAATTTTCGAGT"
}
},
{
"@id": "#MaterialAttributeValue/primer forward_venus insert=TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_forward_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_forward_venus_insert",
"annotationValue": "primer forward_venus insert"
}
},
"value": {
"@id": "#UserTerm_TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
"annotationValue": "TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA"
}
},
{
"@id": "#MaterialAttributeValue/primer reverse_venus insert=AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_reverse_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_reverse_venus_insert",
"annotationValue": "primer reverse_venus insert"
}
},
"value": {
"@id": "#UserTerm_AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
"annotationValue": "AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC"
}
},
{
"@id": "#MaterialAttributeValue/Template=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C45677",
"characteristicType": {
"@id": "NCIT:C45677",
"annotationValue": "Template",
"termSource": "NCIT",
"termAccession": "NCIT:C45677"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_pJC1-PNCgl0177-venus",
"name": "pJC1-PNCgl0177-venus"
}
]
},
{
"@id": "#Process_ReporterPlasmidCloning_9",
"name": "ReporterPlasmidCloning_9",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Gene_of_interest",
"parameterName": {
"@id": "#UserTerm_Gene_of_interest",
"annotationValue": "Gene of interest"
}
},
"value": {
"@id": "#UserTerm_gyrB",
"annotationValue": "gyrB"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Plasmid_backbone",
"parameterName": {
"@id": "#UserTerm_Plasmid_backbone",
"annotationValue": "Plasmid backbone"
}
},
"value": {
"@id": "#UserTerm_pJC1-venus-term-BS",
"annotationValue": "pJC1-venus-term-BS"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Backbone_restriction",
"parameterName": {
"@id": "#UserTerm_Backbone_restriction",
"annotationValue": "Backbone restriction"
}
},
"value": {
"@id": "#UserTerm_BamHI/BcuI",
"annotationValue": "BamHI/BcuI"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Insert_Amplification",
"parameterName": {
"@id": "#UserTerm_Insert_Amplification",
"annotationValue": "Insert Amplification"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_34079",
"annotationValue": "PCR",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Strategy",
"parameterName": {
"@id": "#UserTerm_Strategy",
"annotationValue": "Strategy"
}
},
"value": {
"@id": "#UserTerm_Gibson_Assembly",
"annotationValue": "Gibson Assembly"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Amplification_of_plasmid",
"parameterName": {
"@id": "#UserTerm_Amplification_of_plasmid",
"annotationValue": "Amplification of plasmid"
}
},
"value": {
"@id": "#UserTerm_Transformation_of_E._coli_DH5a_via_heat_shock",
"annotationValue": "Transformation of E. coli DH5a via heat shock"
}
}
],
"inputs": [
{
"@id": "#Source_ReporterPlasmidCloning_Input_9",
"name": "ReporterPlasmidCloning_Input_9",
"characteristics": [
{
"@id": "#MaterialAttributeValue/primer forward=AGCGACGCCGCAGGGGGATCCTATGGGCCACCAATCTGCGCAT",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_forward",
"characteristicType": {
"@id": "#UserTerm_primer_forward",
"annotationValue": "primer forward"
}
},
"value": {
"@id": "#UserTerm_AGCGACGCCGCAGGGGGATCCTATGGGCCACCAATCTGCGCAT",
"annotationValue": "AGCGACGCCGCAGGGGGATCCTATGGGCCACCAATCTGCGCAT"
}
},
{
"@id": "#MaterialAttributeValue/primer reverse=ATGATATCTCCTTCTTAAAGTTCAAGCGTCATAATTGTGTTCAGTGTTTG",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_reverse",
"characteristicType": {
"@id": "#UserTerm_primer_reverse",
"annotationValue": "primer reverse"
}
},
"value": {
"@id": "#UserTerm_ATGATATCTCCTTCTTAAAGTTCAAGCGTCATAATTGTGTTCAGTGTTTG",
"annotationValue": "ATGATATCTCCTTCTTAAAGTTCAAGCGTCATAATTGTGTTCAGTGTTTG"
}
},
{
"@id": "#MaterialAttributeValue/primer forward_venus insert=TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_forward_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_forward_venus_insert",
"annotationValue": "primer forward_venus insert"
}
},
"value": {
"@id": "#UserTerm_TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
"annotationValue": "TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA"
}
},
{
"@id": "#MaterialAttributeValue/primer reverse_venus insert=AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_reverse_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_reverse_venus_insert",
"annotationValue": "primer reverse_venus insert"
}
},
"value": {
"@id": "#UserTerm_AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
"annotationValue": "AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC"
}
},
{
"@id": "#MaterialAttributeValue/Template=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C45677",
"characteristicType": {
"@id": "NCIT:C45677",
"annotationValue": "Template",
"termSource": "NCIT",
"termAccession": "NCIT:C45677"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_pJC1-PgyrB-venus",
"name": "pJC1-PgyrB-venus"
}
]
},
{
"@id": "#Process_ReporterPlasmidCloning_10",
"name": "ReporterPlasmidCloning_10",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Gene_of_interest",
"parameterName": {
"@id": "#UserTerm_Gene_of_interest",
"annotationValue": "Gene of interest"
}
},
"value": {
"@id": "#UserTerm_wzy",
"annotationValue": "wzy"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Plasmid_backbone",
"parameterName": {
"@id": "#UserTerm_Plasmid_backbone",
"annotationValue": "Plasmid backbone"
}
},
"value": {
"@id": "#UserTerm_pJC1-venus-term-BS",
"annotationValue": "pJC1-venus-term-BS"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Backbone_restriction",
"parameterName": {
"@id": "#UserTerm_Backbone_restriction",
"annotationValue": "Backbone restriction"
}
},
"value": {
"@id": "#UserTerm_BamHI/BcuI",
"annotationValue": "BamHI/BcuI"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Insert_Amplification",
"parameterName": {
"@id": "#UserTerm_Insert_Amplification",
"annotationValue": "Insert Amplification"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_34079",
"annotationValue": "PCR",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Strategy",
"parameterName": {
"@id": "#UserTerm_Strategy",
"annotationValue": "Strategy"
}
},
"value": {
"@id": "#UserTerm_Gibson_Assembly",
"annotationValue": "Gibson Assembly"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Amplification_of_plasmid",
"parameterName": {
"@id": "#UserTerm_Amplification_of_plasmid",
"annotationValue": "Amplification of plasmid"
}
},
"value": {
"@id": "#UserTerm_Transformation_of_E._coli_DH5a_via_heat_shock",
"annotationValue": "Transformation of E. coli DH5a via heat shock"
}
}
],
"inputs": [
{
"@id": "#Source_ReporterPlasmidCloning_Input_10",
"name": "ReporterPlasmidCloning_Input_10",
"characteristics": [
{
"@id": "#MaterialAttributeValue/primer forward=AGCGACGCCGCAGGGGGATCCTAAAGCGGTCACCAGTTCGAC",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_forward",
"characteristicType": {
"@id": "#UserTerm_primer_forward",
"annotationValue": "primer forward"
}
},
"value": {
"@id": "#UserTerm_AGCGACGCCGCAGGGGGATCCTAAAGCGGTCACCAGTTCGAC",
"annotationValue": "AGCGACGCCGCAGGGGGATCCTAAAGCGGTCACCAGTTCGAC"
}
},
{
"@id": "#MaterialAttributeValue/primer reverse=ATGATATCTCCTTCTTAAAGTTCAACTTCCGACAGCTAAAGGCTCAC",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_reverse",
"characteristicType": {
"@id": "#UserTerm_primer_reverse",
"annotationValue": "primer reverse"
}
},
"value": {
"@id": "#UserTerm_ATGATATCTCCTTCTTAAAGTTCAACTTCCGACAGCTAAAGGCTCAC",
"annotationValue": "ATGATATCTCCTTCTTAAAGTTCAACTTCCGACAGCTAAAGGCTCAC"
}
},
{
"@id": "#MaterialAttributeValue/primer forward_venus insert=TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_forward_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_forward_venus_insert",
"annotationValue": "primer forward_venus insert"
}
},
"value": {
"@id": "#UserTerm_TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA",
"annotationValue": "TGAACTTTAAGAAGGAGATATCATATGGTGAGCAAGGGCGAGGA"
}
},
{
"@id": "#MaterialAttributeValue/primer reverse_venus insert=AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
"category": {
"@id": "#MaterialAttribute/#UserTerm_primer_reverse_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_reverse_venus_insert",
"annotationValue": "primer reverse_venus insert"
}
},
"value": {
"@id": "#UserTerm_AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC",
"annotationValue": "AAAACGACGGCCAGTACTAGTTTACTTGTACAGCTCGTCCATGCC"
}
},
{
"@id": "#MaterialAttributeValue/Template=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C45677",
"characteristicType": {
"@id": "NCIT:C45677",
"annotationValue": "Template",
"termSource": "NCIT",
"termAccession": "NCIT:C45677"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_pJC1-Pwzy-venus",
"name": "pJC1-Pwzy-venus"
}
]
},
{
"@id": "#Process_ReporterStrainTransformation",
"name": "ReporterStrainTransformation",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Transformation_method",
"parameterName": {
"@id": "#UserTerm_Transformation_method",
"annotationValue": "Transformation method"
}
},
"value": {
"@id": "#UserTerm_Electroporation",
"annotationValue": "Electroporation"
}
}
],
"inputs": [
{
"@id": "#Sample_pJC1-PNCgl1781-venus",
"name": "pJC1-PNCgl1781-venus",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=WT",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
"@id": "#UserTerm_WT",
"annotationValue": "WT"
}
}
]
},
{
"@id": "#Sample_pJC1-PNCgl1781-venus",
"name": "pJC1-PNCgl1781-venus",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=DdtxR",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
"@id": "#UserTerm_DdtxR",
"annotationValue": "DdtxR"
}
}
]
},
{
"@id": "#Sample_pJC1-PxerC-venus",
"name": "pJC1-PxerC-venus",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=WT",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
"@id": "#UserTerm_WT",
"annotationValue": "WT"
}
}
]
},
{
"@id": "#Sample_pJC1-PxerC-venus",
"name": "pJC1-PxerC-venus",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=DdtxR",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
"@id": "#UserTerm_DdtxR",
"annotationValue": "DdtxR"
}
}
]
},
{
"@id": "#Sample_pJC1-Pqor3-venus",
"name": "pJC1-Pqor3-venus",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=WT",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
"@id": "#UserTerm_WT",
"annotationValue": "WT"
}
}
]
},
{
"@id": "#Sample_pJC1-Pqor3-venus",
"name": "pJC1-Pqor3-venus",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=DdtxR",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
"@id": "#UserTerm_DdtxR",
"annotationValue": "DdtxR"
}
}
]
},
{
"@id": "#Sample_pJC1-PcepA-venus",
"name": "pJC1-PcepA-venus",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=WT",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
"@id": "#UserTerm_WT",
"annotationValue": "WT"
}
}
]
},
{
"@id": "#Sample_pJC1-PcepA-venus",
"name": "pJC1-PcepA-venus",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=DdtxR",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
"@id": "#UserTerm_DdtxR",
"annotationValue": "DdtxR"
}
}
]
},
{
"@id": "#Sample_pJC1-PNCgl2766-venus",
"name": "pJC1-PNCgl2766-venus",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=WT",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
"@id": "#UserTerm_WT",
"annotationValue": "WT"
}
}
]
},
{
"@id": "#Sample_pJC1-PNCgl2766-venus",
"name": "pJC1-PNCgl2766-venus",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=DdtxR",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
"@id": "#UserTerm_DdtxR",
"annotationValue": "DdtxR"
}
}
]
},
{
"@id": "#Sample_pJC1-PmetH-venus",
"name": "pJC1-PmetH-venus",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=WT",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
"@id": "#UserTerm_WT",
"annotationValue": "WT"
}
}
]
},
{
"@id": "#Sample_pJC1-PmetH-venus",
"name": "pJC1-PmetH-venus",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=DdtxR",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
"@id": "#UserTerm_DdtxR",
"annotationValue": "DdtxR"
}
}
]
},
{
"@id": "#Sample_pJC1-PNCgl1451-venus",
"name": "pJC1-PNCgl1451-venus",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=WT",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
"@id": "#UserTerm_WT",
"annotationValue": "WT"
}
}
]
},
{
"@id": "#Sample_pJC1-PNCgl1451-venus",
"name": "pJC1-PNCgl1451-venus",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=DdtxR",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
"@id": "#UserTerm_DdtxR",
"annotationValue": "DdtxR"
}
}
]
},
{
"@id": "#Sample_pJC1-PNCgl0176-venus",
"name": "pJC1-PNCgl0176-venus",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
"category": {
"@id": "#MaterialAttribute/NCIT:C14250",
"characteristicType": {
"@id": "NCIT:C14250",
"annotationValue": "Organism",
"termSource": "NCIT",
"termAccession": "NCIT:C14250"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
"termAccession": "http://purl.obolibrary.org/obo/NCBITAXON_196627"
}
},
{
"@id": "#MaterialAttributeValue/Parental strain=WT",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
"@id": "#UserTerm_WT",
"annotationValue": "WT"
}
}
]
},
{
"@id": "#Sample_pJC1-PNCgl0176-venus",
"name": "pJC1-PNCgl0176-venus",
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{
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"characteristicType": {
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"termAccession": "NCIT:C14250"
}
},
"value": {
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"annotationValue": "Corynebacterium glutamicum ATCC 13032",
"termSource": "NCBITAXON",
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}
},
{
"@id": "#MaterialAttributeValue/Parental strain=DdtxR",
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"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
"characteristicType": {
"@id": "#UserTerm_Parental_strain",
"annotationValue": "Parental strain"
}
},
"value": {
"@id": "#UserTerm_DdtxR",
"annotationValue": "DdtxR"
}
}
]
},
{
"@id": "#Sample_pJC1-PNCgl0177-venus",
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{
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}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/NCBITAXON_196627",
"annotationValue": "Corynebacterium glutamicum ATCC 13032",
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}
},
{
"@id": "#MaterialAttributeValue/Parental strain=WT",
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}
},
"value": {
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}
}
]
},
{
"@id": "#Sample_pJC1-PNCgl0177-venus",
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{
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}
},
"value": {
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}
},
{
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}
},
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}
}
]
},
{
"@id": "#Sample_pJC1-PgyrB-venus",
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{
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}
},
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}
},
{
"@id": "#MaterialAttributeValue/Parental strain=WT",
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}
},
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}
}
]
},
{
"@id": "#Sample_pJC1-PgyrB-venus",
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{
"@id": "#MaterialAttributeValue/Organism=Corynebacterium glutamicum ATCC 13032",
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}
},
"value": {
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}
},
{
"@id": "#MaterialAttributeValue/Parental strain=DdtxR",
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}
},
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}
}
]
},
{
"@id": "#Sample_pJC1-Pwzy-venus",
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{
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}
},
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}
},
{
"@id": "#MaterialAttributeValue/Parental strain=WT",
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}
},
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}
}
]
},
{
"@id": "#Sample_pJC1-Pwzy-venus",
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}
},
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}
},
{
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}
},
"value": {
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}
}
]
}
],
"outputs": [
{
"@id": "#Sample_WT-NCgl1781",
"name": "WT-NCgl1781"
},
{
"@id": "#Sample_DdtxR-NCgl1781",
"name": "DdtxR-NCgl1781"
},
{
"@id": "#Sample_WT-xerC",
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},
{
"@id": "#Sample_DdtxR-xerC",
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},
{
"@id": "#Sample_WT-qor3",
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},
{
"@id": "#Sample_DdtxR-qor3",
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},
{
"@id": "#Sample_WT-cepA",
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},
{
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},
{
"@id": "#Sample_WT-NCgl2766",
"name": "WT-NCgl2766"
},
{
"@id": "#Sample_DdtxR-NCgl2766",
"name": "DdtxR-NCgl2766"
},
{
"@id": "#Sample_WT-metH",
"name": "WT-metH"
},
{
"@id": "#Sample_DdtxR-metH",
"name": "DdtxR-metH"
},
{
"@id": "#Sample_WT-NCgl1451",
"name": "WT-NCgl1451"
},
{
"@id": "#Sample_DdtxR-NCgl1451",
"name": "DdtxR-NCgl1451"
},
{
"@id": "#Sample_WT-NCgl0176",
"name": "WT-NCgl0176"
},
{
"@id": "#Sample_DdtxR-NCgl0176",
"name": "DdtxR-NCgl0176"
},
{
"@id": "#Sample_WT-NCgl0177",
"name": "WT-NCgl0177"
},
{
"@id": "#Sample_DdtxR-NCgl0177",
"name": "DdtxR-NCgl0177"
},
{
"@id": "#Sample_WT-gyrB",
"name": "WT-gyrB"
},
{
"@id": "#Sample_DdtxR-gyrB",
"name": "DdtxR-gyrB"
},
{
"@id": "#Sample_WT-wzy",
"name": "WT-wzy"
},
{
"@id": "#Sample_DdtxR-wzy",
"name": "DdtxR-wzy"
}
]
}
],
"characteristicCategories": [
{
"@id": "#MaterialAttribute/#UserTerm_primer_forward",
"characteristicType": {
"@id": "#UserTerm_primer_forward",
"annotationValue": "primer forward"
}
},
{
"@id": "#MaterialAttribute/#UserTerm_primer_reverse",
"characteristicType": {
"@id": "#UserTerm_primer_reverse",
"annotationValue": "primer reverse"
}
},
{
"@id": "#MaterialAttribute/#UserTerm_primer_forward_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_forward_venus_insert",
"annotationValue": "primer forward_venus insert"
}
},
{
"@id": "#MaterialAttribute/#UserTerm_primer_reverse_venus_insert",
"characteristicType": {
"@id": "#UserTerm_primer_reverse_venus_insert",
"annotationValue": "primer reverse_venus insert"
}
},
{
"@id": "#MaterialAttribute/NCIT:C45677",
"characteristicType": {
"@id": "NCIT:C45677",
"annotationValue": "Template",
"termSource": "NCIT",
"termAccession": "NCIT:C45677"
}
},
{
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}
},
{
"@id": "#MaterialAttribute/#UserTerm_Parental_strain",
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"annotationValue": "Parental strain"
}
}
]
},
{
"@id": "studies/4_InVitroBindingOfDtxR/",
"filename": "studies/4_InVitroBindingOfDtxR/isa.study.xlsx",
"identifier": "4_InVitroBindingOfDtxR",
"title": "In vitro Binding of DtxR",
"description": "In order to confirm the binding of DtxR to targets that were identified in ChAP-Seq data as \"weak peaks\" in vitro, electron mobility shift assays should be performed. In course of this study, DNA fragments are generated for selected weak ChAP-Seq targets and DtxR protein is purified as it was done in Wennerhold et al. 2006.",
"people": [
{
"@id": "ul.weber@fz-juelich.de",
"firstName": "Ulrike",
"lastName": "Weber",
"email": "ul.weber@fz-juelich.de",
"affiliation": "IBG-1: Institute of Bio- and Geosciences, Forschungszentrum J\u00fclich GmbH"
},
{
"@id": "0000-0002-4172-2398",
"firstName": "Aileen",
"lastName": "Kr\u00fcger",
"email": "ai.krueger@fz-juelich.de",
"affiliation": "IBG-1: Institute of Bio- and Geosciences, Forschungszentrum J\u00fclich GmbH",
"comments": [
{
"name": "ORCID",
"value": "0000-0002-4172-2398"
}
]
},
{
"@id": "0000-0002-4172-2398",
"firstName": "Aileen",
"lastName": "Kr\u00fcger",
"email": "ai.krueger@fz-juelich.de",
"affiliation": "IBG-1: Institute of Bio- and Geosciences, Forschungszentrum J\u00fclich GmbH",
"comments": [
{
"name": "performer (ARC:00000168) 4_ElectronMobilityShiftAssays_DtxR",
"value": "4_ElectronMobilityShiftAssays_DtxR"
},
{
"name": "ORCID",
"value": "0000-0002-4172-2398"
}
]
},
{
"@id": "ul.weber@fz-juelich.de",
"firstName": "Ulrike",
"lastName": "Weber",
"email": "ul.weber@fz-juelich.de",
"affiliation": "IBG-1: Institute of Bio- and Geosciences, Forschungszentrum J\u00fclich GmbH",
"comments": [
{
"name": "performer (ARC:00000168) 4_ElectronMobilityShiftAssays_DtxR",
"value": "4_ElectronMobilityShiftAssays_DtxR"
}
]
}
],
"protocols": [
{
"@id": "#EmptyProtocol",
"parameters": [
{
"@id": "#ProtocolParameter/#UserTerm_pre-culture",
"parameterName": {
"@id": "#UserTerm_pre-culture",
"annotationValue": "pre-culture"
}
},
{
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
{
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_Cultivation_medium",
"parameterName": {
"@id": "#UserTerm_Cultivation_medium",
"annotationValue": "Cultivation medium"
}
},
{
"@id": "#ProtocolParameter/NCIT:C120268",
"parameterName": {
"@id": "NCIT:C120268",
"annotationValue": "Inducer",
"termSource": "NCIT",
"termAccession": "NCIT:C120268"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_Inducing_condition",
"parameterName": {
"@id": "#UserTerm_Inducing_condition",
"annotationValue": "Inducing condition"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_Induced_cultivation",
"parameterName": {
"@id": "#UserTerm_Induced_cultivation",
"annotationValue": "Induced cultivation"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_cell_disruption",
"parameterName": {
"@id": "#UserTerm_cell_disruption",
"annotationValue": "cell disruption"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_Final_concentration",
"parameterName": {
"@id": "#UserTerm_Final_concentration",
"annotationValue": "Final concentration"
}
},
{
"@id": "#ProtocolParameter/PEFF:0001033",
"parameterName": {
"@id": "PEFF:0001033",
"annotationValue": "Comment",
"termSource": "PEFF",
"termAccession": "PEFF:0001033"
}
}
],
"components": [
{
"componentName": "E. coli BL21 (DE3) ()",
"componentType": {
"@id": "#UserTerm_Overexpressing_strain",
"annotationValue": "Overexpressing strain"
}
},
{
"componentName": "pET24b-dtxR-C (Wennerhold et al. 2006) ()",
"componentType": {
"@id": "OBI:0000430",
"annotationValue": "plasmid",
"termSource": "OBI",
"termAccession": "OBI:0000430"
}
}
]
}
],
"materials": {
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{
"@id": "#Sample_ripA",
"name": "ripA",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Method=PCR",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0088",
"characteristicType": {
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"annotationValue": "Method",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0088"
}
},
"value": {
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"annotationValue": "PCR",
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"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"@id": "#MaterialAttributeValue/cut out of gel?=no",
"category": {
"@id": "#MaterialAttribute/#UserTerm_cut_out_of_gel?",
"characteristicType": {
"@id": "#UserTerm_cut_out_of_gel?",
"annotationValue": "cut out of gel?"
}
},
"value": {
"@id": "#UserTerm_no",
"annotationValue": "no"
}
},
{
"@id": "#MaterialAttributeValue/Concentration=53ng/\u00b5l",
"category": {
"@id": "#MaterialAttribute/NCIT:C41185",
"characteristicType": {
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"termAccession": "NCIT:C41185"
}
},
"value": 53,
"unit": {
"@id": "#UserTerm_ng/\u00b5l",
"annotationValue": "ng/\u00b5l"
}
}
]
},
{
"@id": "#Sample_ripA_fragment",
"name": "ripA_fragment"
},
{
"@id": "#Sample_xerC",
"name": "xerC",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Method=PCR",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0088",
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}
},
"value": {
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}
},
{
"@id": "#MaterialAttributeValue/cut out of gel?=no",
"category": {
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"characteristicType": {
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"annotationValue": "cut out of gel?"
}
},
"value": {
"@id": "#UserTerm_no",
"annotationValue": "no"
}
},
{
"@id": "#MaterialAttributeValue/Concentration=48ng/\u00b5l",
"category": {
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}
},
"value": 48,
"unit": {
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}
}
]
},
{
"@id": "#Sample_xerC_fragment",
"name": "xerC_fragment"
},
{
"@id": "#Sample_NCgl1200",
"name": "NCgl1200",
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{
"@id": "#MaterialAttributeValue/Method=PCR",
"category": {
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}
},
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}
},
{
"@id": "#MaterialAttributeValue/cut out of gel?=yes",
"category": {
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"characteristicType": {
"@id": "#UserTerm_cut_out_of_gel?",
"annotationValue": "cut out of gel?"
}
},
"value": {
"@id": "#UserTerm_yes",
"annotationValue": "yes"
}
},
{
"@id": "#MaterialAttributeValue/Concentration=9ng/\u00b5l",
"category": {
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"characteristicType": {
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}
},
"value": 9,
"unit": {
"@id": "#UserTerm_ng/\u00b5l",
"annotationValue": "ng/\u00b5l"
}
}
]
},
{
"@id": "#Sample_NCgl1200_fragment",
"name": "NCgl1200_fragment"
},
{
"@id": "#Sample_cepA",
"name": "cepA",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Method=PCR",
"category": {
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"annotationValue": "Method",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0088"
}
},
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"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"@id": "#MaterialAttributeValue/cut out of gel?=no",
"category": {
"@id": "#MaterialAttribute/#UserTerm_cut_out_of_gel?",
"characteristicType": {
"@id": "#UserTerm_cut_out_of_gel?",
"annotationValue": "cut out of gel?"
}
},
"value": {
"@id": "#UserTerm_no",
"annotationValue": "no"
}
},
{
"@id": "#MaterialAttributeValue/Concentration=71ng/\u00b5l",
"category": {
"@id": "#MaterialAttribute/NCIT:C41185",
"characteristicType": {
"@id": "NCIT:C41185",
"annotationValue": "Concentration",
"termSource": "NCIT",
"termAccession": "NCIT:C41185"
}
},
"value": 71,
"unit": {
"@id": "#UserTerm_ng/\u00b5l",
"annotationValue": "ng/\u00b5l"
}
}
]
},
{
"@id": "#Sample_cepA_fragment",
"name": "cepA_fragment"
},
{
"@id": "#Sample_NCgl0177",
"name": "NCgl0177",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Method=PCR",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0088",
"characteristicType": {
"@id": "MIAPPE:0088",
"annotationValue": "Method",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0088"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_34079",
"annotationValue": "PCR",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"@id": "#MaterialAttributeValue/cut out of gel?=no",
"category": {
"@id": "#MaterialAttribute/#UserTerm_cut_out_of_gel?",
"characteristicType": {
"@id": "#UserTerm_cut_out_of_gel?",
"annotationValue": "cut out of gel?"
}
},
"value": {
"@id": "#UserTerm_no",
"annotationValue": "no"
}
},
{
"@id": "#MaterialAttributeValue/Concentration=62ng/\u00b5l",
"category": {
"@id": "#MaterialAttribute/NCIT:C41185",
"characteristicType": {
"@id": "NCIT:C41185",
"annotationValue": "Concentration",
"termSource": "NCIT",
"termAccession": "NCIT:C41185"
}
},
"value": 62,
"unit": {
"@id": "#UserTerm_ng/\u00b5l",
"annotationValue": "ng/\u00b5l"
}
}
]
},
{
"@id": "#Sample_NCgl0177_fragment",
"name": "NCgl0177_fragment"
},
{
"@id": "#Sample_NCgl2766",
"name": "NCgl2766",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Method=PCR",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0088",
"characteristicType": {
"@id": "MIAPPE:0088",
"annotationValue": "Method",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0088"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_34079",
"annotationValue": "PCR",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"@id": "#MaterialAttributeValue/cut out of gel?=no",
"category": {
"@id": "#MaterialAttribute/#UserTerm_cut_out_of_gel?",
"characteristicType": {
"@id": "#UserTerm_cut_out_of_gel?",
"annotationValue": "cut out of gel?"
}
},
"value": {
"@id": "#UserTerm_no",
"annotationValue": "no"
}
},
{
"@id": "#MaterialAttributeValue/Concentration=57ng/\u00b5l",
"category": {
"@id": "#MaterialAttribute/NCIT:C41185",
"characteristicType": {
"@id": "NCIT:C41185",
"annotationValue": "Concentration",
"termSource": "NCIT",
"termAccession": "NCIT:C41185"
}
},
"value": 57,
"unit": {
"@id": "#UserTerm_ng/\u00b5l",
"annotationValue": "ng/\u00b5l"
}
}
]
},
{
"@id": "#Sample_NCgl2766_fragment",
"name": "NCgl2766_fragment"
},
{
"@id": "#Sample_metH",
"name": "metH",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Method=PCR",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0088",
"characteristicType": {
"@id": "MIAPPE:0088",
"annotationValue": "Method",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0088"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_34079",
"annotationValue": "PCR",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"@id": "#MaterialAttributeValue/cut out of gel?=no",
"category": {
"@id": "#MaterialAttribute/#UserTerm_cut_out_of_gel?",
"characteristicType": {
"@id": "#UserTerm_cut_out_of_gel?",
"annotationValue": "cut out of gel?"
}
},
"value": {
"@id": "#UserTerm_no",
"annotationValue": "no"
}
},
{
"@id": "#MaterialAttributeValue/Concentration=83ng/\u00b5l",
"category": {
"@id": "#MaterialAttribute/NCIT:C41185",
"characteristicType": {
"@id": "NCIT:C41185",
"annotationValue": "Concentration",
"termSource": "NCIT",
"termAccession": "NCIT:C41185"
}
},
"value": 83,
"unit": {
"@id": "#UserTerm_ng/\u00b5l",
"annotationValue": "ng/\u00b5l"
}
}
]
},
{
"@id": "#Sample_metH_fragment",
"name": "metH_fragment"
},
{
"@id": "#Sample_gyrB",
"name": "gyrB",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Method=PCR",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0088",
"characteristicType": {
"@id": "MIAPPE:0088",
"annotationValue": "Method",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0088"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_34079",
"annotationValue": "PCR",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"@id": "#MaterialAttributeValue/cut out of gel?=yes",
"category": {
"@id": "#MaterialAttribute/#UserTerm_cut_out_of_gel?",
"characteristicType": {
"@id": "#UserTerm_cut_out_of_gel?",
"annotationValue": "cut out of gel?"
}
},
"value": {
"@id": "#UserTerm_yes",
"annotationValue": "yes"
}
},
{
"@id": "#MaterialAttributeValue/Concentration=22ng/\u00b5l",
"category": {
"@id": "#MaterialAttribute/NCIT:C41185",
"characteristicType": {
"@id": "NCIT:C41185",
"annotationValue": "Concentration",
"termSource": "NCIT",
"termAccession": "NCIT:C41185"
}
},
"value": 22,
"unit": {
"@id": "#UserTerm_ng/\u00b5l",
"annotationValue": "ng/\u00b5l"
}
}
]
},
{
"@id": "#Sample_gyrB_fragment",
"name": "gyrB_fragment"
},
{
"@id": "#Sample_acn",
"name": "acn",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Method=PCR",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0088",
"characteristicType": {
"@id": "MIAPPE:0088",
"annotationValue": "Method",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0088"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_34079",
"annotationValue": "PCR",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"@id": "#MaterialAttributeValue/cut out of gel?=no",
"category": {
"@id": "#MaterialAttribute/#UserTerm_cut_out_of_gel?",
"characteristicType": {
"@id": "#UserTerm_cut_out_of_gel?",
"annotationValue": "cut out of gel?"
}
},
"value": {
"@id": "#UserTerm_no",
"annotationValue": "no"
}
},
{
"@id": "#MaterialAttributeValue/Concentration=23ng/\u00b5l",
"category": {
"@id": "#MaterialAttribute/NCIT:C41185",
"characteristicType": {
"@id": "NCIT:C41185",
"annotationValue": "Concentration",
"termSource": "NCIT",
"termAccession": "NCIT:C41185"
}
},
"value": 23,
"unit": {
"@id": "#UserTerm_ng/\u00b5l",
"annotationValue": "ng/\u00b5l"
}
}
]
},
{
"@id": "#Sample_acn_fragment",
"name": "acn_fragment"
},
{
"@id": "#Sample_E.coli_culture",
"name": "E.coli culture",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Protein of interest=DtxR",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Protein_of_interest",
"characteristicType": {
"@id": "#UserTerm_Protein_of_interest",
"annotationValue": "Protein of interest"
}
},
"value": {
"@id": "#UserTerm_DtxR",
"annotationValue": "DtxR"
}
},
{
"@id": "#MaterialAttributeValue/Tag=HHHHLEHHHHHH",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Tag",
"characteristicType": {
"@id": "#UserTerm_Tag",
"annotationValue": "Tag"
}
},
"value": {
"@id": "#UserTerm_HHHHLEHHHHHH",
"annotationValue": "HHHHLEHHHHHH"
}
},
{
"@id": "#MaterialAttributeValue/Method=Ni-NTA agarose column gravity flow protocol",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0088",
"characteristicType": {
"@id": "MIAPPE:0088",
"annotationValue": "Method",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0088"
}
},
"value": {
"@id": "#UserTerm_Ni-NTA_agarose_column_gravity_flow_protocol",
"annotationValue": "Ni-NTA agarose column gravity flow protocol"
}
}
]
},
{
"@id": "#Sample_purified_DtxR",
"name": "purified DtxR"
}
]
},
"processSequence": [
{
"@id": "#Process_DNA_preparation_0",
"name": "DNA preparation_0",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C16612",
"parameterName": {
"@id": "NCIT:C16612",
"annotationValue": "Gene",
"termSource": "NCIT",
"termAccession": "NCIT:C16612"
}
},
"value": {
"@id": "#UserTerm_ripA",
"annotationValue": "ripA"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Primer_forward",
"parameterName": {
"@id": "#UserTerm_Primer_forward",
"annotationValue": "Primer forward"
}
},
"value": {
"@id": "#UserTerm_ATGTAACATCATTTCGAAGATATGAG",
"annotationValue": "ATGTAACATCATTTCGAAGATATGAG"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Primer_reverse",
"parameterName": {
"@id": "#UserTerm_Primer_reverse",
"annotationValue": "Primer reverse"
}
},
"value": {
"@id": "#UserTerm_AACTGTTGACACACCGGAATG",
"annotationValue": "AACTGTTGACACACCGGAATG"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C45677",
"parameterName": {
"@id": "NCIT:C45677",
"annotationValue": "Template",
"termSource": "NCIT",
"termAccession": "NCIT:C45677"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT",
"annotationValue": "C. glutamicum WT"
}
},
{
"category": {
"@id": "#ProtocolParameter/PEFF:0001033",
"parameterName": {
"@id": "PEFF:0001033",
"annotationValue": "Comment",
"termSource": "PEFF",
"termAccession": "PEFF:0001033"
}
},
"value": {
"@id": "#UserTerm_positive_control,_known_from_Wennerhold_et_al._2006",
"annotationValue": "positive control, known from Wennerhold et al. 2006"
}
}
],
"inputs": [
{
"@id": "#Sample_ripA",
"name": "ripA",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Method=PCR",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0088",
"characteristicType": {
"@id": "MIAPPE:0088",
"annotationValue": "Method",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0088"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_34079",
"annotationValue": "PCR",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"@id": "#MaterialAttributeValue/cut out of gel?=no",
"category": {
"@id": "#MaterialAttribute/#UserTerm_cut_out_of_gel?",
"characteristicType": {
"@id": "#UserTerm_cut_out_of_gel?",
"annotationValue": "cut out of gel?"
}
},
"value": {
"@id": "#UserTerm_no",
"annotationValue": "no"
}
},
{
"@id": "#MaterialAttributeValue/Concentration=53ng/\u00b5l",
"category": {
"@id": "#MaterialAttribute/NCIT:C41185",
"characteristicType": {
"@id": "NCIT:C41185",
"annotationValue": "Concentration",
"termSource": "NCIT",
"termAccession": "NCIT:C41185"
}
},
"value": 53,
"unit": {
"@id": "#UserTerm_ng/\u00b5l",
"annotationValue": "ng/\u00b5l"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_ripA_fragment",
"name": "ripA_fragment"
}
]
},
{
"@id": "#Process_DNA_preparation_1",
"name": "DNA preparation_1",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C16612",
"parameterName": {
"@id": "NCIT:C16612",
"annotationValue": "Gene",
"termSource": "NCIT",
"termAccession": "NCIT:C16612"
}
},
"value": {
"@id": "#UserTerm_xerC",
"annotationValue": "xerC"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Primer_forward",
"parameterName": {
"@id": "#UserTerm_Primer_forward",
"annotationValue": "Primer forward"
}
},
"value": {
"@id": "#UserTerm_CCGTCTTCAAGGAACCAG",
"annotationValue": "CCGTCTTCAAGGAACCAG"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Primer_reverse",
"parameterName": {
"@id": "#UserTerm_Primer_reverse",
"annotationValue": "Primer reverse"
}
},
"value": {
"@id": "#UserTerm_AACCTGGGGGTTATATAAAAAACTTC",
"annotationValue": "AACCTGGGGGTTATATAAAAAACTTC"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C45677",
"parameterName": {
"@id": "NCIT:C45677",
"annotationValue": "Template",
"termSource": "NCIT",
"termAccession": "NCIT:C45677"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT",
"annotationValue": "C. glutamicum WT"
}
},
{
"category": {
"@id": "#ProtocolParameter/PEFF:0001033",
"parameterName": {
"@id": "PEFF:0001033",
"annotationValue": "Comment",
"termSource": "PEFF",
"termAccession": "PEFF:0001033"
}
}
}
],
"inputs": [
{
"@id": "#Sample_xerC",
"name": "xerC",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Method=PCR",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0088",
"characteristicType": {
"@id": "MIAPPE:0088",
"annotationValue": "Method",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0088"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_34079",
"annotationValue": "PCR",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"@id": "#MaterialAttributeValue/cut out of gel?=no",
"category": {
"@id": "#MaterialAttribute/#UserTerm_cut_out_of_gel?",
"characteristicType": {
"@id": "#UserTerm_cut_out_of_gel?",
"annotationValue": "cut out of gel?"
}
},
"value": {
"@id": "#UserTerm_no",
"annotationValue": "no"
}
},
{
"@id": "#MaterialAttributeValue/Concentration=48ng/\u00b5l",
"category": {
"@id": "#MaterialAttribute/NCIT:C41185",
"characteristicType": {
"@id": "NCIT:C41185",
"annotationValue": "Concentration",
"termSource": "NCIT",
"termAccession": "NCIT:C41185"
}
},
"value": 48,
"unit": {
"@id": "#UserTerm_ng/\u00b5l",
"annotationValue": "ng/\u00b5l"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_xerC_fragment",
"name": "xerC_fragment"
}
]
},
{
"@id": "#Process_DNA_preparation_2",
"name": "DNA preparation_2",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C16612",
"parameterName": {
"@id": "NCIT:C16612",
"annotationValue": "Gene",
"termSource": "NCIT",
"termAccession": "NCIT:C16612"
}
},
"value": {
"@id": "#UserTerm_NCgl1200",
"annotationValue": "NCgl1200"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Primer_forward",
"parameterName": {
"@id": "#UserTerm_Primer_forward",
"annotationValue": "Primer forward"
}
},
"value": {
"@id": "#UserTerm_ATTGGCTGCCCTCGCATG",
"annotationValue": "ATTGGCTGCCCTCGCATG"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Primer_reverse",
"parameterName": {
"@id": "#UserTerm_Primer_reverse",
"annotationValue": "Primer reverse"
}
},
"value": {
"@id": "#UserTerm_CTTATCGATATATCTTTAACTGACCTAG",
"annotationValue": "CTTATCGATATATCTTTAACTGACCTAG"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C45677",
"parameterName": {
"@id": "NCIT:C45677",
"annotationValue": "Template",
"termSource": "NCIT",
"termAccession": "NCIT:C45677"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT",
"annotationValue": "C. glutamicum WT"
}
},
{
"category": {
"@id": "#ProtocolParameter/PEFF:0001033",
"parameterName": {
"@id": "PEFF:0001033",
"annotationValue": "Comment",
"termSource": "PEFF",
"termAccession": "PEFF:0001033"
}
}
}
],
"inputs": [
{
"@id": "#Sample_NCgl1200",
"name": "NCgl1200",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Method=PCR",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0088",
"characteristicType": {
"@id": "MIAPPE:0088",
"annotationValue": "Method",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0088"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_34079",
"annotationValue": "PCR",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"@id": "#MaterialAttributeValue/cut out of gel?=yes",
"category": {
"@id": "#MaterialAttribute/#UserTerm_cut_out_of_gel?",
"characteristicType": {
"@id": "#UserTerm_cut_out_of_gel?",
"annotationValue": "cut out of gel?"
}
},
"value": {
"@id": "#UserTerm_yes",
"annotationValue": "yes"
}
},
{
"@id": "#MaterialAttributeValue/Concentration=9ng/\u00b5l",
"category": {
"@id": "#MaterialAttribute/NCIT:C41185",
"characteristicType": {
"@id": "NCIT:C41185",
"annotationValue": "Concentration",
"termSource": "NCIT",
"termAccession": "NCIT:C41185"
}
},
"value": 9,
"unit": {
"@id": "#UserTerm_ng/\u00b5l",
"annotationValue": "ng/\u00b5l"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_NCgl1200_fragment",
"name": "NCgl1200_fragment"
}
]
},
{
"@id": "#Process_DNA_preparation_3",
"name": "DNA preparation_3",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C16612",
"parameterName": {
"@id": "NCIT:C16612",
"annotationValue": "Gene",
"termSource": "NCIT",
"termAccession": "NCIT:C16612"
}
},
"value": {
"@id": "#UserTerm_cepA",
"annotationValue": "cepA"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Primer_forward",
"parameterName": {
"@id": "#UserTerm_Primer_forward",
"annotationValue": "Primer forward"
}
},
"value": {
"@id": "#UserTerm_TTTGACGTGCTTTTTTAGCACG",
"annotationValue": "TTTGACGTGCTTTTTTAGCACG"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Primer_reverse",
"parameterName": {
"@id": "#UserTerm_Primer_reverse",
"annotationValue": "Primer reverse"
}
},
"value": {
"@id": "#UserTerm_CTTCATGTGGTAAATGACAATGCG",
"annotationValue": "CTTCATGTGGTAAATGACAATGCG"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C45677",
"parameterName": {
"@id": "NCIT:C45677",
"annotationValue": "Template",
"termSource": "NCIT",
"termAccession": "NCIT:C45677"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT",
"annotationValue": "C. glutamicum WT"
}
},
{
"category": {
"@id": "#ProtocolParameter/PEFF:0001033",
"parameterName": {
"@id": "PEFF:0001033",
"annotationValue": "Comment",
"termSource": "PEFF",
"termAccession": "PEFF:0001033"
}
}
}
],
"inputs": [
{
"@id": "#Sample_cepA",
"name": "cepA",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Method=PCR",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0088",
"characteristicType": {
"@id": "MIAPPE:0088",
"annotationValue": "Method",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0088"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_34079",
"annotationValue": "PCR",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"@id": "#MaterialAttributeValue/cut out of gel?=no",
"category": {
"@id": "#MaterialAttribute/#UserTerm_cut_out_of_gel?",
"characteristicType": {
"@id": "#UserTerm_cut_out_of_gel?",
"annotationValue": "cut out of gel?"
}
},
"value": {
"@id": "#UserTerm_no",
"annotationValue": "no"
}
},
{
"@id": "#MaterialAttributeValue/Concentration=71ng/\u00b5l",
"category": {
"@id": "#MaterialAttribute/NCIT:C41185",
"characteristicType": {
"@id": "NCIT:C41185",
"annotationValue": "Concentration",
"termSource": "NCIT",
"termAccession": "NCIT:C41185"
}
},
"value": 71,
"unit": {
"@id": "#UserTerm_ng/\u00b5l",
"annotationValue": "ng/\u00b5l"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_cepA_fragment",
"name": "cepA_fragment"
}
]
},
{
"@id": "#Process_DNA_preparation_4",
"name": "DNA preparation_4",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C16612",
"parameterName": {
"@id": "NCIT:C16612",
"annotationValue": "Gene",
"termSource": "NCIT",
"termAccession": "NCIT:C16612"
}
},
"value": {
"@id": "#UserTerm_NCgl0177",
"annotationValue": "NCgl0177"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Primer_forward",
"parameterName": {
"@id": "#UserTerm_Primer_forward",
"annotationValue": "Primer forward"
}
},
"value": {
"@id": "#UserTerm_GATTGGTGCTTAAGTAATGGACTG",
"annotationValue": "GATTGGTGCTTAAGTAATGGACTG"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Primer_reverse",
"parameterName": {
"@id": "#UserTerm_Primer_reverse",
"annotationValue": "Primer reverse"
}
},
"value": {
"@id": "#UserTerm_GAGTAGTAGCAGTGGGTATTTGC",
"annotationValue": "GAGTAGTAGCAGTGGGTATTTGC"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C45677",
"parameterName": {
"@id": "NCIT:C45677",
"annotationValue": "Template",
"termSource": "NCIT",
"termAccession": "NCIT:C45677"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT",
"annotationValue": "C. glutamicum WT"
}
},
{
"category": {
"@id": "#ProtocolParameter/PEFF:0001033",
"parameterName": {
"@id": "PEFF:0001033",
"annotationValue": "Comment",
"termSource": "PEFF",
"termAccession": "PEFF:0001033"
}
}
}
],
"inputs": [
{
"@id": "#Sample_NCgl0177",
"name": "NCgl0177",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Method=PCR",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0088",
"characteristicType": {
"@id": "MIAPPE:0088",
"annotationValue": "Method",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0088"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_34079",
"annotationValue": "PCR",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"@id": "#MaterialAttributeValue/cut out of gel?=no",
"category": {
"@id": "#MaterialAttribute/#UserTerm_cut_out_of_gel?",
"characteristicType": {
"@id": "#UserTerm_cut_out_of_gel?",
"annotationValue": "cut out of gel?"
}
},
"value": {
"@id": "#UserTerm_no",
"annotationValue": "no"
}
},
{
"@id": "#MaterialAttributeValue/Concentration=62ng/\u00b5l",
"category": {
"@id": "#MaterialAttribute/NCIT:C41185",
"characteristicType": {
"@id": "NCIT:C41185",
"annotationValue": "Concentration",
"termSource": "NCIT",
"termAccession": "NCIT:C41185"
}
},
"value": 62,
"unit": {
"@id": "#UserTerm_ng/\u00b5l",
"annotationValue": "ng/\u00b5l"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_NCgl0177_fragment",
"name": "NCgl0177_fragment"
}
]
},
{
"@id": "#Process_DNA_preparation_5",
"name": "DNA preparation_5",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C16612",
"parameterName": {
"@id": "NCIT:C16612",
"annotationValue": "Gene",
"termSource": "NCIT",
"termAccession": "NCIT:C16612"
}
},
"value": {
"@id": "#UserTerm_NCgl2766",
"annotationValue": "NCgl2766"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Primer_forward",
"parameterName": {
"@id": "#UserTerm_Primer_forward",
"annotationValue": "Primer forward"
}
},
"value": {
"@id": "#UserTerm_TAGTCGTATCAAAAAGTGCTCTG",
"annotationValue": "TAGTCGTATCAAAAAGTGCTCTG"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Primer_reverse",
"parameterName": {
"@id": "#UserTerm_Primer_reverse",
"annotationValue": "Primer reverse"
}
},
"value": {
"@id": "#UserTerm_TTGCAATGTTTGTTAATAAATGGGTTC",
"annotationValue": "TTGCAATGTTTGTTAATAAATGGGTTC"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C45677",
"parameterName": {
"@id": "NCIT:C45677",
"annotationValue": "Template",
"termSource": "NCIT",
"termAccession": "NCIT:C45677"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT",
"annotationValue": "C. glutamicum WT"
}
},
{
"category": {
"@id": "#ProtocolParameter/PEFF:0001033",
"parameterName": {
"@id": "PEFF:0001033",
"annotationValue": "Comment",
"termSource": "PEFF",
"termAccession": "PEFF:0001033"
}
}
}
],
"inputs": [
{
"@id": "#Sample_NCgl2766",
"name": "NCgl2766",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Method=PCR",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0088",
"characteristicType": {
"@id": "MIAPPE:0088",
"annotationValue": "Method",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0088"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_34079",
"annotationValue": "PCR",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"@id": "#MaterialAttributeValue/cut out of gel?=no",
"category": {
"@id": "#MaterialAttribute/#UserTerm_cut_out_of_gel?",
"characteristicType": {
"@id": "#UserTerm_cut_out_of_gel?",
"annotationValue": "cut out of gel?"
}
},
"value": {
"@id": "#UserTerm_no",
"annotationValue": "no"
}
},
{
"@id": "#MaterialAttributeValue/Concentration=57ng/\u00b5l",
"category": {
"@id": "#MaterialAttribute/NCIT:C41185",
"characteristicType": {
"@id": "NCIT:C41185",
"annotationValue": "Concentration",
"termSource": "NCIT",
"termAccession": "NCIT:C41185"
}
},
"value": 57,
"unit": {
"@id": "#UserTerm_ng/\u00b5l",
"annotationValue": "ng/\u00b5l"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_NCgl2766_fragment",
"name": "NCgl2766_fragment"
}
]
},
{
"@id": "#Process_DNA_preparation_6",
"name": "DNA preparation_6",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C16612",
"parameterName": {
"@id": "NCIT:C16612",
"annotationValue": "Gene",
"termSource": "NCIT",
"termAccession": "NCIT:C16612"
}
},
"value": {
"@id": "#UserTerm_metH",
"annotationValue": "metH"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Primer_forward",
"parameterName": {
"@id": "#UserTerm_Primer_forward",
"annotationValue": "Primer forward"
}
},
"value": {
"@id": "#UserTerm_GCTGGTGAAGTAACTGAAGTAGACATTG",
"annotationValue": "GCTGGTGAAGTAACTGAAGTAGACATTG"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Primer_reverse",
"parameterName": {
"@id": "#UserTerm_Primer_reverse",
"annotationValue": "Primer reverse"
}
},
"value": {
"@id": "#UserTerm_GTGGCGCTTTGCCTGTGTTG",
"annotationValue": "GTGGCGCTTTGCCTGTGTTG"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C45677",
"parameterName": {
"@id": "NCIT:C45677",
"annotationValue": "Template",
"termSource": "NCIT",
"termAccession": "NCIT:C45677"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT",
"annotationValue": "C. glutamicum WT"
}
},
{
"category": {
"@id": "#ProtocolParameter/PEFF:0001033",
"parameterName": {
"@id": "PEFF:0001033",
"annotationValue": "Comment",
"termSource": "PEFF",
"termAccession": "PEFF:0001033"
}
}
}
],
"inputs": [
{
"@id": "#Sample_metH",
"name": "metH",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Method=PCR",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0088",
"characteristicType": {
"@id": "MIAPPE:0088",
"annotationValue": "Method",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0088"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_34079",
"annotationValue": "PCR",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"@id": "#MaterialAttributeValue/cut out of gel?=no",
"category": {
"@id": "#MaterialAttribute/#UserTerm_cut_out_of_gel?",
"characteristicType": {
"@id": "#UserTerm_cut_out_of_gel?",
"annotationValue": "cut out of gel?"
}
},
"value": {
"@id": "#UserTerm_no",
"annotationValue": "no"
}
},
{
"@id": "#MaterialAttributeValue/Concentration=83ng/\u00b5l",
"category": {
"@id": "#MaterialAttribute/NCIT:C41185",
"characteristicType": {
"@id": "NCIT:C41185",
"annotationValue": "Concentration",
"termSource": "NCIT",
"termAccession": "NCIT:C41185"
}
},
"value": 83,
"unit": {
"@id": "#UserTerm_ng/\u00b5l",
"annotationValue": "ng/\u00b5l"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_metH_fragment",
"name": "metH_fragment"
}
]
},
{
"@id": "#Process_DNA_preparation_7",
"name": "DNA preparation_7",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C16612",
"parameterName": {
"@id": "NCIT:C16612",
"annotationValue": "Gene",
"termSource": "NCIT",
"termAccession": "NCIT:C16612"
}
},
"value": {
"@id": "#UserTerm_gyrB",
"annotationValue": "gyrB"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Primer_forward",
"parameterName": {
"@id": "#UserTerm_Primer_forward",
"annotationValue": "Primer forward"
}
},
"value": {
"@id": "#UserTerm_GGACCTAAGCGTGTAAGATG",
"annotationValue": "GGACCTAAGCGTGTAAGATG"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Primer_reverse",
"parameterName": {
"@id": "#UserTerm_Primer_reverse",
"annotationValue": "Primer reverse"
}
},
"value": {
"@id": "#UserTerm_CAAGACCTTCAAGGATGGTG",
"annotationValue": "CAAGACCTTCAAGGATGGTG"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C45677",
"parameterName": {
"@id": "NCIT:C45677",
"annotationValue": "Template",
"termSource": "NCIT",
"termAccession": "NCIT:C45677"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT",
"annotationValue": "C. glutamicum WT"
}
},
{
"category": {
"@id": "#ProtocolParameter/PEFF:0001033",
"parameterName": {
"@id": "PEFF:0001033",
"annotationValue": "Comment",
"termSource": "PEFF",
"termAccession": "PEFF:0001033"
}
}
}
],
"inputs": [
{
"@id": "#Sample_gyrB",
"name": "gyrB",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Method=PCR",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0088",
"characteristicType": {
"@id": "MIAPPE:0088",
"annotationValue": "Method",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0088"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_34079",
"annotationValue": "PCR",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"@id": "#MaterialAttributeValue/cut out of gel?=yes",
"category": {
"@id": "#MaterialAttribute/#UserTerm_cut_out_of_gel?",
"characteristicType": {
"@id": "#UserTerm_cut_out_of_gel?",
"annotationValue": "cut out of gel?"
}
},
"value": {
"@id": "#UserTerm_yes",
"annotationValue": "yes"
}
},
{
"@id": "#MaterialAttributeValue/Concentration=22ng/\u00b5l",
"category": {
"@id": "#MaterialAttribute/NCIT:C41185",
"characteristicType": {
"@id": "NCIT:C41185",
"annotationValue": "Concentration",
"termSource": "NCIT",
"termAccession": "NCIT:C41185"
}
},
"value": 22,
"unit": {
"@id": "#UserTerm_ng/\u00b5l",
"annotationValue": "ng/\u00b5l"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_gyrB_fragment",
"name": "gyrB_fragment"
}
]
},
{
"@id": "#Process_DNA_preparation_8",
"name": "DNA preparation_8",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NCIT:C16612",
"parameterName": {
"@id": "NCIT:C16612",
"annotationValue": "Gene",
"termSource": "NCIT",
"termAccession": "NCIT:C16612"
}
},
"value": {
"@id": "#UserTerm_acn",
"annotationValue": "acn"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Primer_forward",
"parameterName": {
"@id": "#UserTerm_Primer_forward",
"annotationValue": "Primer forward"
}
},
"value": {
"@id": "#UserTerm_AGGATAATGAAGACGTAGGGTC",
"annotationValue": "AGGATAATGAAGACGTAGGGTC"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Primer_reverse",
"parameterName": {
"@id": "#UserTerm_Primer_reverse",
"annotationValue": "Primer reverse"
}
},
"value": {
"@id": "#UserTerm_TTCTAACTTTTTTAGGGTGAGATTTCG",
"annotationValue": "TTCTAACTTTTTTAGGGTGAGATTTCG"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C45677",
"parameterName": {
"@id": "NCIT:C45677",
"annotationValue": "Template",
"termSource": "NCIT",
"termAccession": "NCIT:C45677"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT",
"annotationValue": "C. glutamicum WT"
}
},
{
"category": {
"@id": "#ProtocolParameter/PEFF:0001033",
"parameterName": {
"@id": "PEFF:0001033",
"annotationValue": "Comment",
"termSource": "PEFF",
"termAccession": "PEFF:0001033"
}
},
"value": {
"@id": "#UserTerm_negative_control_taken_from_Wennerhold_et_al._2006",
"annotationValue": "negative control taken from Wennerhold et al. 2006"
}
}
],
"inputs": [
{
"@id": "#Sample_acn",
"name": "acn",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Method=PCR",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0088",
"characteristicType": {
"@id": "MIAPPE:0088",
"annotationValue": "Method",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0088"
}
},
"value": {
"@id": "http://purl.obolibrary.org/obo/C_34079",
"annotationValue": "PCR",
"termSource": "C",
"termAccession": "http://purl.obolibrary.org/obo/C_34079"
}
},
{
"@id": "#MaterialAttributeValue/cut out of gel?=no",
"category": {
"@id": "#MaterialAttribute/#UserTerm_cut_out_of_gel?",
"characteristicType": {
"@id": "#UserTerm_cut_out_of_gel?",
"annotationValue": "cut out of gel?"
}
},
"value": {
"@id": "#UserTerm_no",
"annotationValue": "no"
}
},
{
"@id": "#MaterialAttributeValue/Concentration=23ng/\u00b5l",
"category": {
"@id": "#MaterialAttribute/NCIT:C41185",
"characteristicType": {
"@id": "NCIT:C41185",
"annotationValue": "Concentration",
"termSource": "NCIT",
"termAccession": "NCIT:C41185"
}
},
"value": 23,
"unit": {
"@id": "#UserTerm_ng/\u00b5l",
"annotationValue": "ng/\u00b5l"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_acn_fragment",
"name": "acn_fragment"
}
]
},
{
"@id": "#Process_Protein_purification",
"name": "Protein purification",
"executesProtocol": {
"@id": "#Protocol_4_InVitroBindingOfDtxR_Protein_purification",
"parameters": [
{
"@id": "#ProtocolParameter/#UserTerm_pre-culture",
"parameterName": {
"@id": "#UserTerm_pre-culture",
"annotationValue": "pre-culture"
}
},
{
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
{
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_Cultivation_medium",
"parameterName": {
"@id": "#UserTerm_Cultivation_medium",
"annotationValue": "Cultivation medium"
}
},
{
"@id": "#ProtocolParameter/NCIT:C120268",
"parameterName": {
"@id": "NCIT:C120268",
"annotationValue": "Inducer",
"termSource": "NCIT",
"termAccession": "NCIT:C120268"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_Inducing_condition",
"parameterName": {
"@id": "#UserTerm_Inducing_condition",
"annotationValue": "Inducing condition"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_Induced_cultivation",
"parameterName": {
"@id": "#UserTerm_Induced_cultivation",
"annotationValue": "Induced cultivation"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_cell_disruption",
"parameterName": {
"@id": "#UserTerm_cell_disruption",
"annotationValue": "cell disruption"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_Final_concentration",
"parameterName": {
"@id": "#UserTerm_Final_concentration",
"annotationValue": "Final concentration"
}
},
{
"@id": "#ProtocolParameter/PEFF:0001033",
"parameterName": {
"@id": "PEFF:0001033",
"annotationValue": "Comment",
"termSource": "PEFF",
"termAccession": "PEFF:0001033"
}
}
],
"components": [
{
"componentName": "E. coli BL21 (DE3) ()",
"componentType": {
"@id": "#UserTerm_Overexpressing_strain",
"annotationValue": "Overexpressing strain"
}
},
{
"componentName": "pET24b-dtxR-C (Wennerhold et al. 2006) ()",
"componentType": {
"@id": "OBI:0000430",
"annotationValue": "plasmid",
"termSource": "OBI",
"termAccession": "OBI:0000430"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_pre-culture",
"parameterName": {
"@id": "#UserTerm_pre-culture",
"annotationValue": "pre-culture"
}
},
"value": {
"@id": "#UserTerm_LB-Kan50,_10_ml_in_100_ml_flask,_overnight",
"annotationValue": "LB-Kan50, 10 ml in 100 ml flask, overnight"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_37\u00b0C",
"annotationValue": "37\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_0.1",
"annotationValue": "0.1"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Cultivation_medium",
"parameterName": {
"@id": "#UserTerm_Cultivation_medium",
"annotationValue": "Cultivation medium"
}
},
"value": {
"@id": "#UserTerm_LB-Kan50,_100_ml_in_1_l_flask",
"annotationValue": "LB-Kan50, 100 ml in 1 l flask"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C120268",
"parameterName": {
"@id": "NCIT:C120268",
"annotationValue": "Inducer",
"termSource": "NCIT",
"termAccession": "NCIT:C120268"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_IPTG",
"annotationValue": "100 \u00b5M IPTG"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Inducing_condition",
"parameterName": {
"@id": "#UserTerm_Inducing_condition",
"annotationValue": "Inducing condition"
}
},
"value": {
"@id": "#UserTerm_OD600=0.6_(approx._2_h)",
"annotationValue": "OD600=0.6 (approx. 2 h)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Induced_cultivation",
"parameterName": {
"@id": "#UserTerm_Induced_cultivation",
"annotationValue": "Induced cultivation"
}
},
"value": {
"@id": "#UserTerm_18\u00b0C,_overnight",
"annotationValue": "18\u00b0C, overnight"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cell_disruption",
"parameterName": {
"@id": "#UserTerm_cell_disruption",
"annotationValue": "cell disruption"
}
},
"value": {
"@id": "#UserTerm_MultiShot_Cell_Disruptor",
"annotationValue": "MultiShot Cell Disruptor"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Final_concentration",
"parameterName": {
"@id": "#UserTerm_Final_concentration",
"annotationValue": "Final concentration"
}
},
"value": {
"@id": "#UserTerm_926_\u00b5g/ml",
"annotationValue": "926 \u00b5g/ml"
}
},
{
"category": {
"@id": "#ProtocolParameter/PEFF:0001033",
"parameterName": {
"@id": "PEFF:0001033",
"annotationValue": "Comment",
"termSource": "PEFF",
"termAccession": "PEFF:0001033"
}
},
"value": {
"@id": "#UserTerm_only_half_of_the_whole_approach_was_purified_(50_ml_pellet)",
"annotationValue": "only half of the whole approach was purified (50 ml pellet)"
}
}
],
"inputs": [
{
"@id": "#Sample_E.coli_culture",
"name": "E.coli culture",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Protein of interest=DtxR",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Protein_of_interest",
"characteristicType": {
"@id": "#UserTerm_Protein_of_interest",
"annotationValue": "Protein of interest"
}
},
"value": {
"@id": "#UserTerm_DtxR",
"annotationValue": "DtxR"
}
},
{
"@id": "#MaterialAttributeValue/Tag=HHHHLEHHHHHH",
"category": {
"@id": "#MaterialAttribute/#UserTerm_Tag",
"characteristicType": {
"@id": "#UserTerm_Tag",
"annotationValue": "Tag"
}
},
"value": {
"@id": "#UserTerm_HHHHLEHHHHHH",
"annotationValue": "HHHHLEHHHHHH"
}
},
{
"@id": "#MaterialAttributeValue/Method=Ni-NTA agarose column gravity flow protocol",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0088",
"characteristicType": {
"@id": "MIAPPE:0088",
"annotationValue": "Method",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0088"
}
},
"value": {
"@id": "#UserTerm_Ni-NTA_agarose_column_gravity_flow_protocol",
"annotationValue": "Ni-NTA agarose column gravity flow protocol"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_purified_DtxR",
"name": "purified DtxR"
}
]
}
],
"assays": [
{
"filename": "assays/4_ElectronMobilityShiftAssays_DtxR/isa.assay.xlsx",
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/",
"measurementType": {
"@id": "#UserTerm_Electron_mobility_shift_assay",
"annotationValue": "Electron mobility shift assay"
},
"dataFiles": [
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel2.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel2.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel1.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel1.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel2.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel2.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel3.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel3.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel4.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel4.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel5.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel5.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel6.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel6.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff\t\t\t\t",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff\t\t\t\t",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff\t\t\t",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff\t\t\t",
"type": "Raw Data File"
}
],
"materials": {
"samples": [
{
"@id": "#Sample_hmuO",
"name": "hmuO"
},
{
"@id": "#Sample_ripA_fragment",
"name": "ripA_fragment"
},
{
"@id": "#Sample_metH_fragment",
"name": "metH_fragment"
},
{
"@id": "#Sample_gyrB_fragment",
"name": "gyrB_fragment"
},
{
"@id": "#Sample_cepA_fragment",
"name": "cepA_fragment"
},
{
"@id": "#Sample_acn_fragment",
"name": "acn_fragment"
},
{
"@id": "#Sample_xerC_fragment",
"name": "xerC_fragment"
},
{
"@id": "#Sample_NCgl1200_fragment",
"name": "NCgl1200_fragment"
},
{
"@id": "#Sample_wzy",
"name": "wzy"
},
{
"@id": "#Sample_pta",
"name": "pta"
},
{
"@id": "#Sample_NCgl0177_fragment",
"name": "NCgl0177_fragment"
},
{
"@id": "#Sample_NCgl2766_fragment",
"name": "NCgl2766_fragment"
}
]
},
"processSequence": [
{
"@id": "#Process_ElectronMobilityShift_Gel_0",
"name": "ElectronMobilityShift Gel_0",
"executesProtocol": {
"@id": "#Protocol_4_InVitroBindingOfDtxR_4_ElectronMobilityShiftAssays_DtxR_ElectronMobilityShift_Gel_0",
"parameters": [
{
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
}
],
"components": [
{
"componentName": "purified DtxR ()",
"componentType": {
"@id": "PR:000000001",
"annotationValue": "protein",
"termSource": "PR",
"termAccession": "PR:000000001"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
"value": {
"@id": "#UserTerm_1",
"annotationValue": "1"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
},
"value": {
"@id": "#UserTerm_0x",
"annotationValue": "0x"
}
}
],
"inputs": [
{
"@id": "#Sample_hmuO",
"name": "hmuO"
},
{
"@id": "#Sample_ripA_fragment",
"name": "ripA_fragment"
},
{
"@id": "#Sample_metH_fragment",
"name": "metH_fragment"
},
{
"@id": "#Sample_ripA_fragment",
"name": "ripA_fragment"
},
{
"@id": "#Sample_gyrB_fragment",
"name": "gyrB_fragment"
},
{
"@id": "#Sample_hmuO",
"name": "hmuO"
},
{
"@id": "#Sample_cepA_fragment",
"name": "cepA_fragment"
},
{
"@id": "#Sample_metH_fragment",
"name": "metH_fragment"
}
],
"outputs": [
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel2.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel2.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel1.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel1.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel2.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel2.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel3.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel3.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel4.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel4.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel5.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel5.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel6.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel6.tiff",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_ElectronMobilityShift_Gel_1",
"name": "ElectronMobilityShift Gel_1",
"executesProtocol": {
"@id": "#Protocol_4_InVitroBindingOfDtxR_4_ElectronMobilityShiftAssays_DtxR_ElectronMobilityShift_Gel_1",
"parameters": [
{
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
}
],
"components": [
{
"componentName": "purified DtxR ()",
"componentType": {
"@id": "PR:000000001",
"annotationValue": "protein",
"termSource": "PR",
"termAccession": "PR:000000001"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
"value": {
"@id": "#UserTerm_2",
"annotationValue": "2"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
},
"value": {
"@id": "#UserTerm_25x",
"annotationValue": "25x"
}
}
],
"inputs": [
{
"@id": "#Sample_hmuO",
"name": "hmuO"
},
{
"@id": "#Sample_ripA_fragment",
"name": "ripA_fragment"
}
],
"outputs": [
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel2.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel2.tiff",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_ElectronMobilityShift_Gel_2",
"name": "ElectronMobilityShift Gel_2",
"executesProtocol": {
"@id": "#Protocol_4_InVitroBindingOfDtxR_4_ElectronMobilityShiftAssays_DtxR_ElectronMobilityShift_Gel_2",
"parameters": [
{
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
}
],
"components": [
{
"componentName": "purified DtxR ()",
"componentType": {
"@id": "PR:000000001",
"annotationValue": "protein",
"termSource": "PR",
"termAccession": "PR:000000001"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
},
"value": {
"@id": "#UserTerm_50x",
"annotationValue": "50x"
}
}
],
"inputs": [
{
"@id": "#Sample_hmuO",
"name": "hmuO"
},
{
"@id": "#Sample_ripA_fragment",
"name": "ripA_fragment"
}
],
"outputs": [
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel2.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel2.tiff",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_ElectronMobilityShift_Gel_3",
"name": "ElectronMobilityShift Gel_3",
"executesProtocol": {
"@id": "#Protocol_4_InVitroBindingOfDtxR_4_ElectronMobilityShiftAssays_DtxR_ElectronMobilityShift_Gel_3",
"parameters": [
{
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
}
],
"components": [
{
"componentName": "purified DtxR ()",
"componentType": {
"@id": "PR:000000001",
"annotationValue": "protein",
"termSource": "PR",
"termAccession": "PR:000000001"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
"value": {
"@id": "#UserTerm_4",
"annotationValue": "4"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
},
"value": {
"@id": "#UserTerm_100x",
"annotationValue": "100x"
}
}
],
"inputs": [
{
"@id": "#Sample_hmuO",
"name": "hmuO"
},
{
"@id": "#Sample_ripA_fragment",
"name": "ripA_fragment"
}
],
"outputs": [
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel2.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel2.tiff",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_ElectronMobilityShift_Gel_4",
"name": "ElectronMobilityShift Gel_4",
"executesProtocol": {
"@id": "#Protocol_4_InVitroBindingOfDtxR_4_ElectronMobilityShiftAssays_DtxR_ElectronMobilityShift_Gel_4",
"parameters": [
{
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
}
],
"components": [
{
"componentName": "purified DtxR ()",
"componentType": {
"@id": "PR:000000001",
"annotationValue": "protein",
"termSource": "PR",
"termAccession": "PR:000000001"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
"value": {
"@id": "#UserTerm_5",
"annotationValue": "5"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
},
"value": {
"@id": "#UserTerm_200x",
"annotationValue": "200x"
}
}
],
"inputs": [
{
"@id": "#Sample_hmuO",
"name": "hmuO"
},
{
"@id": "#Sample_ripA_fragment",
"name": "ripA_fragment"
}
],
"outputs": [
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel2.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel2.tiff",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_ElectronMobilityShift_Gel_5",
"name": "ElectronMobilityShift Gel_5",
"executesProtocol": {
"@id": "#Protocol_4_InVitroBindingOfDtxR_4_ElectronMobilityShiftAssays_DtxR_ElectronMobilityShift_Gel_5",
"parameters": [
{
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
}
],
"components": [
{
"componentName": "purified DtxR ()",
"componentType": {
"@id": "PR:000000001",
"annotationValue": "protein",
"termSource": "PR",
"termAccession": "PR:000000001"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
"value": {
"@id": "#UserTerm_6",
"annotationValue": "6"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
},
"value": {
"@id": "#UserTerm_0x",
"annotationValue": "0x"
}
}
],
"inputs": [
{
"@id": "#Sample_acn_fragment",
"name": "acn_fragment"
},
{
"@id": "#Sample_hmuO",
"name": "hmuO"
}
],
"outputs": [
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff\t\t\t\t",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff\t\t\t\t",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel2.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel2.tiff",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_ElectronMobilityShift_Gel_6",
"name": "ElectronMobilityShift Gel_6",
"executesProtocol": {
"@id": "#Protocol_4_InVitroBindingOfDtxR_4_ElectronMobilityShiftAssays_DtxR_ElectronMobilityShift_Gel_6",
"parameters": [
{
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
}
],
"components": [
{
"componentName": "purified DtxR ()",
"componentType": {
"@id": "PR:000000001",
"annotationValue": "protein",
"termSource": "PR",
"termAccession": "PR:000000001"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
"value": {
"@id": "#UserTerm_7",
"annotationValue": "7"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
},
"value": {
"@id": "#UserTerm_25x",
"annotationValue": "25x"
}
}
],
"inputs": [
{
"@id": "#Sample_acn_fragment",
"name": "acn_fragment"
},
{
"@id": "#Sample_hmuO",
"name": "hmuO"
}
],
"outputs": [
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff\t\t\t",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff\t\t\t",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel2.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel2.tiff",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_ElectronMobilityShift_Gel_7",
"name": "ElectronMobilityShift Gel_7",
"executesProtocol": {
"@id": "#Protocol_4_InVitroBindingOfDtxR_4_ElectronMobilityShiftAssays_DtxR_ElectronMobilityShift_Gel_7",
"parameters": [
{
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
}
],
"components": [
{
"componentName": "purified DtxR ()",
"componentType": {
"@id": "PR:000000001",
"annotationValue": "protein",
"termSource": "PR",
"termAccession": "PR:000000001"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
"value": {
"@id": "#UserTerm_8",
"annotationValue": "8"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
},
"value": {
"@id": "#UserTerm_50x",
"annotationValue": "50x"
}
}
],
"inputs": [
{
"@id": "#Sample_acn_fragment",
"name": "acn_fragment"
},
{
"@id": "#Sample_hmuO",
"name": "hmuO"
},
{
"@id": "#Sample_acn_fragment",
"name": "acn_fragment"
}
],
"outputs": [
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff\t\t\t",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff\t\t\t",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel2.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel2.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel3.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel3.tiff",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_ElectronMobilityShift_Gel_8",
"name": "ElectronMobilityShift Gel_8",
"executesProtocol": {
"@id": "#Protocol_4_InVitroBindingOfDtxR_4_ElectronMobilityShiftAssays_DtxR_ElectronMobilityShift_Gel_8",
"parameters": [
{
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
}
],
"components": [
{
"componentName": "purified DtxR ()",
"componentType": {
"@id": "PR:000000001",
"annotationValue": "protein",
"termSource": "PR",
"termAccession": "PR:000000001"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
"value": {
"@id": "#UserTerm_9",
"annotationValue": "9"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
},
"value": {
"@id": "#UserTerm_100x",
"annotationValue": "100x"
}
}
],
"inputs": [
{
"@id": "#Sample_acn_fragment",
"name": "acn_fragment"
},
{
"@id": "#Sample_hmuO",
"name": "hmuO"
}
],
"outputs": [
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff\t\t\t",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff\t\t\t",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel2.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel2.tiff",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_ElectronMobilityShift_Gel_9",
"name": "ElectronMobilityShift Gel_9",
"executesProtocol": {
"@id": "#Protocol_4_InVitroBindingOfDtxR_4_ElectronMobilityShiftAssays_DtxR_ElectronMobilityShift_Gel_9",
"parameters": [
{
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
}
],
"components": [
{
"componentName": "purified DtxR ()",
"componentType": {
"@id": "PR:000000001",
"annotationValue": "protein",
"termSource": "PR",
"termAccession": "PR:000000001"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
"value": {
"@id": "#UserTerm_10",
"annotationValue": "10"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
},
"value": {
"@id": "#UserTerm_200x",
"annotationValue": "200x"
}
}
],
"inputs": [
{
"@id": "#Sample_acn_fragment",
"name": "acn_fragment"
},
{
"@id": "#Sample_hmuO",
"name": "hmuO"
}
],
"outputs": [
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff\t\t\t",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel1.tiff\t\t\t",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel2.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/controlgel2.tiff",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_ElectronMobilityShift_Gel_10",
"name": "ElectronMobilityShift Gel_10",
"executesProtocol": {
"@id": "#Protocol_4_InVitroBindingOfDtxR_4_ElectronMobilityShiftAssays_DtxR_ElectronMobilityShift_Gel_10",
"parameters": [
{
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
}
],
"components": [
{
"componentName": "purified DtxR ()",
"componentType": {
"@id": "PR:000000001",
"annotationValue": "protein",
"termSource": "PR",
"termAccession": "PR:000000001"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
"value": {
"@id": "#UserTerm_2",
"annotationValue": "2"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
},
"value": {
"@id": "#UserTerm_50x",
"annotationValue": "50x"
}
}
],
"inputs": [
{
"@id": "#Sample_metH_fragment",
"name": "metH_fragment"
},
{
"@id": "#Sample_ripA_fragment",
"name": "ripA_fragment"
},
{
"@id": "#Sample_gyrB_fragment",
"name": "gyrB_fragment"
},
{
"@id": "#Sample_hmuO",
"name": "hmuO"
}
],
"outputs": [
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel1.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel1.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel2.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel2.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel3.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel3.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel4.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel4.tiff",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_ElectronMobilityShift_Gel_11",
"name": "ElectronMobilityShift Gel_11",
"executesProtocol": {
"@id": "#Protocol_4_InVitroBindingOfDtxR_4_ElectronMobilityShiftAssays_DtxR_ElectronMobilityShift_Gel_11",
"parameters": [
{
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
}
],
"components": [
{
"componentName": "purified DtxR ()",
"componentType": {
"@id": "PR:000000001",
"annotationValue": "protein",
"termSource": "PR",
"termAccession": "PR:000000001"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
},
"value": {
"@id": "#UserTerm_200x",
"annotationValue": "200x"
}
}
],
"inputs": [
{
"@id": "#Sample_metH_fragment",
"name": "metH_fragment"
},
{
"@id": "#Sample_ripA_fragment",
"name": "ripA_fragment"
},
{
"@id": "#Sample_gyrB_fragment",
"name": "gyrB_fragment"
},
{
"@id": "#Sample_hmuO",
"name": "hmuO"
}
],
"outputs": [
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel1.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel1.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel2.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel2.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel3.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel3.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel4.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel4.tiff",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_ElectronMobilityShift_Gel_12",
"name": "ElectronMobilityShift Gel_12",
"executesProtocol": {
"@id": "#Protocol_4_InVitroBindingOfDtxR_4_ElectronMobilityShiftAssays_DtxR_ElectronMobilityShift_Gel_12",
"parameters": [
{
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
}
],
"components": [
{
"componentName": "purified DtxR ()",
"componentType": {
"@id": "PR:000000001",
"annotationValue": "protein",
"termSource": "PR",
"termAccession": "PR:000000001"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
"value": {
"@id": "#UserTerm_4",
"annotationValue": "4"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
},
"value": {
"@id": "#UserTerm_0x",
"annotationValue": "0x"
}
}
],
"inputs": [
{
"@id": "#Sample_xerC_fragment",
"name": "xerC_fragment"
},
{
"@id": "#Sample_NCgl1200_fragment",
"name": "NCgl1200_fragment"
},
{
"@id": "#Sample_wzy",
"name": "wzy"
},
{
"@id": "#Sample_pta",
"name": "pta"
},
{
"@id": "#Sample_NCgl0177_fragment",
"name": "NCgl0177_fragment"
},
{
"@id": "#Sample_gyrB_fragment",
"name": "gyrB_fragment"
}
],
"outputs": [
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel1.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel1.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel2.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel2.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel3.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel3.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel4.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel4.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel5.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel5.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel6.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel6.tiff",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_ElectronMobilityShift_Gel_13",
"name": "ElectronMobilityShift Gel_13",
"executesProtocol": {
"@id": "#Protocol_4_InVitroBindingOfDtxR_4_ElectronMobilityShiftAssays_DtxR_ElectronMobilityShift_Gel_13",
"parameters": [
{
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
}
],
"components": [
{
"componentName": "purified DtxR ()",
"componentType": {
"@id": "PR:000000001",
"annotationValue": "protein",
"termSource": "PR",
"termAccession": "PR:000000001"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
"value": {
"@id": "#UserTerm_5",
"annotationValue": "5"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
},
"value": {
"@id": "#UserTerm_50x",
"annotationValue": "50x"
}
}
],
"inputs": [
{
"@id": "#Sample_xerC_fragment",
"name": "xerC_fragment"
},
{
"@id": "#Sample_NCgl1200_fragment",
"name": "NCgl1200_fragment"
},
{
"@id": "#Sample_wzy",
"name": "wzy"
},
{
"@id": "#Sample_pta",
"name": "pta"
}
],
"outputs": [
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel1.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel1.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel2.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel2.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel3.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel3.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel4.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel4.tiff",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_ElectronMobilityShift_Gel_14",
"name": "ElectronMobilityShift Gel_14",
"executesProtocol": {
"@id": "#Protocol_4_InVitroBindingOfDtxR_4_ElectronMobilityShiftAssays_DtxR_ElectronMobilityShift_Gel_14",
"parameters": [
{
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
}
],
"components": [
{
"componentName": "purified DtxR ()",
"componentType": {
"@id": "PR:000000001",
"annotationValue": "protein",
"termSource": "PR",
"termAccession": "PR:000000001"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
"value": {
"@id": "#UserTerm_6",
"annotationValue": "6"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
},
"value": {
"@id": "#UserTerm_200x",
"annotationValue": "200x"
}
}
],
"inputs": [
{
"@id": "#Sample_xerC_fragment",
"name": "xerC_fragment"
},
{
"@id": "#Sample_NCgl1200_fragment",
"name": "NCgl1200_fragment"
},
{
"@id": "#Sample_wzy",
"name": "wzy"
},
{
"@id": "#Sample_pta",
"name": "pta"
}
],
"outputs": [
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel1.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel1.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel2.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel2.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel3.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel3.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel4.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel4.tiff",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_ElectronMobilityShift_Gel_15",
"name": "ElectronMobilityShift Gel_15",
"executesProtocol": {
"@id": "#Protocol_4_InVitroBindingOfDtxR_4_ElectronMobilityShiftAssays_DtxR_ElectronMobilityShift_Gel_15",
"parameters": [
{
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
}
],
"components": [
{
"componentName": "purified DtxR ()",
"componentType": {
"@id": "PR:000000001",
"annotationValue": "protein",
"termSource": "PR",
"termAccession": "PR:000000001"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
"value": {
"@id": "#UserTerm_7",
"annotationValue": "7"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
},
"value": {
"@id": "#UserTerm_0x",
"annotationValue": "0x"
}
}
],
"inputs": [
{
"@id": "#Sample_acn_fragment",
"name": "acn_fragment"
},
{
"@id": "#Sample_NCgl2766_fragment",
"name": "NCgl2766_fragment"
},
{
"@id": "#Sample_acn_fragment",
"name": "acn_fragment"
}
],
"outputs": [
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel3.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel3.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel5.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel5.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel6.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel6.tiff",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_ElectronMobilityShift_Gel_16",
"name": "ElectronMobilityShift Gel_16",
"executesProtocol": {
"@id": "#Protocol_4_InVitroBindingOfDtxR_4_ElectronMobilityShiftAssays_DtxR_ElectronMobilityShift_Gel_16",
"parameters": [
{
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
}
],
"components": [
{
"componentName": "purified DtxR ()",
"componentType": {
"@id": "PR:000000001",
"annotationValue": "protein",
"termSource": "PR",
"termAccession": "PR:000000001"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
"value": {
"@id": "#UserTerm_9",
"annotationValue": "9"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
},
"value": {
"@id": "#UserTerm_200x",
"annotationValue": "200x"
}
}
],
"inputs": [
{
"@id": "#Sample_acn_fragment",
"name": "acn_fragment"
}
],
"outputs": [
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel3.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel3.tiff",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_ElectronMobilityShift_Gel_17",
"name": "ElectronMobilityShift Gel_17",
"executesProtocol": {
"@id": "#Protocol_4_InVitroBindingOfDtxR_4_ElectronMobilityShiftAssays_DtxR_ElectronMobilityShift_Gel_17",
"parameters": [
{
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
}
],
"components": [
{
"componentName": "purified DtxR ()",
"componentType": {
"@id": "PR:000000001",
"annotationValue": "protein",
"termSource": "PR",
"termAccession": "PR:000000001"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
"value": {
"@id": "#UserTerm_2",
"annotationValue": "2"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
},
"value": {
"@id": "#UserTerm_300x",
"annotationValue": "300x"
}
}
],
"inputs": [
{
"@id": "#Sample_cepA_fragment",
"name": "cepA_fragment"
},
{
"@id": "#Sample_metH_fragment",
"name": "metH_fragment"
}
],
"outputs": [
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel5.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel5.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel6.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel6.tiff",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_ElectronMobilityShift_Gel_18",
"name": "ElectronMobilityShift Gel_18",
"executesProtocol": {
"@id": "#Protocol_4_InVitroBindingOfDtxR_4_ElectronMobilityShiftAssays_DtxR_ElectronMobilityShift_Gel_18",
"parameters": [
{
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
}
],
"components": [
{
"componentName": "purified DtxR ()",
"componentType": {
"@id": "PR:000000001",
"annotationValue": "protein",
"termSource": "PR",
"termAccession": "PR:000000001"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
},
"value": {
"@id": "#UserTerm_400x",
"annotationValue": "400x"
}
}
],
"inputs": [
{
"@id": "#Sample_cepA_fragment",
"name": "cepA_fragment"
},
{
"@id": "#Sample_metH_fragment",
"name": "metH_fragment"
}
],
"outputs": [
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel5.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel5.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel6.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel6.tiff",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_ElectronMobilityShift_Gel_19",
"name": "ElectronMobilityShift Gel_19",
"executesProtocol": {
"@id": "#Protocol_4_InVitroBindingOfDtxR_4_ElectronMobilityShiftAssays_DtxR_ElectronMobilityShift_Gel_19",
"parameters": [
{
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
}
],
"components": [
{
"componentName": "purified DtxR ()",
"componentType": {
"@id": "PR:000000001",
"annotationValue": "protein",
"termSource": "PR",
"termAccession": "PR:000000001"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
"value": {
"@id": "#UserTerm_5",
"annotationValue": "5"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
},
"value": {
"@id": "#UserTerm_300x",
"annotationValue": "300x"
}
}
],
"inputs": [
{
"@id": "#Sample_NCgl0177_fragment",
"name": "NCgl0177_fragment"
},
{
"@id": "#Sample_gyrB_fragment",
"name": "gyrB_fragment"
}
],
"outputs": [
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel5.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel5.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel6.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel6.tiff",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_ElectronMobilityShift_Gel_20",
"name": "ElectronMobilityShift Gel_20",
"executesProtocol": {
"@id": "#Protocol_4_InVitroBindingOfDtxR_4_ElectronMobilityShiftAssays_DtxR_ElectronMobilityShift_Gel_20",
"parameters": [
{
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
}
],
"components": [
{
"componentName": "purified DtxR ()",
"componentType": {
"@id": "PR:000000001",
"annotationValue": "protein",
"termSource": "PR",
"termAccession": "PR:000000001"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
"value": {
"@id": "#UserTerm_6",
"annotationValue": "6"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
},
"value": {
"@id": "#UserTerm_400x",
"annotationValue": "400x"
}
}
],
"inputs": [
{
"@id": "#Sample_NCgl0177_fragment",
"name": "NCgl0177_fragment"
},
{
"@id": "#Sample_gyrB_fragment",
"name": "gyrB_fragment"
}
],
"outputs": [
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel5.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel5.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel6.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel6.tiff",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_ElectronMobilityShift_Gel_21",
"name": "ElectronMobilityShift Gel_21",
"executesProtocol": {
"@id": "#Protocol_4_InVitroBindingOfDtxR_4_ElectronMobilityShiftAssays_DtxR_ElectronMobilityShift_Gel_21",
"parameters": [
{
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
}
],
"components": [
{
"componentName": "purified DtxR ()",
"componentType": {
"@id": "PR:000000001",
"annotationValue": "protein",
"termSource": "PR",
"termAccession": "PR:000000001"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
"value": {
"@id": "#UserTerm_8",
"annotationValue": "8"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
},
"value": {
"@id": "#UserTerm_300x",
"annotationValue": "300x"
}
}
],
"inputs": [
{
"@id": "#Sample_NCgl2766_fragment",
"name": "NCgl2766_fragment"
},
{
"@id": "#Sample_acn_fragment",
"name": "acn_fragment"
}
],
"outputs": [
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel5.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel5.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel6.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel6.tiff",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_ElectronMobilityShift_Gel_22",
"name": "ElectronMobilityShift Gel_22",
"executesProtocol": {
"@id": "#Protocol_4_InVitroBindingOfDtxR_4_ElectronMobilityShiftAssays_DtxR_ElectronMobilityShift_Gel_22",
"parameters": [
{
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
"@id": "#UserTerm_protein_concentration",
"annotationValue": "protein concentration"
}
}
],
"components": [
{
"componentName": "purified DtxR ()",
"componentType": {
"@id": "PR:000000001",
"annotationValue": "protein",
"termSource": "PR",
"termAccession": "PR:000000001"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000153",
"parameterName": {
"@id": "DPBO:0000153",
"annotationValue": "gel lane number",
"termSource": "DPBO",
"termAccession": "DPBO:0000153"
}
},
"value": {
"@id": "#UserTerm_9",
"annotationValue": "9"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_protein_concentration",
"parameterName": {
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"annotationValue": "protein concentration"
}
},
"value": {
"@id": "#UserTerm_400x",
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}
}
],
"inputs": [
{
"@id": "#Sample_NCgl2766_fragment",
"name": "NCgl2766_fragment"
},
{
"@id": "#Sample_acn_fragment",
"name": "acn_fragment"
}
],
"outputs": [
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel5.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel5.tiff",
"type": "Raw Data File"
},
{
"@id": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel6.tiff",
"name": "assays/4_ElectronMobilityShiftAssays_DtxR/dataset/Gel6.tiff",
"type": "Raw Data File"
}
]
}
]
}
],
"characteristicCategories": [
{
"@id": "#MaterialAttribute/MIAPPE:0088",
"characteristicType": {
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"annotationValue": "Method",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0088"
}
},
{
"@id": "#MaterialAttribute/#UserTerm_cut_out_of_gel?",
"characteristicType": {
"@id": "#UserTerm_cut_out_of_gel?",
"annotationValue": "cut out of gel?"
}
},
{
"@id": "#MaterialAttribute/NCIT:C41185",
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"annotationValue": "Concentration",
"termSource": "NCIT",
"termAccession": "NCIT:C41185"
}
},
{
"@id": "#MaterialAttribute/#UserTerm_Protein_of_interest",
"characteristicType": {
"@id": "#UserTerm_Protein_of_interest",
"annotationValue": "Protein of interest"
}
},
{
"@id": "#MaterialAttribute/#UserTerm_Tag",
"characteristicType": {
"@id": "#UserTerm_Tag",
"annotationValue": "Tag"
}
}
],
"unitCategories": [
{
"@id": "#UserTerm_ng/\u00b5l",
"annotationValue": "ng/\u00b5l"
}
]
},
{
"@id": "studies/PLACEHOLDER_STUDY_1-2_qPCR-taggedVariants/",
"filename": "studies/PLACEHOLDER_STUDY_1-2_qPCR-taggedVariants/isa.study.xlsx",
"identifier": "PLACEHOLDER_STUDY_1-2_qPCR-taggedVariants",
"people": [
{
"@id": "ai.krueger@fz-juelich.de",
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"comments": [
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"name": "performer (ARC:00000168) 1-2_qPCR-taggedVariants",
"value": "1-2_qPCR-taggedVariants"
}
]
}
],
"assays": [
{
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"annotationValue": "qPCR"
},
"technologyType": {
"@id": "#UserTerm_NEB_Luna_Universal_One-Step_RT-qPCR_Kit",
"annotationValue": "NEB Luna Universal One-Step RT-qPCR Kit"
},
"technologyPlatform": "qTower (analytikjena)",
"dataFiles": [
{
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"type": "Raw Data File"
}
],
"materials": {
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"name": "C. glutamicum ATCC13032 WT",
"characteristics": [
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"@id": "#MaterialAttributeValue/replicate=1",
"category": {
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}
},
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}
}
]
},
{
"@id": "#Sample_C._glutamicum_ATCC13032_WT",
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"characteristics": [
{
"@id": "#MaterialAttributeValue/replicate=2",
"category": {
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}
},
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}
]
},
{
"@id": "#Sample_C._glutamicum_ATCC13032::dtxR-His-Cterm-2link\t\t",
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}
},
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}
}
]
},
{
"@id": "#Sample_C._glutamicum_ATCC13032::dtxR-His-Cterm-2link",
"name": "C. glutamicum ATCC13032::dtxR-His-Cterm-2link",
"characteristics": [
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"@id": "#MaterialAttributeValue/replicate=2",
"category": {
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}
},
"value": {
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}
}
]
},
{
"@id": "#Sample_C._glutamicum_ATCC13032::dtxR-Strep-Nterm-4link",
"name": "C. glutamicum ATCC13032::dtxR-Strep-Nterm-4link",
"characteristics": [
{
"@id": "#MaterialAttributeValue/replicate=1",
"category": {
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}
},
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}
}
]
},
{
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"characteristics": [
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"characteristicType": {
"@id": "#UserTerm_replicate",
"annotationValue": "replicate"
}
},
"value": {
"@id": "#UserTerm_2",
"annotationValue": "2"
}
}
]
},
{
"@id": "#Sample_C._glutamicum_ATCC13032::dtxR-His-Cterm-2link",
"name": "C. glutamicum ATCC13032::dtxR-His-Cterm-2link",
"characteristics": [
{
"@id": "#MaterialAttributeValue/replicate=1",
"category": {
"@id": "#MaterialAttribute/#UserTerm_replicate",
"characteristicType": {
"@id": "#UserTerm_replicate",
"annotationValue": "replicate"
}
},
"value": {
"@id": "#UserTerm_1",
"annotationValue": "1"
}
}
]
}
]
},
"characteristicCategories": [
{
"@id": "#MaterialAttribute/#UserTerm_replicate",
"characteristicType": {
"@id": "#UserTerm_replicate",
"annotationValue": "replicate"
}
}
],
"unitCategories": [
{
"@id": "#UserTerm_ng/\u00b5l",
"annotationValue": "ng/\u00b5l"
}
],
"processSequence": [
{
"@id": "#Process_qPCRsamples_0",
"name": "qPCRsamples_0",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Main_culture_cultivation_condition",
"parameterName": {
"@id": "#UserTerm_Main_culture_cultivation_condition",
"annotationValue": "Main culture cultivation condition"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose",
"annotationValue": "CGXII + 2% glucose"
}
},
{
"category": {
"@id": "#ProtocolParameter/TO:0006049",
"parameterName": {
"@id": "TO:0006049",
"annotationValue": "iron concentration",
"termSource": "TO",
"termAccession": "TO:0006049"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Cultivation_volume",
"parameterName": {
"@id": "#UserTerm_Cultivation_volume",
"annotationValue": "Cultivation volume"
}
},
"value": {
"@id": "#UserTerm_20_ml",
"annotationValue": "20 ml"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Harvesting_OD600",
"parameterName": {
"@id": "#UserTerm_Harvesting_OD600",
"annotationValue": "Harvesting OD600"
}
},
"value": {
"@id": "#UserTerm_5.28",
"annotationValue": "5.28"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Harvesting_timepoint",
"parameterName": {
"@id": "#UserTerm_Harvesting_timepoint",
"annotationValue": "Harvesting timepoint"
}
},
"value": {
"@id": "#UserTerm_4.75_h",
"annotationValue": "4.75 h"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_RNA_isolation",
"parameterName": {
"@id": "#UserTerm_RNA_isolation",
"annotationValue": "RNA isolation"
}
},
"value": {
"@id": "#UserTerm_NEB_Monarch_RNA_Isolation_Kit",
"annotationValue": "NEB Monarch RNA Isolation Kit"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_RNA_concentration",
"parameterName": {
"@id": "#UserTerm_RNA_concentration",
"annotationValue": "RNA concentration"
}
},
"value": 528,
"unit": {
"@id": "#UserTerm_ng/\u00b5l",
"annotationValue": "ng/\u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_dtxR_forward",
"parameterName": {
"@id": "#UserTerm_qPCR_primer_dtxR_forward",
"annotationValue": "qPCR primer dtxR forward"
}
},
"value": {
"@id": "#UserTerm_TTGAGCAGTTCCAGGCACTC",
"annotationValue": "TTGAGCAGTTCCAGGCACTC"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_dtxR_reverse",
"parameterName": {
"@id": "#UserTerm_qPCR_primer_dtxR_reverse",
"annotationValue": "qPCR primer dtxR reverse"
}
},
"value": {
"@id": "#UserTerm_TTTCTACGCGGACTGCATGT",
"annotationValue": "TTTCTACGCGGACTGCATGT"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_ddh_forward",
"parameterName": {
"@id": "#UserTerm_qPCR_primer_ddh_forward",
"annotationValue": "qPCR primer ddh forward"
}
},
"value": {
"@id": "#UserTerm_CCGGAAAGCAAACCCACAAG",
"annotationValue": "CCGGAAAGCAAACCCACAAG"
}
},
{
"category": {
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"@id": "#UserTerm_qPCR_primer_ddh_reverse",
"annotationValue": "qPCR primer ddh reverse"
}
},
"value": {
"@id": "#UserTerm_CTCGGAGTCGAAGGTTGCTT",
"annotationValue": "CTCGGAGTCGAAGGTTGCTT"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR",
"parameterName": {
"@id": "#UserTerm_qPCR",
"annotationValue": "qPCR"
}
},
"value": {
"@id": "#UserTerm_Luna_Universal_One_Step_RT-qPCR_Kit",
"annotationValue": "Luna Universal One Step RT-qPCR Kit"
}
}
],
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{
"@id": "#Sample_C._glutamicum_ATCC13032_WT",
"name": "C. glutamicum ATCC13032 WT",
"characteristics": [
{
"@id": "#MaterialAttributeValue/replicate=1",
"category": {
"@id": "#MaterialAttribute/#UserTerm_replicate",
"characteristicType": {
"@id": "#UserTerm_replicate",
"annotationValue": "replicate"
}
},
"value": {
"@id": "#UserTerm_1",
"annotationValue": "1"
}
}
]
}
],
"outputs": [
{
"@id": "assays/1-2_qPCR-taggedVariants/dataset/20210403_qPCR_DtxR_Tags.rtp",
"name": "assays/1-2_qPCR-taggedVariants/dataset/20210403_qPCR_DtxR_Tags.rtp",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_qPCRsamples_1",
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{
"category": {
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}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose",
"annotationValue": "CGXII + 2% glucose"
}
},
{
"category": {
"@id": "#ProtocolParameter/TO:0006049",
"parameterName": {
"@id": "TO:0006049",
"annotationValue": "iron concentration",
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"termAccession": "TO:0006049"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Cultivation_volume",
"parameterName": {
"@id": "#UserTerm_Cultivation_volume",
"annotationValue": "Cultivation volume"
}
},
"value": {
"@id": "#UserTerm_20_ml",
"annotationValue": "20 ml"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Harvesting_OD600",
"parameterName": {
"@id": "#UserTerm_Harvesting_OD600",
"annotationValue": "Harvesting OD600"
}
},
"value": {
"@id": "#UserTerm_5.26",
"annotationValue": "5.26"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Harvesting_timepoint",
"parameterName": {
"@id": "#UserTerm_Harvesting_timepoint",
"annotationValue": "Harvesting timepoint"
}
},
"value": {
"@id": "#UserTerm_4.75_h",
"annotationValue": "4.75 h"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_RNA_isolation",
"parameterName": {
"@id": "#UserTerm_RNA_isolation",
"annotationValue": "RNA isolation"
}
},
"value": {
"@id": "#UserTerm_NEB_Monarch_RNA_Isolation_Kit",
"annotationValue": "NEB Monarch RNA Isolation Kit"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_RNA_concentration",
"parameterName": {
"@id": "#UserTerm_RNA_concentration",
"annotationValue": "RNA concentration"
}
},
"value": "128 ng/\u00b5l"
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_dtxR_forward",
"parameterName": {
"@id": "#UserTerm_qPCR_primer_dtxR_forward",
"annotationValue": "qPCR primer dtxR forward"
}
},
"value": {
"@id": "#UserTerm_TTGAGCAGTTCCAGGCACTC",
"annotationValue": "TTGAGCAGTTCCAGGCACTC"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_dtxR_reverse",
"parameterName": {
"@id": "#UserTerm_qPCR_primer_dtxR_reverse",
"annotationValue": "qPCR primer dtxR reverse"
}
},
"value": {
"@id": "#UserTerm_TTTCTACGCGGACTGCATGT",
"annotationValue": "TTTCTACGCGGACTGCATGT"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_ddh_forward",
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"@id": "#UserTerm_qPCR_primer_ddh_forward",
"annotationValue": "qPCR primer ddh forward"
}
},
"value": {
"@id": "#UserTerm_CCGGAAAGCAAACCCACAAG",
"annotationValue": "CCGGAAAGCAAACCCACAAG"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_ddh_reverse",
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"@id": "#UserTerm_qPCR_primer_ddh_reverse",
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}
},
"value": {
"@id": "#UserTerm_CTCGGAGTCGAAGGTTGCTT",
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR",
"parameterName": {
"@id": "#UserTerm_qPCR",
"annotationValue": "qPCR"
}
},
"value": {
"@id": "#UserTerm_Luna_Universal_One_Step_RT-qPCR_Kit",
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}
}
],
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{
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"characteristics": [
{
"@id": "#MaterialAttributeValue/replicate=2",
"category": {
"@id": "#MaterialAttribute/#UserTerm_replicate",
"characteristicType": {
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"annotationValue": "replicate"
}
},
"value": {
"@id": "#UserTerm_2",
"annotationValue": "2"
}
}
]
}
],
"outputs": [
{
"@id": "assays/1-2_qPCR-taggedVariants/dataset/20210403_qPCR_DtxR_Tags.rtp",
"name": "assays/1-2_qPCR-taggedVariants/dataset/20210403_qPCR_DtxR_Tags.rtp",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_qPCRsamples_2",
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{
"category": {
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}
},
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}
},
{
"category": {
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"parameterName": {
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"termAccession": "TO:0006049"
}
},
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}
},
{
"category": {
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"annotationValue": "Cultivation volume"
}
},
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"annotationValue": "20 ml"
}
},
{
"category": {
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"@id": "#UserTerm_Harvesting_OD600",
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}
},
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"@id": "#UserTerm_5.3",
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Harvesting_timepoint",
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"annotationValue": "Harvesting timepoint"
}
},
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},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_RNA_isolation",
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}
},
"value": {
"@id": "#UserTerm_NEB_Monarch_RNA_Isolation_Kit",
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},
{
"category": {
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"parameterName": {
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}
},
"value": "480 ng/\u00b5l"
},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
"@id": "#UserTerm_TTTCTACGCGGACTGCATGT",
"annotationValue": "TTTCTACGCGGACTGCATGT"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_ddh_forward",
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}
},
"value": {
"@id": "#UserTerm_CCGGAAAGCAAACCCACAAG",
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}
},
{
"category": {
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}
},
"value": {
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},
{
"category": {
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}
},
"value": {
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}
],
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{
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"characteristics": [
{
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"category": {
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"annotationValue": "replicate"
}
},
"value": {
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}
}
]
}
],
"outputs": [
{
"@id": "assays/1-2_qPCR-taggedVariants/dataset/20210403_qPCR_DtxR_Tags.rtp",
"name": "assays/1-2_qPCR-taggedVariants/dataset/20210403_qPCR_DtxR_Tags.rtp",
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}
]
},
{
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{
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}
},
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}
},
{
"category": {
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"termAccession": "TO:0006049"
}
},
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"annotationValue": "100 \u00b5M FeSO4"
}
},
{
"category": {
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}
},
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"annotationValue": "20 ml"
}
},
{
"category": {
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}
},
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"@id": "#UserTerm_4.97",
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}
},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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}
},
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},
{
"category": {
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"parameterName": {
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}
},
"value": "378 ng/\u00b5l"
},
{
"category": {
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}
},
"value": {
"@id": "#UserTerm_TTGAGCAGTTCCAGGCACTC",
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}
},
{
"category": {
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}
},
"value": {
"@id": "#UserTerm_TTTCTACGCGGACTGCATGT",
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_ddh_forward",
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}
},
"value": {
"@id": "#UserTerm_CCGGAAAGCAAACCCACAAG",
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}
},
{
"category": {
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}
},
"value": {
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},
{
"category": {
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}
},
"value": {
"@id": "#UserTerm_Luna_Universal_One_Step_RT-qPCR_Kit",
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}
}
],
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{
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"characteristics": [
{
"@id": "#MaterialAttributeValue/replicate=2",
"category": {
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"characteristicType": {
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"annotationValue": "replicate"
}
},
"value": {
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}
}
]
}
],
"outputs": [
{
"@id": "assays/1-2_qPCR-taggedVariants/dataset/20210403_qPCR_DtxR_Tags.rtp",
"name": "assays/1-2_qPCR-taggedVariants/dataset/20210403_qPCR_DtxR_Tags.rtp",
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}
]
},
{
"@id": "#Process_qPCRsamples_4",
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{
"category": {
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}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose",
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}
},
{
"category": {
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"parameterName": {
"@id": "TO:0006049",
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"termSource": "TO",
"termAccession": "TO:0006049"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
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}
},
{
"category": {
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}
},
"value": {
"@id": "#UserTerm_20_ml",
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}
},
{
"category": {
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"@id": "#UserTerm_Harvesting_OD600",
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}
},
"value": {
"@id": "#UserTerm_5.41",
"annotationValue": "5.41"
}
},
{
"category": {
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"annotationValue": "Harvesting timepoint"
}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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"parameterName": {
"@id": "#UserTerm_RNA_concentration",
"annotationValue": "RNA concentration"
}
},
"value": "354 ng/\u00b5l"
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_dtxR_forward",
"parameterName": {
"@id": "#UserTerm_qPCR_primer_dtxR_forward",
"annotationValue": "qPCR primer dtxR forward"
}
},
"value": {
"@id": "#UserTerm_TTGAGCAGTTCCAGGCACTC",
"annotationValue": "TTGAGCAGTTCCAGGCACTC"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_dtxR_reverse",
"parameterName": {
"@id": "#UserTerm_qPCR_primer_dtxR_reverse",
"annotationValue": "qPCR primer dtxR reverse"
}
},
"value": {
"@id": "#UserTerm_TTTCTACGCGGACTGCATGT",
"annotationValue": "TTTCTACGCGGACTGCATGT"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_ddh_forward",
"parameterName": {
"@id": "#UserTerm_qPCR_primer_ddh_forward",
"annotationValue": "qPCR primer ddh forward"
}
},
"value": {
"@id": "#UserTerm_CCGGAAAGCAAACCCACAAG",
"annotationValue": "CCGGAAAGCAAACCCACAAG"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_ddh_reverse",
"parameterName": {
"@id": "#UserTerm_qPCR_primer_ddh_reverse",
"annotationValue": "qPCR primer ddh reverse"
}
},
"value": {
"@id": "#UserTerm_CTCGGAGTCGAAGGTTGCTT",
"annotationValue": "CTCGGAGTCGAAGGTTGCTT"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR",
"parameterName": {
"@id": "#UserTerm_qPCR",
"annotationValue": "qPCR"
}
},
"value": {
"@id": "#UserTerm_Luna_Universal_One_Step_RT-qPCR_Kit",
"annotationValue": "Luna Universal One Step RT-qPCR Kit"
}
}
],
"inputs": [
{
"@id": "#Sample_C._glutamicum_ATCC13032::dtxR-Strep-Nterm-4link",
"name": "C. glutamicum ATCC13032::dtxR-Strep-Nterm-4link",
"characteristics": [
{
"@id": "#MaterialAttributeValue/replicate=1",
"category": {
"@id": "#MaterialAttribute/#UserTerm_replicate",
"characteristicType": {
"@id": "#UserTerm_replicate",
"annotationValue": "replicate"
}
},
"value": {
"@id": "#UserTerm_1",
"annotationValue": "1"
}
}
]
}
],
"outputs": [
{
"@id": "assays/1-2_qPCR-taggedVariants/dataset/20210403_qPCR_DtxR_Tags.rtp",
"name": "assays/1-2_qPCR-taggedVariants/dataset/20210403_qPCR_DtxR_Tags.rtp",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_qPCRsamples_5",
"name": "qPCRsamples_5",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Main_culture_cultivation_condition",
"parameterName": {
"@id": "#UserTerm_Main_culture_cultivation_condition",
"annotationValue": "Main culture cultivation condition"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose",
"annotationValue": "CGXII + 2% glucose"
}
},
{
"category": {
"@id": "#ProtocolParameter/TO:0006049",
"parameterName": {
"@id": "TO:0006049",
"annotationValue": "iron concentration",
"termSource": "TO",
"termAccession": "TO:0006049"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Cultivation_volume",
"parameterName": {
"@id": "#UserTerm_Cultivation_volume",
"annotationValue": "Cultivation volume"
}
},
"value": {
"@id": "#UserTerm_20_ml",
"annotationValue": "20 ml"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Harvesting_OD600",
"parameterName": {
"@id": "#UserTerm_Harvesting_OD600",
"annotationValue": "Harvesting OD600"
}
},
"value": {
"@id": "#UserTerm_4.58",
"annotationValue": "4.58"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Harvesting_timepoint",
"parameterName": {
"@id": "#UserTerm_Harvesting_timepoint",
"annotationValue": "Harvesting timepoint"
}
},
"value": {
"@id": "#UserTerm_4.75_h",
"annotationValue": "4.75 h"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_RNA_isolation",
"parameterName": {
"@id": "#UserTerm_RNA_isolation",
"annotationValue": "RNA isolation"
}
},
"value": {
"@id": "#UserTerm_NEB_Monarch_RNA_Isolation_Kit",
"annotationValue": "NEB Monarch RNA Isolation Kit"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_RNA_concentration",
"parameterName": {
"@id": "#UserTerm_RNA_concentration",
"annotationValue": "RNA concentration"
}
},
"value": "210 ng/\u00b5l"
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_dtxR_forward",
"parameterName": {
"@id": "#UserTerm_qPCR_primer_dtxR_forward",
"annotationValue": "qPCR primer dtxR forward"
}
},
"value": {
"@id": "#UserTerm_TTGAGCAGTTCCAGGCACTC",
"annotationValue": "TTGAGCAGTTCCAGGCACTC"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_dtxR_reverse",
"parameterName": {
"@id": "#UserTerm_qPCR_primer_dtxR_reverse",
"annotationValue": "qPCR primer dtxR reverse"
}
},
"value": {
"@id": "#UserTerm_TTTCTACGCGGACTGCATGT",
"annotationValue": "TTTCTACGCGGACTGCATGT"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_ddh_forward",
"parameterName": {
"@id": "#UserTerm_qPCR_primer_ddh_forward",
"annotationValue": "qPCR primer ddh forward"
}
},
"value": {
"@id": "#UserTerm_CCGGAAAGCAAACCCACAAG",
"annotationValue": "CCGGAAAGCAAACCCACAAG"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_ddh_reverse",
"parameterName": {
"@id": "#UserTerm_qPCR_primer_ddh_reverse",
"annotationValue": "qPCR primer ddh reverse"
}
},
"value": {
"@id": "#UserTerm_CTCGGAGTCGAAGGTTGCTT",
"annotationValue": "CTCGGAGTCGAAGGTTGCTT"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR",
"parameterName": {
"@id": "#UserTerm_qPCR",
"annotationValue": "qPCR"
}
},
"value": {
"@id": "#UserTerm_Luna_Universal_One_Step_RT-qPCR_Kit",
"annotationValue": "Luna Universal One Step RT-qPCR Kit"
}
}
],
"inputs": [
{
"@id": "#Sample_C._glutamicum_ATCC13032::dtxR-Strep-Nterm-4link",
"name": "C. glutamicum ATCC13032::dtxR-Strep-Nterm-4link",
"characteristics": [
{
"@id": "#MaterialAttributeValue/replicate=2",
"category": {
"@id": "#MaterialAttribute/#UserTerm_replicate",
"characteristicType": {
"@id": "#UserTerm_replicate",
"annotationValue": "replicate"
}
},
"value": {
"@id": "#UserTerm_2",
"annotationValue": "2"
}
}
]
}
],
"outputs": [
{
"@id": "assays/1-2_qPCR-taggedVariants/dataset/20210403_qPCR_DtxR_Tags.rtp",
"name": "assays/1-2_qPCR-taggedVariants/dataset/20210403_qPCR_DtxR_Tags.rtp",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_qPCRsamples_6",
"name": "qPCRsamples_6",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Main_culture_cultivation_condition",
"parameterName": {
"@id": "#UserTerm_Main_culture_cultivation_condition",
"annotationValue": "Main culture cultivation condition"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose",
"annotationValue": "CGXII + 2% glucose"
}
},
{
"category": {
"@id": "#ProtocolParameter/TO:0006049",
"parameterName": {
"@id": "TO:0006049",
"annotationValue": "iron concentration",
"termSource": "TO",
"termAccession": "TO:0006049"
}
},
"value": {
"@id": "#UserTerm_36_\u00b5M_FeSO4",
"annotationValue": "36 \u00b5M FeSO4"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Cultivation_volume",
"parameterName": {
"@id": "#UserTerm_Cultivation_volume",
"annotationValue": "Cultivation volume"
}
},
"value": {
"@id": "#UserTerm_2_ml",
"annotationValue": "2 ml"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Harvesting_OD600",
"parameterName": {
"@id": "#UserTerm_Harvesting_OD600",
"annotationValue": "Harvesting OD600"
}
},
"value": {
"@id": "#UserTerm_n.d.",
"annotationValue": "n.d."
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Harvesting_timepoint",
"parameterName": {
"@id": "#UserTerm_Harvesting_timepoint",
"annotationValue": "Harvesting timepoint"
}
},
"value": {
"@id": "#UserTerm_4.75_h",
"annotationValue": "4.75 h"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_RNA_isolation",
"parameterName": {
"@id": "#UserTerm_RNA_isolation",
"annotationValue": "RNA isolation"
}
},
"value": {
"@id": "#UserTerm_NEB_Monarch_RNA_Isolation_Kit",
"annotationValue": "NEB Monarch RNA Isolation Kit"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_RNA_concentration",
"parameterName": {
"@id": "#UserTerm_RNA_concentration",
"annotationValue": "RNA concentration"
}
},
"value": "218 ng/\u00b5l"
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_dtxR_forward",
"parameterName": {
"@id": "#UserTerm_qPCR_primer_dtxR_forward",
"annotationValue": "qPCR primer dtxR forward"
}
},
"value": {
"@id": "#UserTerm_TTGAGCAGTTCCAGGCACTC",
"annotationValue": "TTGAGCAGTTCCAGGCACTC"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_dtxR_reverse",
"parameterName": {
"@id": "#UserTerm_qPCR_primer_dtxR_reverse",
"annotationValue": "qPCR primer dtxR reverse"
}
},
"value": {
"@id": "#UserTerm_TTTCTACGCGGACTGCATGT",
"annotationValue": "TTTCTACGCGGACTGCATGT"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_ddh_forward",
"parameterName": {
"@id": "#UserTerm_qPCR_primer_ddh_forward",
"annotationValue": "qPCR primer ddh forward"
}
},
"value": {
"@id": "#UserTerm_CCGGAAAGCAAACCCACAAG",
"annotationValue": "CCGGAAAGCAAACCCACAAG"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_ddh_reverse",
"parameterName": {
"@id": "#UserTerm_qPCR_primer_ddh_reverse",
"annotationValue": "qPCR primer ddh reverse"
}
},
"value": {
"@id": "#UserTerm_CTCGGAGTCGAAGGTTGCTT",
"annotationValue": "CTCGGAGTCGAAGGTTGCTT"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR",
"parameterName": {
"@id": "#UserTerm_qPCR",
"annotationValue": "qPCR"
}
},
"value": {
"@id": "#UserTerm_Luna_Universal_One_Step_RT-qPCR_Kit",
"annotationValue": "Luna Universal One Step RT-qPCR Kit"
}
}
],
"inputs": [
{
"@id": "#Sample_C._glutamicum_ATCC13032_WT",
"name": "C. glutamicum ATCC13032 WT",
"characteristics": [
{
"@id": "#MaterialAttributeValue/replicate=1",
"category": {
"@id": "#MaterialAttribute/#UserTerm_replicate",
"characteristicType": {
"@id": "#UserTerm_replicate",
"annotationValue": "replicate"
}
},
"value": {
"@id": "#UserTerm_1",
"annotationValue": "1"
}
}
]
}
],
"outputs": [
{
"@id": "assays/1-2_qPCR-taggedVariants/dataset/20210403_qPCR_DtxR_Tags.rtp",
"name": "assays/1-2_qPCR-taggedVariants/dataset/20210403_qPCR_DtxR_Tags.rtp",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_qPCRsamples_7",
"name": "qPCRsamples_7",
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{
"category": {
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}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose",
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}
},
{
"category": {
"@id": "#ProtocolParameter/TO:0006049",
"parameterName": {
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"annotationValue": "iron concentration",
"termSource": "TO",
"termAccession": "TO:0006049"
}
},
"value": {
"@id": "#UserTerm_36_\u00b5M_FeSO4",
"annotationValue": "36 \u00b5M FeSO4"
}
},
{
"category": {
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"parameterName": {
"@id": "#UserTerm_Cultivation_volume",
"annotationValue": "Cultivation volume"
}
},
"value": {
"@id": "#UserTerm_2_ml",
"annotationValue": "2 ml"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Harvesting_OD600",
"parameterName": {
"@id": "#UserTerm_Harvesting_OD600",
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}
},
"value": {
"@id": "#UserTerm_n.d.",
"annotationValue": "n.d."
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Harvesting_timepoint",
"parameterName": {
"@id": "#UserTerm_Harvesting_timepoint",
"annotationValue": "Harvesting timepoint"
}
},
"value": {
"@id": "#UserTerm_4.75_h",
"annotationValue": "4.75 h"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_RNA_isolation",
"parameterName": {
"@id": "#UserTerm_RNA_isolation",
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}
},
"value": {
"@id": "#UserTerm_NEB_Monarch_RNA_Isolation_Kit",
"annotationValue": "NEB Monarch RNA Isolation Kit"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_RNA_concentration",
"parameterName": {
"@id": "#UserTerm_RNA_concentration",
"annotationValue": "RNA concentration"
}
},
"value": "82 ng/\u00b5l"
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_dtxR_forward",
"parameterName": {
"@id": "#UserTerm_qPCR_primer_dtxR_forward",
"annotationValue": "qPCR primer dtxR forward"
}
},
"value": {
"@id": "#UserTerm_TTGAGCAGTTCCAGGCACTC",
"annotationValue": "TTGAGCAGTTCCAGGCACTC"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_dtxR_reverse",
"parameterName": {
"@id": "#UserTerm_qPCR_primer_dtxR_reverse",
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}
},
"value": {
"@id": "#UserTerm_TTTCTACGCGGACTGCATGT",
"annotationValue": "TTTCTACGCGGACTGCATGT"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_ddh_forward",
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"@id": "#UserTerm_qPCR_primer_ddh_forward",
"annotationValue": "qPCR primer ddh forward"
}
},
"value": {
"@id": "#UserTerm_CCGGAAAGCAAACCCACAAG",
"annotationValue": "CCGGAAAGCAAACCCACAAG"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_ddh_reverse",
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"@id": "#UserTerm_qPCR_primer_ddh_reverse",
"annotationValue": "qPCR primer ddh reverse"
}
},
"value": {
"@id": "#UserTerm_CTCGGAGTCGAAGGTTGCTT",
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR",
"parameterName": {
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"annotationValue": "qPCR"
}
},
"value": {
"@id": "#UserTerm_Luna_Universal_One_Step_RT-qPCR_Kit",
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}
}
],
"inputs": [
{
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"name": "C. glutamicum ATCC13032 WT",
"characteristics": [
{
"@id": "#MaterialAttributeValue/replicate=2",
"category": {
"@id": "#MaterialAttribute/#UserTerm_replicate",
"characteristicType": {
"@id": "#UserTerm_replicate",
"annotationValue": "replicate"
}
},
"value": {
"@id": "#UserTerm_2",
"annotationValue": "2"
}
}
]
}
],
"outputs": [
{
"@id": "assays/1-2_qPCR-taggedVariants/dataset/20210403_qPCR_DtxR_Tags.rtp",
"name": "assays/1-2_qPCR-taggedVariants/dataset/20210403_qPCR_DtxR_Tags.rtp",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_qPCRsamples_8",
"name": "qPCRsamples_8",
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{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Main_culture_cultivation_condition",
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"annotationValue": "Main culture cultivation condition"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose",
"annotationValue": "CGXII + 2% glucose"
}
},
{
"category": {
"@id": "#ProtocolParameter/TO:0006049",
"parameterName": {
"@id": "TO:0006049",
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"termSource": "TO",
"termAccession": "TO:0006049"
}
},
"value": {
"@id": "#UserTerm_36_\u00b5M_FeSO4",
"annotationValue": "36 \u00b5M FeSO4"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Cultivation_volume",
"parameterName": {
"@id": "#UserTerm_Cultivation_volume",
"annotationValue": "Cultivation volume"
}
},
"value": {
"@id": "#UserTerm_2_ml",
"annotationValue": "2 ml"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Harvesting_OD600",
"parameterName": {
"@id": "#UserTerm_Harvesting_OD600",
"annotationValue": "Harvesting OD600"
}
},
"value": {
"@id": "#UserTerm_n.d.",
"annotationValue": "n.d."
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Harvesting_timepoint",
"parameterName": {
"@id": "#UserTerm_Harvesting_timepoint",
"annotationValue": "Harvesting timepoint"
}
},
"value": {
"@id": "#UserTerm_4.75_h",
"annotationValue": "4.75 h"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_RNA_isolation",
"parameterName": {
"@id": "#UserTerm_RNA_isolation",
"annotationValue": "RNA isolation"
}
},
"value": {
"@id": "#UserTerm_NEB_Monarch_RNA_Isolation_Kit",
"annotationValue": "NEB Monarch RNA Isolation Kit"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_RNA_concentration",
"parameterName": {
"@id": "#UserTerm_RNA_concentration",
"annotationValue": "RNA concentration"
}
},
"value": "140 ng/\u00b5l"
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_dtxR_forward",
"parameterName": {
"@id": "#UserTerm_qPCR_primer_dtxR_forward",
"annotationValue": "qPCR primer dtxR forward"
}
},
"value": {
"@id": "#UserTerm_TTGAGCAGTTCCAGGCACTC",
"annotationValue": "TTGAGCAGTTCCAGGCACTC"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_dtxR_reverse",
"parameterName": {
"@id": "#UserTerm_qPCR_primer_dtxR_reverse",
"annotationValue": "qPCR primer dtxR reverse"
}
},
"value": {
"@id": "#UserTerm_TTTCTACGCGGACTGCATGT",
"annotationValue": "TTTCTACGCGGACTGCATGT"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_ddh_forward",
"parameterName": {
"@id": "#UserTerm_qPCR_primer_ddh_forward",
"annotationValue": "qPCR primer ddh forward"
}
},
"value": {
"@id": "#UserTerm_CCGGAAAGCAAACCCACAAG",
"annotationValue": "CCGGAAAGCAAACCCACAAG"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR_primer_ddh_reverse",
"parameterName": {
"@id": "#UserTerm_qPCR_primer_ddh_reverse",
"annotationValue": "qPCR primer ddh reverse"
}
},
"value": {
"@id": "#UserTerm_CTCGGAGTCGAAGGTTGCTT",
"annotationValue": "CTCGGAGTCGAAGGTTGCTT"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_qPCR",
"parameterName": {
"@id": "#UserTerm_qPCR",
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}
},
"value": {
"@id": "#UserTerm_Luna_Universal_One_Step_RT-qPCR_Kit",
"annotationValue": "Luna Universal One Step RT-qPCR Kit"
}
}
],
"inputs": [
{
"@id": "#Sample_C._glutamicum_ATCC13032::dtxR-His-Cterm-2link",
"name": "C. glutamicum ATCC13032::dtxR-His-Cterm-2link",
"characteristics": [
{
"@id": "#MaterialAttributeValue/replicate=1",
"category": {
"@id": "#MaterialAttribute/#UserTerm_replicate",
"characteristicType": {
"@id": "#UserTerm_replicate",
"annotationValue": "replicate"
}
},
"value": {
"@id": "#UserTerm_1",
"annotationValue": "1"
}
}
]
}
],
"outputs": [
{
"@id": "assays/1-2_qPCR-taggedVariants/dataset/20210403_qPCR_DtxR_Tags.rtp",
"name": "assays/1-2_qPCR-taggedVariants/dataset/20210403_qPCR_DtxR_Tags.rtp",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_qPCRsamples_9",
"name": "qPCRsamples_9",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Main_culture_cultivation_condition",
"parameterName": {
"@id": "#UserTerm_Main_culture_cultivation_condition",
"annotationValue": "Main culture cultivation condition"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose",
"annotationValue": "CGXII + 2% glucose"
}
},
{
"category": {
"@id": "#ProtocolParameter/TO:0006049",
"parameterName": {
"@id": "TO:0006049",
"annotationValue": "iron concentration",
"termSource": "TO",
"termAccession": "TO:0006049"
}
},
"value": {
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},
{
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},
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}
]
},
{
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{
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},
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},
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},
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},
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}
},
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}
]
},
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}
},
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}
]
},
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},
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}
]
},
{
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},
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}
]
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{
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},
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},
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}
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},
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}
},
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},
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},
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},
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},
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},
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}
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},
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},
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},
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},
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},
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},
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},
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},
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},
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},
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},
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},
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{
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},
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},
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},
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},
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}
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},
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},
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},
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},
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}
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},
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},
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}
]
},
{
"@id": "#Sample_WT-cepA-heme-3",
"name": "WT-cepA-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PcepA-venus",
"category": {
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"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum WT + pJC1-PcepA-venus"
}
}
]
},
{
"@id": "#Sample_WT-cepA-iron-1",
"name": "WT-cepA-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum WT + pJC1-PcepA-venus"
}
}
]
},
{
"@id": "#Sample_WT-cepA-iron-2",
"name": "WT-cepA-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum WT + pJC1-PcepA-venus"
}
}
]
},
{
"@id": "#Sample_WT-cepA-iron-3",
"name": "WT-cepA-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PcepA-venus",
"category": {
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"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum WT + pJC1-PcepA-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl1781-heme-1",
"name": "DdtxR-NCgl1781-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1781-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl1781-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl1781-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl1781-heme-2",
"name": "DdtxR-NCgl1781-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1781-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl1781-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl1781-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl1781-heme-3",
"name": "DdtxR-NCgl1781-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1781-venus",
"category": {
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"characteristicType": {
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"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl1781-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl1781-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl1781-iron-1",
"name": "DdtxR-NCgl1781-iron-1",
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1781-venus",
"category": {
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"characteristicType": {
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"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl1781-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl1781-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl1781-iron-2",
"name": "DdtxR-NCgl1781-iron-2",
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1781-venus",
"category": {
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"characteristicType": {
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"annotationValue": "Organism",
"termSource": "MIAPPE",
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl1781-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl1781-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl1781-iron-3",
"name": "DdtxR-NCgl1781-iron-3",
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1781-venus",
"category": {
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl1781-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl1781-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-xerC-heme-1",
"name": "DdtxR-xerC-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PxerC-venus",
"category": {
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"characteristicType": {
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"termSource": "MIAPPE",
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PxerC-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-xerC-heme-2",
"name": "DdtxR-xerC-heme-2",
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PxerC-venus",
"category": {
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"characteristicType": {
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"termSource": "MIAPPE",
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PxerC-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-xerC-heme-3",
"name": "DdtxR-xerC-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PxerC-venus",
"category": {
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"characteristicType": {
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"termSource": "MIAPPE",
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PxerC-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-xerC-iron-1",
"name": "DdtxR-xerC-iron-1",
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PxerC-venus",
"category": {
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"characteristicType": {
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"annotationValue": "Organism",
"termSource": "MIAPPE",
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PxerC-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-xerC-iron-2",
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{
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"category": {
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PxerC-venus",
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}
}
]
},
{
"@id": "#Sample_DdtxR-xerC-iron-3",
"name": "DdtxR-xerC-iron-3",
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PxerC-venus",
"category": {
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PxerC-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-qor3-heme-1",
"name": "DdtxR-qor3-heme-1",
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pqor3-venus",
"category": {
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"characteristicType": {
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pqor3-venus",
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}
}
]
},
{
"@id": "#Sample_DdtxR-qor3-heme-2",
"name": "DdtxR-qor3-heme-2",
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pqor3-venus",
"category": {
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pqor3-venus",
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}
}
]
},
{
"@id": "#Sample_DdtxR-qor3-heme-3",
"name": "DdtxR-qor3-heme-3",
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{
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pqor3-venus",
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}
}
]
},
{
"@id": "#Sample_DdtxR-qor3-iron-1",
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pqor3-venus",
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pqor3-venus",
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}
]
},
{
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{
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pqor3-venus",
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}
}
]
},
{
"@id": "#Sample_DdtxR-qor3-iron-3",
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pqor3-venus",
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pqor3-venus",
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}
]
},
{
"@id": "#Sample_DdtxR-cepA-heme-1",
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PcepA-venus",
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PcepA-venus",
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}
}
]
},
{
"@id": "#Sample_DdtxR-cepA-heme-2",
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{
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"category": {
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PcepA-venus",
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}
]
},
{
"@id": "#Sample_DdtxR-cepA-heme-3",
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{
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PcepA-venus",
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}
]
},
{
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{
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}
},
"value": {
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}
]
},
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}
},
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}
]
},
{
"@id": "#Sample_DdtxR-cepA-iron-3",
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{
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PcepA-venus",
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}
]
},
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"@id": "#Sample_WT-NCgl2776-heme-1",
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{
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl2776-venus",
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}
]
},
{
"@id": "#Sample_WT-NCgl2776-heme-2",
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"characteristics": [
{
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl2776-venus",
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}
]
},
{
"@id": "#Sample_WT-NCgl2776-heme-3",
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{
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl2776-venus",
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}
]
},
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"@id": "#Sample_WT-NCgl2776-iron-1",
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{
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}
},
"value": {
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}
]
},
{
"@id": "#Sample_WT-NCgl2776-iron-2",
"name": "WT-NCgl2776-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl2776-venus",
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"termSource": "MIAPPE",
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl2776-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl2776-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl2776-iron-3",
"name": "WT-NCgl2776-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl2776-venus",
"category": {
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"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl2776-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl2776-venus"
}
}
]
},
{
"@id": "#Sample_WT-gyrB-heme-1",
"name": "WT-gyrB-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PgyrB-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PgyrB-venus",
"annotationValue": "C. glutamicum WT + pJC1-PgyrB-venus"
}
}
]
},
{
"@id": "#Sample_WT-gyrB-heme-2",
"name": "WT-gyrB-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PgyrB-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PgyrB-venus",
"annotationValue": "C. glutamicum WT + pJC1-PgyrB-venus"
}
}
]
},
{
"@id": "#Sample_WT-gyrB-heme-3",
"name": "WT-gyrB-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PgyrB-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PgyrB-venus",
"annotationValue": "C. glutamicum WT + pJC1-PgyrB-venus"
}
}
]
},
{
"@id": "#Sample_WT-gyrB-iron-1",
"name": "WT-gyrB-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PgyrB-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PgyrB-venus",
"annotationValue": "C. glutamicum WT + pJC1-PgyrB-venus"
}
}
]
},
{
"@id": "#Sample_WT-gyrB-iron-2",
"name": "WT-gyrB-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PgyrB-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PgyrB-venus",
"annotationValue": "C. glutamicum WT + pJC1-PgyrB-venus"
}
}
]
},
{
"@id": "#Sample_WT-gyrB-iron-3",
"name": "WT-gyrB-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PgyrB-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PgyrB-venus",
"annotationValue": "C. glutamicum WT + pJC1-PgyrB-venus"
}
}
]
},
{
"@id": "#Sample_WT-ssuD1-heme-1",
"name": "WT-ssuD1-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PssuD1-venus",
"category": {
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"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PssuD1-venus",
"annotationValue": "C. glutamicum WT + pJC1-PssuD1-venus"
}
}
]
},
{
"@id": "#Sample_WT-ssuD1-heme-2",
"name": "WT-ssuD1-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PssuD1-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PssuD1-venus",
"annotationValue": "C. glutamicum WT + pJC1-PssuD1-venus"
}
}
]
},
{
"@id": "#Sample_WT-ssuD1-heme-3",
"name": "WT-ssuD1-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PssuD1-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PssuD1-venus",
"annotationValue": "C. glutamicum WT + pJC1-PssuD1-venus"
}
}
]
},
{
"@id": "#Sample_WT-ssuD1-iron-1",
"name": "WT-ssuD1-iron-1",
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PssuD1-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PssuD1-venus",
"annotationValue": "C. glutamicum WT + pJC1-PssuD1-venus"
}
}
]
},
{
"@id": "#Sample_WT-ssuD1-iron-2",
"name": "WT-ssuD1-iron-2",
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PssuD1-venus",
"category": {
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"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PssuD1-venus",
"annotationValue": "C. glutamicum WT + pJC1-PssuD1-venus"
}
}
]
},
{
"@id": "#Sample_WT-ssuD1-iron-3",
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PssuD1-venus",
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"characteristicType": {
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"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PssuD1-venus",
"annotationValue": "C. glutamicum WT + pJC1-PssuD1-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl2776-heme-1",
"name": "DdtxR-NCgl2776-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl2776-venus",
"category": {
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"annotationValue": "Organism",
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl2776-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl2776-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl2776-heme-2",
"name": "DdtxR-NCgl2776-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl2776-venus",
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"characteristicType": {
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl2776-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl2776-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl2776-heme-3",
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{
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl2776-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl2776-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl2776-iron-1",
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl2776-venus",
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl2776-venus",
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}
}
]
},
{
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl2776-venus",
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl2776-venus",
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}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl2776-iron-3",
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl2776-venus",
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl2776-venus",
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}
]
},
{
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{
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"characteristicType": {
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PgyrB-venus",
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}
}
]
},
{
"@id": "#Sample_DdtxR-gyrB-heme-2",
"name": "DdtxR-gyrB-heme-2",
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{
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PgyrB-venus",
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}
]
},
{
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{
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PgyrB-venus",
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}
}
]
},
{
"@id": "#Sample_DdtxR-gyrB-iron-1",
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{
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PgyrB-venus",
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}
}
]
},
{
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{
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PgyrB-venus",
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}
]
},
{
"@id": "#Sample_DdtxR-gyrB-iron-3",
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{
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}
},
"value": {
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}
]
},
{
"@id": "#Sample_DdtxR-ssuD1-heme-1",
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{
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}
},
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}
]
},
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{
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}
},
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}
]
},
{
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{
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},
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}
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},
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{
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}
},
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}
]
},
{
"@id": "#Sample_DdtxR-ssuD1-iron-2",
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{
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}
},
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}
]
},
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{
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}
},
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"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PssuD1-venus",
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}
]
},
{
"@id": "#Sample_DdtxR-wzy-heme-1",
"name": "DdtxR-wzy-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-Pwzy-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-wzy-heme-2",
"name": "DdtxR-wzy-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-Pwzy-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-wzy-heme-3",
"name": "DdtxR-wzy-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-Pwzy-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-wzy-iron-1",
"name": "DdtxR-wzy-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-Pwzy-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-wzy-iron-2",
"name": "DdtxR-wzy-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-Pwzy-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-wzy-iron-3",
"name": "DdtxR-wzy-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-Pwzy-venus"
}
}
]
}
]
},
"characteristicCategories": [
{
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
}
],
"processSequence": [
{
"@id": "#Process_Biolector-metH-NCgl1451_0",
"name": "Biolector-metH-NCgl1451_0",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A1",
"annotationValue": "A1"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(EX:_620nm,_gain_20);_YFP_(EX:_508nm,_EM:532nm;gain_80)",
"annotationValue": "backscatter (EX: 620nm, gain 20); YFP (EX: 508nm, EM:532nm;gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl0176-heme-1",
"name": "WT-NCgl0176-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0176-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl0176-heme-1",
"name": "WT-NCgl0176-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0176-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_1",
"name": "Biolector-metH-NCgl1451_1",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B1",
"annotationValue": "B1"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl0176-heme-2",
"name": "WT-NCgl0176-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0176-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl0176-heme-2",
"name": "WT-NCgl0176-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0176-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_2",
"name": "Biolector-metH-NCgl1451_2",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C1",
"annotationValue": "C1"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl0176-heme-3",
"name": "WT-NCgl0176-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0176-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl0176-heme-3",
"name": "WT-NCgl0176-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0176-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_3",
"name": "Biolector-metH-NCgl1451_3",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D1",
"annotationValue": "D1"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl0176-iron-1",
"name": "WT-NCgl0176-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0176-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl0176-iron-1",
"name": "WT-NCgl0176-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0176-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_4",
"name": "Biolector-metH-NCgl1451_4",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E1",
"annotationValue": "E1"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl0176-iron-2",
"name": "WT-NCgl0176-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0176-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl0176-iron-2",
"name": "WT-NCgl0176-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0176-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_5",
"name": "Biolector-metH-NCgl1451_5",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F1",
"annotationValue": "F1"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl0176-iron-3",
"name": "WT-NCgl0176-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0176-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl0176-iron-3",
"name": "WT-NCgl0176-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0176-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_6",
"name": "Biolector-metH-NCgl1451_6",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A2",
"annotationValue": "A2"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl0177-heme-1",
"name": "WT-NCgl0177-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0177-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl0177-heme-1",
"name": "WT-NCgl0177-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0177-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_7",
"name": "Biolector-metH-NCgl1451_7",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B2",
"annotationValue": "B2"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl0177-heme-2",
"name": "WT-NCgl0177-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0177-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl0177-heme-2",
"name": "WT-NCgl0177-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0177-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_8",
"name": "Biolector-metH-NCgl1451_8",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C2",
"annotationValue": "C2"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl0177-heme-3",
"name": "WT-NCgl0177-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0177-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl0177-heme-3",
"name": "WT-NCgl0177-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0177-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_9",
"name": "Biolector-metH-NCgl1451_9",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D2",
"annotationValue": "D2"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl0177-iron-1",
"name": "WT-NCgl0177-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0177-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl0177-iron-1",
"name": "WT-NCgl0177-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0177-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_10",
"name": "Biolector-metH-NCgl1451_10",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E2",
"annotationValue": "E2"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl0177-iron-2",
"name": "WT-NCgl0177-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0177-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl0177-iron-2",
"name": "WT-NCgl0177-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0177-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_11",
"name": "Biolector-metH-NCgl1451_11",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F2",
"annotationValue": "F2"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl0177-iron-3",
"name": "WT-NCgl0177-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0177-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl0177-iron-3",
"name": "WT-NCgl0177-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0177-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_12",
"name": "Biolector-metH-NCgl1451_12",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A3",
"annotationValue": "A3"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-metH-heme-1",
"name": "WT-metH-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PmetH-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PmetH-venus",
"annotationValue": "C. glutamicum WT + pJC1-PmetH-venus"
}
}
]
},
{
"@id": "#Sample_WT-metH-heme-1",
"name": "WT-metH-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PmetH-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PmetH-venus",
"annotationValue": "C. glutamicum WT + pJC1-PmetH-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_13",
"name": "Biolector-metH-NCgl1451_13",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B3",
"annotationValue": "B3"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-metH-heme-2",
"name": "WT-metH-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PmetH-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PmetH-venus",
"annotationValue": "C. glutamicum WT + pJC1-PmetH-venus"
}
}
]
},
{
"@id": "#Sample_WT-metH-heme-2",
"name": "WT-metH-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PmetH-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PmetH-venus",
"annotationValue": "C. glutamicum WT + pJC1-PmetH-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_14",
"name": "Biolector-metH-NCgl1451_14",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C3",
"annotationValue": "C3"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-metH-heme-3",
"name": "WT-metH-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PmetH-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PmetH-venus",
"annotationValue": "C. glutamicum WT + pJC1-PmetH-venus"
}
}
]
},
{
"@id": "#Sample_WT-metH-heme-3",
"name": "WT-metH-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PmetH-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PmetH-venus",
"annotationValue": "C. glutamicum WT + pJC1-PmetH-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_15",
"name": "Biolector-metH-NCgl1451_15",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D3",
"annotationValue": "D3"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-metH-iron-1",
"name": "WT-metH-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PmetH-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PmetH-venus",
"annotationValue": "C. glutamicum WT + pJC1-PmetH-venus"
}
}
]
},
{
"@id": "#Sample_WT-metH-iron-1",
"name": "WT-metH-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PmetH-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PmetH-venus",
"annotationValue": "C. glutamicum WT + pJC1-PmetH-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_16",
"name": "Biolector-metH-NCgl1451_16",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E3",
"annotationValue": "E3"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-metH-iron-2",
"name": "WT-metH-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PmetH-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PmetH-venus",
"annotationValue": "C. glutamicum WT + pJC1-PmetH-venus"
}
}
]
},
{
"@id": "#Sample_WT-metH-iron-2",
"name": "WT-metH-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PmetH-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PmetH-venus",
"annotationValue": "C. glutamicum WT + pJC1-PmetH-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_17",
"name": "Biolector-metH-NCgl1451_17",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F3",
"annotationValue": "F3"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-metH-iron-3",
"name": "WT-metH-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PmetH-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PmetH-venus",
"annotationValue": "C. glutamicum WT + pJC1-PmetH-venus"
}
}
]
},
{
"@id": "#Sample_WT-metH-iron-3",
"name": "WT-metH-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PmetH-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PmetH-venus",
"annotationValue": "C. glutamicum WT + pJC1-PmetH-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_18",
"name": "Biolector-metH-NCgl1451_18",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A4",
"annotationValue": "A4"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl1451-heme-1",
"name": "WT-NCgl1451-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl1451-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl1451-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl1451-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl1451-heme-1",
"name": "WT-NCgl1451-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl1451-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl1451-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl1451-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_19",
"name": "Biolector-metH-NCgl1451_19",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B4",
"annotationValue": "B4"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl1451-heme-2",
"name": "WT-NCgl1451-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl1451-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl1451-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl1451-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl1451-heme-2",
"name": "WT-NCgl1451-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl1451-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl1451-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl1451-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_20",
"name": "Biolector-metH-NCgl1451_20",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C4",
"annotationValue": "C4"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl1451-heme-3",
"name": "WT-NCgl1451-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl1451-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl1451-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl1451-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl1451-heme-3",
"name": "WT-NCgl1451-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl1451-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl1451-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl1451-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_21",
"name": "Biolector-metH-NCgl1451_21",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D4",
"annotationValue": "D4"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl1451-iron-1",
"name": "WT-NCgl1451-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl1451-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl1451-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl1451-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl1451-iron-1",
"name": "WT-NCgl1451-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl1451-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl1451-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl1451-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_22",
"name": "Biolector-metH-NCgl1451_22",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E4",
"annotationValue": "E4"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl1451-iron-2",
"name": "WT-NCgl1451-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl1451-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl1451-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl1451-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl1451-iron-2",
"name": "WT-NCgl1451-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl1451-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl1451-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl1451-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_23",
"name": "Biolector-metH-NCgl1451_23",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F4",
"annotationValue": "F4"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl1451-iron-3",
"name": "WT-NCgl1451-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl1451-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl1451-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl1451-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl1451-iron-3",
"name": "WT-NCgl1451-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl1451-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl1451-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl1451-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_24",
"name": "Biolector-metH-NCgl1451_24",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A5",
"annotationValue": "A5"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl0176-heme-1",
"name": "DdtxR-NCgl0176-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0176-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl0176-heme-1",
"name": "DdtxR-NCgl0176-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0176-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_25",
"name": "Biolector-metH-NCgl1451_25",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B5",
"annotationValue": "B5"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl0176-heme-2",
"name": "DdtxR-NCgl0176-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0176-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl0176-heme-2",
"name": "DdtxR-NCgl0176-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0176-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_26",
"name": "Biolector-metH-NCgl1451_26",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C5",
"annotationValue": "C5"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl0176-heme-3",
"name": "DdtxR-NCgl0176-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0176-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl0176-heme-3",
"name": "DdtxR-NCgl0176-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0176-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_27",
"name": "Biolector-metH-NCgl1451_27",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D5",
"annotationValue": "D5"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl0176-iron-1",
"name": "DdtxR-NCgl0176-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0176-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl0176-iron-1",
"name": "DdtxR-NCgl0176-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0176-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_28",
"name": "Biolector-metH-NCgl1451_28",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E5",
"annotationValue": "E5"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl0176-iron-2",
"name": "DdtxR-NCgl0176-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0176-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl0176-iron-2",
"name": "DdtxR-NCgl0176-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0176-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_29",
"name": "Biolector-metH-NCgl1451_29",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F5",
"annotationValue": "F5"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl0176-iron-3",
"name": "DdtxR-NCgl0176-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0176-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl0176-iron-3",
"name": "DdtxR-NCgl0176-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0176-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_30",
"name": "Biolector-metH-NCgl1451_30",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A6",
"annotationValue": "A6"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl0177-heme-1",
"name": "DdtxR-NCgl0177-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0177-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl0177-heme-1",
"name": "DdtxR-NCgl0177-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0177-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_31",
"name": "Biolector-metH-NCgl1451_31",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B6",
"annotationValue": "B6"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl0177-heme-2",
"name": "DdtxR-NCgl0177-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0177-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl0177-heme-2",
"name": "DdtxR-NCgl0177-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0177-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_32",
"name": "Biolector-metH-NCgl1451_32",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C6",
"annotationValue": "C6"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl0177-heme-3",
"name": "DdtxR-NCgl0177-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0177-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl0177-heme-3",
"name": "DdtxR-NCgl0177-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0177-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_33",
"name": "Biolector-metH-NCgl1451_33",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D6",
"annotationValue": "D6"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl0177-iron-1",
"name": "DdtxR-NCgl0177-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0177-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl0177-iron-1",
"name": "DdtxR-NCgl0177-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0177-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_34",
"name": "Biolector-metH-NCgl1451_34",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E6",
"annotationValue": "E6"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl0177-iron-2",
"name": "DdtxR-NCgl0177-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0177-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl0177-iron-2",
"name": "DdtxR-NCgl0177-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0177-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_35",
"name": "Biolector-metH-NCgl1451_35",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F6",
"annotationValue": "F6"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl0177-iron-3",
"name": "DdtxR-NCgl0177-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0177-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl0177-iron-3",
"name": "DdtxR-NCgl0177-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0177-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_36",
"name": "Biolector-metH-NCgl1451_36",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A7",
"annotationValue": "A7"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-metH-heme-1",
"name": "DdtxR-metH-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PmetH-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PmetH-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PmetH-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-metH-heme-1",
"name": "DdtxR-metH-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PmetH-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PmetH-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PmetH-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_37",
"name": "Biolector-metH-NCgl1451_37",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B7",
"annotationValue": "B7"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-metH-heme-2",
"name": "DdtxR-metH-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PmetH-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PmetH-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PmetH-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-metH-heme-2",
"name": "DdtxR-metH-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PmetH-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PmetH-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PmetH-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_38",
"name": "Biolector-metH-NCgl1451_38",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C7",
"annotationValue": "C7"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-metH-heme-3",
"name": "DdtxR-metH-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PmetH-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PmetH-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PmetH-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-metH-heme-3",
"name": "DdtxR-metH-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PmetH-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PmetH-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PmetH-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_39",
"name": "Biolector-metH-NCgl1451_39",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D7",
"annotationValue": "D7"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-metH-iron-1",
"name": "DdtxR-metH-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PmetH-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PmetH-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PmetH-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-metH-iron-1",
"name": "DdtxR-metH-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PmetH-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PmetH-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PmetH-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_40",
"name": "Biolector-metH-NCgl1451_40",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E7",
"annotationValue": "E7"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-metH-iron-2",
"name": "DdtxR-metH-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PmetH-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PmetH-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PmetH-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-metH-iron-2",
"name": "DdtxR-metH-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PmetH-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PmetH-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PmetH-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_41",
"name": "Biolector-metH-NCgl1451_41",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F7",
"annotationValue": "F7"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-metH-iron-3",
"name": "DdtxR-metH-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PmetH-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PmetH-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PmetH-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-metH-iron-3",
"name": "DdtxR-metH-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PmetH-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PmetH-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PmetH-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_42",
"name": "Biolector-metH-NCgl1451_42",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A8",
"annotationValue": "A8"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl1451-heme-1",
"name": "DdtxR-NCgl1451-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1451-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl1451-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl1451-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl1451-heme-1",
"name": "DdtxR-NCgl1451-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1451-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl1451-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl1451-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_43",
"name": "Biolector-metH-NCgl1451_43",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B8",
"annotationValue": "B8"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl1451-heme-2",
"name": "DdtxR-NCgl1451-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1451-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl1451-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl1451-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl1451-heme-2",
"name": "DdtxR-NCgl1451-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1451-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl1451-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl1451-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_44",
"name": "Biolector-metH-NCgl1451_44",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C8",
"annotationValue": "C8"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl1451-heme-3",
"name": "DdtxR-NCgl1451-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1451-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl1451-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl1451-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl1451-heme-3",
"name": "DdtxR-NCgl1451-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1451-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl1451-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl1451-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_45",
"name": "Biolector-metH-NCgl1451_45",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D8",
"annotationValue": "D8"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl1451-iron-1",
"name": "DdtxR-NCgl1451-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1451-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl1451-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl1451-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl1451-iron-1",
"name": "DdtxR-NCgl1451-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1451-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl1451-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl1451-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_46",
"name": "Biolector-metH-NCgl1451_46",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E8",
"annotationValue": "E8"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl1451-iron-2",
"name": "DdtxR-NCgl1451-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1451-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl1451-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl1451-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl1451-iron-2",
"name": "DdtxR-NCgl1451-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1451-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl1451-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl1451-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-metH-NCgl1451_47",
"name": "Biolector-metH-NCgl1451_47",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F8",
"annotationValue": "F8"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_22,56112_h",
"annotationValue": "22,56112 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl1451-iron-3",
"name": "DdtxR-NCgl1451-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1451-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl1451-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl1451-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl1451-iron-3",
"name": "DdtxR-NCgl1451-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1451-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl1451-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl1451-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/metH-NCgl1451/20240215_BiolectorAK114_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_0",
"name": "Biolector-NCgl0176-NCgl0177-wzy_0",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A1",
"annotationValue": "A1"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(EX:_620nm,_gain_20);_YFP_(EX:_508nm,_EM:532nm;gain_80)",
"annotationValue": "backscatter (EX: 620nm, gain 20); YFP (EX: 508nm, EM:532nm;gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-wzy-heme-1",
"name": "WT-wzy-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pwzy-venus"
}
}
]
},
{
"@id": "#Sample_WT-wzy-heme-1",
"name": "WT-wzy-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pwzy-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_1",
"name": "Biolector-NCgl0176-NCgl0177-wzy_1",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B1",
"annotationValue": "B1"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-wzy-heme-2",
"name": "WT-wzy-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pwzy-venus"
}
}
]
},
{
"@id": "#Sample_WT-wzy-heme-2",
"name": "WT-wzy-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pwzy-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_2",
"name": "Biolector-NCgl0176-NCgl0177-wzy_2",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C1",
"annotationValue": "C1"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-wzy-heme-3",
"name": "WT-wzy-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pwzy-venus"
}
}
]
},
{
"@id": "#Sample_WT-wzy-heme-3",
"name": "WT-wzy-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pwzy-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_3",
"name": "Biolector-NCgl0176-NCgl0177-wzy_3",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D1",
"annotationValue": "D1"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-wzy-iron-1",
"name": "WT-wzy-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pwzy-venus"
}
}
]
},
{
"@id": "#Sample_WT-wzy-iron-1",
"name": "WT-wzy-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pwzy-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_4",
"name": "Biolector-NCgl0176-NCgl0177-wzy_4",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E1",
"annotationValue": "E1"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-wzy-iron-2",
"name": "WT-wzy-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pwzy-venus"
}
}
]
},
{
"@id": "#Sample_WT-wzy-iron-2",
"name": "WT-wzy-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pwzy-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_5",
"name": "Biolector-NCgl0176-NCgl0177-wzy_5",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F1",
"annotationValue": "F1"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-wzy-iron-3",
"name": "WT-wzy-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pwzy-venus"
}
}
]
},
{
"@id": "#Sample_WT-wzy-iron-3",
"name": "WT-wzy-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pwzy-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_6",
"name": "Biolector-NCgl0176-NCgl0177-wzy_6",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A2",
"annotationValue": "A2"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DhrrA-wzy-heme-1",
"name": "DhrrA-wzy-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DhrrA + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DhrrA_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum DhrrA + pJC1-Pwzy-venus"
}
}
]
},
{
"@id": "#Sample_DhrrA-wzy-heme-1",
"name": "DhrrA-wzy-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DhrrA + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DhrrA_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum DhrrA + pJC1-Pwzy-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_7",
"name": "Biolector-NCgl0176-NCgl0177-wzy_7",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B2",
"annotationValue": "B2"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DhrrA-wzy-heme-2",
"name": "DhrrA-wzy-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DhrrA + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DhrrA_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum DhrrA + pJC1-Pwzy-venus"
}
}
]
},
{
"@id": "#Sample_DhrrA-wzy-heme-2",
"name": "DhrrA-wzy-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DhrrA + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DhrrA_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum DhrrA + pJC1-Pwzy-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_8",
"name": "Biolector-NCgl0176-NCgl0177-wzy_8",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C2",
"annotationValue": "C2"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DhrrA-wzy-heme-3",
"name": "DhrrA-wzy-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DhrrA + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DhrrA_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum DhrrA + pJC1-Pwzy-venus"
}
}
]
},
{
"@id": "#Sample_DhrrA-wzy-heme-3",
"name": "DhrrA-wzy-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DhrrA + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DhrrA_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum DhrrA + pJC1-Pwzy-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_9",
"name": "Biolector-NCgl0176-NCgl0177-wzy_9",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D2",
"annotationValue": "D2"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DhrrA-wzy-iron-1",
"name": "DhrrA-wzy-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DhrrA + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DhrrA_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum DhrrA + pJC1-Pwzy-venus"
}
}
]
},
{
"@id": "#Sample_DhrrA-wzy-iron-1",
"name": "DhrrA-wzy-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DhrrA + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DhrrA_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum DhrrA + pJC1-Pwzy-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_10",
"name": "Biolector-NCgl0176-NCgl0177-wzy_10",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E2",
"annotationValue": "E2"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DhrrA-wzy-iron-2",
"name": "DhrrA-wzy-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DhrrA + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DhrrA_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum DhrrA + pJC1-Pwzy-venus"
}
}
]
},
{
"@id": "#Sample_DhrrA-wzy-iron-2",
"name": "DhrrA-wzy-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DhrrA + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DhrrA_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum DhrrA + pJC1-Pwzy-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_11",
"name": "Biolector-NCgl0176-NCgl0177-wzy_11",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F2",
"annotationValue": "F2"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DhrrA-wzy-iron-3",
"name": "DhrrA-wzy-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DhrrA + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DhrrA_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum DhrrA + pJC1-Pwzy-venus"
}
}
]
},
{
"@id": "#Sample_DhrrA-wzy-iron-3",
"name": "DhrrA-wzy-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DhrrA + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DhrrA_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum DhrrA + pJC1-Pwzy-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_12",
"name": "Biolector-NCgl0176-NCgl0177-wzy_12",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A3",
"annotationValue": "A3"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl0176-heme-1",
"name": "WT-NCgl0176-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0176-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl0176-heme-1",
"name": "WT-NCgl0176-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0176-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_13",
"name": "Biolector-NCgl0176-NCgl0177-wzy_13",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B3",
"annotationValue": "B3"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl0176-heme-2",
"name": "WT-NCgl0176-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0176-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl0176-heme-2",
"name": "WT-NCgl0176-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0176-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_14",
"name": "Biolector-NCgl0176-NCgl0177-wzy_14",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C3",
"annotationValue": "C3"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl0176-heme-3",
"name": "WT-NCgl0176-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0176-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl0176-heme-3",
"name": "WT-NCgl0176-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0176-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_15",
"name": "Biolector-NCgl0176-NCgl0177-wzy_15",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D3",
"annotationValue": "D3"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl0176-iron-1",
"name": "WT-NCgl0176-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0176-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl0176-iron-1",
"name": "WT-NCgl0176-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0176-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_16",
"name": "Biolector-NCgl0176-NCgl0177-wzy_16",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E3",
"annotationValue": "E3"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl0176-iron-2",
"name": "WT-NCgl0176-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0176-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl0176-iron-2",
"name": "WT-NCgl0176-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0176-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_17",
"name": "Biolector-NCgl0176-NCgl0177-wzy_17",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F3",
"annotationValue": "F3"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl0176-iron-3",
"name": "WT-NCgl0176-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0176-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl0176-iron-3",
"name": "WT-NCgl0176-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0176-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_18",
"name": "Biolector-NCgl0176-NCgl0177-wzy_18",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A4",
"annotationValue": "A4"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl0176-heme-1",
"name": "DdtxR-NCgl0176-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0176-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl0176-heme-1",
"name": "DdtxR-NCgl0176-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0176-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_19",
"name": "Biolector-NCgl0176-NCgl0177-wzy_19",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B4",
"annotationValue": "B4"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl0176-heme-2",
"name": "DdtxR-NCgl0176-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0176-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl0176-heme-2",
"name": "DdtxR-NCgl0176-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0176-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_20",
"name": "Biolector-NCgl0176-NCgl0177-wzy_20",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C4",
"annotationValue": "C4"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl0176-heme-3",
"name": "DdtxR-NCgl0176-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0176-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl0176-heme-3",
"name": "DdtxR-NCgl0176-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0176-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_21",
"name": "Biolector-NCgl0176-NCgl0177-wzy_21",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D4",
"annotationValue": "D4"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl0176-iron-1",
"name": "DdtxR-NCgl0176-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0176-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl0176-iron-1",
"name": "DdtxR-NCgl0176-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0176-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_22",
"name": "Biolector-NCgl0176-NCgl0177-wzy_22",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E4",
"annotationValue": "E4"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl0176-iron-2",
"name": "DdtxR-NCgl0176-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0176-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl0176-iron-2",
"name": "DdtxR-NCgl0176-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0176-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_23",
"name": "Biolector-NCgl0176-NCgl0177-wzy_23",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F4",
"annotationValue": "F4"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl0176-iron-3",
"name": "DdtxR-NCgl0176-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0176-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl0176-iron-3",
"name": "DdtxR-NCgl0176-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0176-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0176-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0176-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_24",
"name": "Biolector-NCgl0176-NCgl0177-wzy_24",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A5",
"annotationValue": "A5"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl0177-heme-1",
"name": "WT-NCgl0177-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0177-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl0177-heme-1",
"name": "WT-NCgl0177-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0177-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_25",
"name": "Biolector-NCgl0176-NCgl0177-wzy_25",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B5",
"annotationValue": "B5"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl0177-heme-2",
"name": "WT-NCgl0177-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0177-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl0177-heme-2",
"name": "WT-NCgl0177-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0177-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_26",
"name": "Biolector-NCgl0176-NCgl0177-wzy_26",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C5",
"annotationValue": "C5"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl0177-heme-3",
"name": "WT-NCgl0177-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0177-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl0177-heme-3",
"name": "WT-NCgl0177-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0177-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_27",
"name": "Biolector-NCgl0176-NCgl0177-wzy_27",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D5",
"annotationValue": "D5"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl0177-iron-1",
"name": "WT-NCgl0177-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0177-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl0177-iron-1",
"name": "WT-NCgl0177-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0177-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_28",
"name": "Biolector-NCgl0176-NCgl0177-wzy_28",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E5",
"annotationValue": "E5"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl0177-iron-2",
"name": "WT-NCgl0177-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0177-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl0177-iron-2",
"name": "WT-NCgl0177-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0177-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_29",
"name": "Biolector-NCgl0176-NCgl0177-wzy_29",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F5",
"annotationValue": "F5"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl0177-iron-3",
"name": "WT-NCgl0177-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0177-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl0177-iron-3",
"name": "WT-NCgl0177-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl0177-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_30",
"name": "Biolector-NCgl0176-NCgl0177-wzy_30",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A6",
"annotationValue": "A6"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl0177-heme-1",
"name": "DdtxR-NCgl0177-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0177-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl0177-heme-1",
"name": "DdtxR-NCgl0177-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0177-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_31",
"name": "Biolector-NCgl0176-NCgl0177-wzy_31",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B6",
"annotationValue": "B6"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl0177-heme-2",
"name": "DdtxR-NCgl0177-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0177-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl0177-heme-2",
"name": "DdtxR-NCgl0177-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0177-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_32",
"name": "Biolector-NCgl0176-NCgl0177-wzy_32",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C6",
"annotationValue": "C6"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl0177-heme-3",
"name": "DdtxR-NCgl0177-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0177-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl0177-heme-3",
"name": "DdtxR-NCgl0177-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0177-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_33",
"name": "Biolector-NCgl0176-NCgl0177-wzy_33",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D6",
"annotationValue": "D6"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl0177-iron-1",
"name": "DdtxR-NCgl0177-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0177-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl0177-iron-1",
"name": "DdtxR-NCgl0177-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0177-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_34",
"name": "Biolector-NCgl0176-NCgl0177-wzy_34",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E6",
"annotationValue": "E6"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl0177-iron-2",
"name": "DdtxR-NCgl0177-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0177-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl0177-iron-2",
"name": "DdtxR-NCgl0177-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0177-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_35",
"name": "Biolector-NCgl0176-NCgl0177-wzy_35",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F6",
"annotationValue": "F6"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_26,06198_h",
"annotationValue": "26,06198 h"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl0177-iron-3",
"name": "DdtxR-NCgl0177-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0177-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0177-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl0177-iron-3",
"name": "DdtxR-NCgl0177-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl0177-venus",
"category": {
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"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl0177-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl0177-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_36",
"name": "Biolector-NCgl0176-NCgl0177-wzy_36",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
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"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A7",
"annotationValue": "A7"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
}
}
],
"inputs": [
{
"@id": "#Sample_",
"name": "",
"characteristics": [
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
}
}
]
},
{
"@id": "#Sample_",
"name": "",
"characteristics": [
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
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"characteristicType": {
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"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#EmptyFactorValue",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_37",
"name": "Biolector-NCgl0176-NCgl0177-wzy_37",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B7",
"annotationValue": "B7"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
}
}
],
"inputs": [
{
"@id": "#Sample_",
"name": "",
"characteristics": [
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
}
}
]
},
{
"@id": "#Sample_",
"name": "",
"characteristics": [
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#EmptyFactorValue",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_38",
"name": "Biolector-NCgl0176-NCgl0177-wzy_38",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
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"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C7",
"annotationValue": "C7"
}
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{
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"termAccession": "MS:1001938"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
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"annotationValue": "experiment time"
}
}
}
],
"inputs": [
{
"@id": "#Sample_",
"name": "",
"characteristics": [
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
}
}
]
},
{
"@id": "#Sample_",
"name": "",
"characteristics": [
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
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"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#EmptyFactorValue",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl0176-NCgl0177-wzy_47",
"name": "Biolector-NCgl0176-NCgl0177-wzy_47",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F8",
"annotationValue": "F8"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
}
}
],
"inputs": [
{
"@id": "#Sample_",
"name": "",
"characteristics": [
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
}
}
]
},
{
"@id": "#Sample_",
"name": "",
"characteristics": [
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl0176_NCgl0177_wzy/20240423_BiolectorAK123_Raw.csv",
"factorValues": [
{
"@id": "#EmptyFactorValue",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_0",
"name": "Biolector-N01781-xerC-cepA-qor3_0",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A1",
"annotationValue": "A1"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
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"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
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"parameterName": {
"@id": "DPBO:0000101",
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"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(EX:_620nm,_gain_20);_YFP_(EX:_508nm,_EM:532nm;gain_80)",
"annotationValue": "backscatter (EX: 620nm, gain 20); YFP (EX: 508nm, EM:532nm;gain 80)"
}
},
{
"category": {
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"parameterName": {
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"termSource": "EFO",
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}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
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"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
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}
},
{
"category": {
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"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
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}
},
{
"category": {
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}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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"parameterName": {
"@id": "#UserTerm_shaker_frequency",
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}
},
"value": {
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"annotationValue": "1200 rpm"
}
},
{
"category": {
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"parameterName": {
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}
},
"value": {
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
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}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl1781-heme-1",
"name": "WT-NCgl1781-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl1781-venus",
"category": {
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"termSource": "MIAPPE",
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},
"value": {
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}
}
]
},
{
"@id": "#Sample_WT-NCgl1781-heme-1",
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl1781-venus",
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},
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}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
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"type": "Raw Data File"
},
{
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"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
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"category": {
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"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
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}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_1",
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},
"value": {
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},
{
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},
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},
{
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}
},
"value": {
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}
},
{
"category": {
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},
"value": {
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}
},
{
"category": {
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}
},
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}
},
{
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},
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},
{
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},
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},
{
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},
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},
{
"category": {
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},
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}
},
{
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},
"value": {
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}
},
{
"category": {
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},
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}
},
{
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}
},
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}
},
{
"category": {
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},
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},
{
"category": {
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},
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},
{
"category": {
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}
},
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}
],
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{
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"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl1781-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl1781-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl1781-heme-2",
"name": "WT-NCgl1781-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl1781-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl1781-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl1781-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_2",
"name": "Biolector-N01781-xerC-cepA-qor3_2",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C1",
"annotationValue": "C1"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl1781-heme-3",
"name": "WT-NCgl1781-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl1781-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl1781-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl1781-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl1781-heme-3",
"name": "WT-NCgl1781-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl1781-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl1781-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl1781-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_3",
"name": "Biolector-N01781-xerC-cepA-qor3_3",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D1",
"annotationValue": "D1"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl1781-iron-1",
"name": "WT-NCgl1781-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl1781-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl1781-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl1781-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl1781-iron-1",
"name": "WT-NCgl1781-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl1781-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl1781-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl1781-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_4",
"name": "Biolector-N01781-xerC-cepA-qor3_4",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E1",
"annotationValue": "E1"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl1781-iron-2",
"name": "WT-NCgl1781-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl1781-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl1781-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl1781-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl1781-iron-2",
"name": "WT-NCgl1781-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl1781-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl1781-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl1781-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_5",
"name": "Biolector-N01781-xerC-cepA-qor3_5",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F1",
"annotationValue": "F1"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl1781-iron-3",
"name": "WT-NCgl1781-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl1781-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl1781-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl1781-venus"
}
}
]
},
{
"@id": "#Sample_WT-NCgl1781-iron-3",
"name": "WT-NCgl1781-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl1781-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl1781-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl1781-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_6",
"name": "Biolector-N01781-xerC-cepA-qor3_6",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A2",
"annotationValue": "A2"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-xerC-heme-1",
"name": "WT-xerC-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PxerC-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum WT + pJC1-PxerC-venus"
}
}
]
},
{
"@id": "#Sample_WT-xerC-heme-1",
"name": "WT-xerC-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PxerC-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum WT + pJC1-PxerC-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_7",
"name": "Biolector-N01781-xerC-cepA-qor3_7",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B2",
"annotationValue": "B2"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-xerC-heme-2",
"name": "WT-xerC-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PxerC-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum WT + pJC1-PxerC-venus"
}
}
]
},
{
"@id": "#Sample_WT-xerC-heme-2",
"name": "WT-xerC-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PxerC-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum WT + pJC1-PxerC-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_8",
"name": "Biolector-N01781-xerC-cepA-qor3_8",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C2",
"annotationValue": "C2"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-xerC-heme-3",
"name": "WT-xerC-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PxerC-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum WT + pJC1-PxerC-venus"
}
}
]
},
{
"@id": "#Sample_WT-xerC-heme-3",
"name": "WT-xerC-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PxerC-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum WT + pJC1-PxerC-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_9",
"name": "Biolector-N01781-xerC-cepA-qor3_9",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D2",
"annotationValue": "D2"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-xerC-iron-1",
"name": "WT-xerC-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PxerC-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum WT + pJC1-PxerC-venus"
}
}
]
},
{
"@id": "#Sample_WT-xerC-iron-1",
"name": "WT-xerC-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PxerC-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum WT + pJC1-PxerC-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_10",
"name": "Biolector-N01781-xerC-cepA-qor3_10",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E2",
"annotationValue": "E2"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-xerC-iron-2",
"name": "WT-xerC-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PxerC-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum WT + pJC1-PxerC-venus"
}
}
]
},
{
"@id": "#Sample_WT-xerC-iron-2",
"name": "WT-xerC-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PxerC-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum WT + pJC1-PxerC-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_11",
"name": "Biolector-N01781-xerC-cepA-qor3_11",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F2",
"annotationValue": "F2"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-xerC-iron-3",
"name": "WT-xerC-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PxerC-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum WT + pJC1-PxerC-venus"
}
}
]
},
{
"@id": "#Sample_WT-xerC-iron-3",
"name": "WT-xerC-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PxerC-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum WT + pJC1-PxerC-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_12",
"name": "Biolector-N01781-xerC-cepA-qor3_12",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A3",
"annotationValue": "A3"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-qor3-heme-1",
"name": "WT-qor3-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pqor3-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pqor3-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pqor3-venus"
}
}
]
},
{
"@id": "#Sample_WT-qor3-heme-1",
"name": "WT-qor3-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pqor3-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pqor3-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pqor3-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_13",
"name": "Biolector-N01781-xerC-cepA-qor3_13",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B3",
"annotationValue": "B3"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-qor3-heme-2",
"name": "WT-qor3-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pqor3-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pqor3-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pqor3-venus"
}
}
]
},
{
"@id": "#Sample_WT-qor3-heme-2",
"name": "WT-qor3-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pqor3-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pqor3-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pqor3-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_14",
"name": "Biolector-N01781-xerC-cepA-qor3_14",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C3",
"annotationValue": "C3"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-qor3-heme-3",
"name": "WT-qor3-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pqor3-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pqor3-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pqor3-venus"
}
}
]
},
{
"@id": "#Sample_WT-qor3-heme-3",
"name": "WT-qor3-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pqor3-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pqor3-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pqor3-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_15",
"name": "Biolector-N01781-xerC-cepA-qor3_15",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D3",
"annotationValue": "D3"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-qor3-iron-1",
"name": "WT-qor3-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pqor3-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pqor3-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pqor3-venus"
}
}
]
},
{
"@id": "#Sample_WT-qor3-iron-1",
"name": "WT-qor3-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pqor3-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pqor3-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pqor3-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_16",
"name": "Biolector-N01781-xerC-cepA-qor3_16",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E3",
"annotationValue": "E3"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-qor3-iron-2",
"name": "WT-qor3-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pqor3-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pqor3-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pqor3-venus"
}
}
]
},
{
"@id": "#Sample_WT-qor3-iron-2",
"name": "WT-qor3-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pqor3-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pqor3-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pqor3-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_17",
"name": "Biolector-N01781-xerC-cepA-qor3_17",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F3",
"annotationValue": "F3"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-qor3-iron-3",
"name": "WT-qor3-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pqor3-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pqor3-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pqor3-venus"
}
}
]
},
{
"@id": "#Sample_WT-qor3-iron-3",
"name": "WT-qor3-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pqor3-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pqor3-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pqor3-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_18",
"name": "Biolector-N01781-xerC-cepA-qor3_18",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A4",
"annotationValue": "A4"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-cepA-heme-1",
"name": "WT-cepA-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum WT + pJC1-PcepA-venus"
}
}
]
},
{
"@id": "#Sample_WT-cepA-heme-1",
"name": "WT-cepA-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum WT + pJC1-PcepA-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_19",
"name": "Biolector-N01781-xerC-cepA-qor3_19",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B4",
"annotationValue": "B4"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-cepA-heme-2",
"name": "WT-cepA-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum WT + pJC1-PcepA-venus"
}
}
]
},
{
"@id": "#Sample_WT-cepA-heme-2",
"name": "WT-cepA-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum WT + pJC1-PcepA-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_20",
"name": "Biolector-N01781-xerC-cepA-qor3_20",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C4",
"annotationValue": "C4"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-cepA-heme-3",
"name": "WT-cepA-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum WT + pJC1-PcepA-venus"
}
}
]
},
{
"@id": "#Sample_WT-cepA-heme-3",
"name": "WT-cepA-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum WT + pJC1-PcepA-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_21",
"name": "Biolector-N01781-xerC-cepA-qor3_21",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D4",
"annotationValue": "D4"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-cepA-iron-1",
"name": "WT-cepA-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum WT + pJC1-PcepA-venus"
}
}
]
},
{
"@id": "#Sample_WT-cepA-iron-1",
"name": "WT-cepA-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum WT + pJC1-PcepA-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_22",
"name": "Biolector-N01781-xerC-cepA-qor3_22",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E4",
"annotationValue": "E4"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-cepA-iron-2",
"name": "WT-cepA-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum WT + pJC1-PcepA-venus"
}
}
]
},
{
"@id": "#Sample_WT-cepA-iron-2",
"name": "WT-cepA-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum WT + pJC1-PcepA-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_23",
"name": "Biolector-N01781-xerC-cepA-qor3_23",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F4",
"annotationValue": "F4"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-cepA-iron-3",
"name": "WT-cepA-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum WT + pJC1-PcepA-venus"
}
}
]
},
{
"@id": "#Sample_WT-cepA-iron-3",
"name": "WT-cepA-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum WT + pJC1-PcepA-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_24",
"name": "Biolector-N01781-xerC-cepA-qor3_24",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A5",
"annotationValue": "A5"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl1781-heme-1",
"name": "DdtxR-NCgl1781-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1781-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl1781-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl1781-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl1781-heme-1",
"name": "DdtxR-NCgl1781-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1781-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl1781-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl1781-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
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}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_25",
"name": "Biolector-N01781-xerC-cepA-qor3_25",
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{
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"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B5",
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},
{
"category": {
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}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
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}
},
{
"category": {
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"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
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"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
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"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
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"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
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},
{
"category": {
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"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
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"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
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"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
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"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
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}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl1781-heme-2",
"name": "DdtxR-NCgl1781-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1781-venus",
"category": {
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"termAccession": "MIAPPE:0041"
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},
"value": {
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}
]
},
{
"@id": "#Sample_DdtxR-NCgl1781-heme-2",
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1781-venus",
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"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
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"termAccession": "MIAPPE:0041"
}
},
"value": {
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"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl1781-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_26",
"name": "Biolector-N01781-xerC-cepA-qor3_26",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C5",
"annotationValue": "C5"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
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"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
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}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
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"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
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"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
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"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
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"termAccession": "NCIT:C65288"
}
},
"value": {
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"annotationValue": "0%"
}
},
{
"category": {
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"parameterName": {
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"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
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"parameterName": {
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}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl1781-heme-3",
"name": "DdtxR-NCgl1781-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1781-venus",
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"characteristicType": {
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"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
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}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl1781-heme-3",
"name": "DdtxR-NCgl1781-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1781-venus",
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"characteristicType": {
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},
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}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
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"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
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"category": {
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}
},
"value": {
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}
}
]
}
]
},
{
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"termAccession": "NFDI4PSO:1000101"
}
},
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}
},
{
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}
},
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}
},
{
"category": {
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}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
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}
},
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"annotationValue": "Biolector I"
}
},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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"parameterName": {
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}
},
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},
{
"category": {
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}
},
"value": {
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},
{
"category": {
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},
"value": {
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}
},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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}
},
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}
},
{
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}
},
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}
},
{
"category": {
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}
},
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},
{
"category": {
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},
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}
},
{
"category": {
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}
},
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}
}
],
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{
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}
},
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}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl1781-iron-1",
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{
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},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl1781-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl1781-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_28",
"name": "Biolector-N01781-xerC-cepA-qor3_28",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E5",
"annotationValue": "E5"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl1781-iron-2",
"name": "DdtxR-NCgl1781-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1781-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl1781-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl1781-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl1781-iron-2",
"name": "DdtxR-NCgl1781-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1781-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl1781-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl1781-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_29",
"name": "Biolector-N01781-xerC-cepA-qor3_29",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F5",
"annotationValue": "F5"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
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"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
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"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
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"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
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"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
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"parameterName": {
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}
},
"value": {
"@id": "#UserTerm_30_min",
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}
},
{
"category": {
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"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl1781-iron-3",
"name": "DdtxR-NCgl1781-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1781-venus",
"category": {
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"characteristicType": {
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"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
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}
}
]
},
{
"@id": "#Sample_DdtxR-NCgl1781-iron-3",
"name": "DdtxR-NCgl1781-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl1781-venus",
"category": {
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"characteristicType": {
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"termSource": "MIAPPE",
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},
"value": {
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}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
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"category": {
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"factorName": "Factor [iron source]",
"factorType": {
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"annotationValue": "iron source"
}
},
"value": {
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}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_30",
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"parameterValues": [
{
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"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
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"annotationValue": "A6"
}
},
{
"category": {
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"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
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}
},
{
"category": {
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"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
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"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
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"annotationValue": "Biolector I"
}
},
{
"category": {
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},
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}
},
{
"category": {
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"parameterName": {
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}
},
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},
{
"category": {
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"parameterName": {
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}
},
"value": {
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},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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"parameterName": {
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"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
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}
},
{
"category": {
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"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
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}
},
{
"category": {
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"parameterName": {
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}
},
"value": {
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},
{
"category": {
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"parameterName": {
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}
},
"value": {
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}
},
{
"category": {
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}
},
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}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-xerC-heme-1",
"name": "DdtxR-xerC-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PxerC-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PxerC-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-xerC-heme-1",
"name": "DdtxR-xerC-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PxerC-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PxerC-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_31",
"name": "Biolector-N01781-xerC-cepA-qor3_31",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B6",
"annotationValue": "B6"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-xerC-heme-2",
"name": "DdtxR-xerC-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PxerC-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PxerC-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-xerC-heme-2",
"name": "DdtxR-xerC-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PxerC-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PxerC-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_32",
"name": "Biolector-N01781-xerC-cepA-qor3_32",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C6",
"annotationValue": "C6"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-xerC-heme-3",
"name": "DdtxR-xerC-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PxerC-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PxerC-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-xerC-heme-3",
"name": "DdtxR-xerC-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PxerC-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PxerC-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_33",
"name": "Biolector-N01781-xerC-cepA-qor3_33",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D6",
"annotationValue": "D6"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
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"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
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"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-xerC-iron-1",
"name": "DdtxR-xerC-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PxerC-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PxerC-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-xerC-iron-1",
"name": "DdtxR-xerC-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PxerC-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PxerC-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_34",
"name": "Biolector-N01781-xerC-cepA-qor3_34",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E6",
"annotationValue": "E6"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-xerC-iron-2",
"name": "DdtxR-xerC-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PxerC-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PxerC-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-xerC-iron-2",
"name": "DdtxR-xerC-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PxerC-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PxerC-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_35",
"name": "Biolector-N01781-xerC-cepA-qor3_35",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F6",
"annotationValue": "F6"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-xerC-iron-3",
"name": "DdtxR-xerC-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PxerC-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PxerC-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-xerC-iron-3",
"name": "DdtxR-xerC-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PxerC-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PxerC-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PxerC-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_36",
"name": "Biolector-N01781-xerC-cepA-qor3_36",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A7",
"annotationValue": "A7"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-qor3-heme-1",
"name": "DdtxR-qor3-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pqor3-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pqor3-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-Pqor3-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-qor3-heme-1",
"name": "DdtxR-qor3-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pqor3-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pqor3-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-Pqor3-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_37",
"name": "Biolector-N01781-xerC-cepA-qor3_37",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B7",
"annotationValue": "B7"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-qor3-heme-2",
"name": "DdtxR-qor3-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pqor3-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pqor3-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-Pqor3-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-qor3-heme-2",
"name": "DdtxR-qor3-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pqor3-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pqor3-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-Pqor3-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_38",
"name": "Biolector-N01781-xerC-cepA-qor3_38",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C7",
"annotationValue": "C7"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-qor3-heme-3",
"name": "DdtxR-qor3-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pqor3-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pqor3-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-Pqor3-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-qor3-heme-3",
"name": "DdtxR-qor3-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pqor3-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pqor3-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-Pqor3-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_39",
"name": "Biolector-N01781-xerC-cepA-qor3_39",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D7",
"annotationValue": "D7"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-qor3-iron-1",
"name": "DdtxR-qor3-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pqor3-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pqor3-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-Pqor3-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-qor3-iron-1",
"name": "DdtxR-qor3-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pqor3-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pqor3-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-Pqor3-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_40",
"name": "Biolector-N01781-xerC-cepA-qor3_40",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E7",
"annotationValue": "E7"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-qor3-iron-2",
"name": "DdtxR-qor3-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pqor3-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pqor3-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-Pqor3-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-qor3-iron-2",
"name": "DdtxR-qor3-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pqor3-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pqor3-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-Pqor3-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_41",
"name": "Biolector-N01781-xerC-cepA-qor3_41",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F7",
"annotationValue": "F7"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-qor3-iron-3",
"name": "DdtxR-qor3-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pqor3-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pqor3-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-Pqor3-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-qor3-iron-3",
"name": "DdtxR-qor3-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pqor3-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pqor3-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-Pqor3-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_42",
"name": "Biolector-N01781-xerC-cepA-qor3_42",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A8",
"annotationValue": "A8"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-cepA-heme-1",
"name": "DdtxR-cepA-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PcepA-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-cepA-heme-1",
"name": "DdtxR-cepA-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PcepA-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_43",
"name": "Biolector-N01781-xerC-cepA-qor3_43",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B8",
"annotationValue": "B8"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-cepA-heme-2",
"name": "DdtxR-cepA-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PcepA-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-cepA-heme-2",
"name": "DdtxR-cepA-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PcepA-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_44",
"name": "Biolector-N01781-xerC-cepA-qor3_44",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C8",
"annotationValue": "C8"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-cepA-heme-3",
"name": "DdtxR-cepA-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PcepA-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-cepA-heme-3",
"name": "DdtxR-cepA-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PcepA-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=4 \u00b5M hemin",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_4_\u00b5M_hemin",
"annotationValue": "4 \u00b5M hemin"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_45",
"name": "Biolector-N01781-xerC-cepA-qor3_45",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D8",
"annotationValue": "D8"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-cepA-iron-1",
"name": "DdtxR-cepA-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PcepA-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-cepA-iron-1",
"name": "DdtxR-cepA-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PcepA-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_46",
"name": "Biolector-N01781-xerC-cepA-qor3_46",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E8",
"annotationValue": "E8"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-cepA-iron-2",
"name": "DdtxR-cepA-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PcepA-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-cepA-iron-2",
"name": "DdtxR-cepA-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PcepA-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-N01781-xerC-cepA-qor3_47",
"name": "Biolector-N01781-xerC-cepA-qor3_47",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F8",
"annotationValue": "F8"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin",
"annotationValue": "CGXII + 2% glucose + Kanamycin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.56134",
"annotationValue": "23.56134"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-cepA-iron-3",
"name": "DdtxR-cepA-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PcepA-venus"
}
}
]
},
{
"@id": "#Sample_DdtxR-cepA-iron-3",
"name": "DdtxR-cepA-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PcepA-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PcepA-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PcepA-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"type": "Raw Data File"
},
{
"@id": "#Sample_assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION_Gain_60.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl1781_xerC_qor3_cepA/Johanna-coryne_20240130_TRANSFORM__CRITERION Gain 60.csv",
"factorValues": [
{
"@id": "#FactorValue/iron source=100 \u00b5M FeSO4",
"category": {
"@id": "#Factor/Factor [iron source]",
"factorName": "Factor [iron source]",
"factorType": {
"@id": "#UserTerm_iron_source",
"annotationValue": "iron source"
}
},
"value": {
"@id": "#UserTerm_100_\u00b5M_FeSO4",
"annotationValue": "100 \u00b5M FeSO4"
}
}
]
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_0",
"name": "Biolector-NCgl2776-gyrB-wzy_0",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A1",
"annotationValue": "A1"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_0_\u00b5M_FeSO4_+_4_\u00b5M_hemin",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 0 \u00b5M FeSO4 + 4 \u00b5M hemin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(EX:_620nm,_gain_20);_YFP_(EX:_508nm,_EM:532nm;gain_80)",
"annotationValue": "backscatter (EX: 620nm, gain 20); YFP (EX: 508nm, EM:532nm;gain 80)"
}
},
{
"category": {
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"parameterName": {
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"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl2776-heme-1",
"name": "WT-NCgl2776-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl2776-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
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"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl2776-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl2776-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_1",
"name": "Biolector-NCgl2776-gyrB-wzy_1",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B1",
"annotationValue": "B1"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_0_\u00b5M_FeSO4_+_4_\u00b5M_hemin",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 0 \u00b5M FeSO4 + 4 \u00b5M hemin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
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"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
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"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
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}
},
{
"category": {
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"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
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"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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"termAccession": "UO:0000196"
}
},
"value": {
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"annotationValue": "not applicable"
}
},
{
"category": {
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"@id": "#UserTerm_shaker_frequency",
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}
},
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},
{
"category": {
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}
},
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}
},
{
"category": {
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"annotationValue": "experiment time"
}
},
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}
],
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{
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl2776-venus",
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"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
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"annotationValue": "C. glutamicum WT + pJC1-PNCgl2776-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
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{
"category": {
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"parameterName": {
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"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
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}
},
{
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}
},
"value": {
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},
{
"category": {
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"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
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"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
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}
},
{
"category": {
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}
},
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}
},
{
"category": {
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}
},
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}
},
{
"category": {
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"parameterName": {
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"annotationValue": "filterset"
}
},
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}
},
{
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}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
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},
{
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}
},
"value": {
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}
},
{
"category": {
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}
},
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}
},
{
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"termSource": "NCIT",
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}
},
"value": {
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}
},
{
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"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
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}
},
"value": {
"@id": "#UserTerm_1200_rpm",
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}
},
{
"category": {
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}
},
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},
{
"category": {
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},
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}
],
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{
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{
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},
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}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
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}
]
},
{
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{
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}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
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"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
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}
},
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}
},
{
"category": {
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}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
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}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
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}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
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}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
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"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl2776-iron-1",
"name": "WT-NCgl2776-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl2776-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl2776-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl2776-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_4",
"name": "Biolector-NCgl2776-gyrB-wzy_4",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E1",
"annotationValue": "E1"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_100_\u00b5M_FeSO4_",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 100 \u00b5M FeSO4 "
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-NCgl2776-iron-2",
"name": "WT-NCgl2776-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl2776-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PNCgl2776-venus",
"annotationValue": "C. glutamicum WT + pJC1-PNCgl2776-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_5",
"name": "Biolector-NCgl2776-gyrB-wzy_5",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F1",
"annotationValue": "F1"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_100_\u00b5M_FeSO4_",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 100 \u00b5M FeSO4 "
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
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"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
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"@id": "MS:1001938",
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}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
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}
},
{
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},
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},
{
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}
},
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}
},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
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"annotationValue": "not applicable"
}
},
{
"category": {
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}
},
"value": {
"@id": "#UserTerm_1200_rpm",
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}
},
{
"category": {
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},
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},
{
"category": {
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}
},
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}
],
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{
"@id": "#Sample_WT-NCgl2776-iron-3",
"name": "WT-NCgl2776-iron-3",
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PNCgl2776-venus",
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}
},
"value": {
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"annotationValue": "C. glutamicum WT + pJC1-PNCgl2776-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_6",
"name": "Biolector-NCgl2776-gyrB-wzy_6",
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{
"category": {
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"parameterName": {
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"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A2",
"annotationValue": "A2"
}
},
{
"category": {
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"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_0_\u00b5M_FeSO4_+_4_\u00b5M_hemin",
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}
},
{
"category": {
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"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
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"parameterName": {
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"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
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}
},
{
"category": {
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"@id": "#UserTerm_cultivation_device",
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}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
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"@id": "MS:1001938",
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"termSource": "MS",
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}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
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}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
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}
},
{
"category": {
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"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
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}
},
"value": {
"@id": "#UserTerm_20,95%",
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}
},
{
"category": {
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"parameterName": {
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"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
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}
},
{
"category": {
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"annotationValue": "pH",
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"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
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}
},
"value": {
"@id": "#UserTerm_30_min",
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
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}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-gyrB-heme-1",
"name": "WT-gyrB-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PgyrB-venus",
"category": {
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"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PgyrB-venus",
"annotationValue": "C. glutamicum WT + pJC1-PgyrB-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_7",
"name": "Biolector-NCgl2776-gyrB-wzy_7",
"parameterValues": [
{
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"parameterName": {
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"annotationValue": "Well",
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"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B2",
"annotationValue": "B2"
}
},
{
"category": {
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"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_0_\u00b5M_FeSO4_+_4_\u00b5M_hemin",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 0 \u00b5M FeSO4 + 4 \u00b5M hemin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-gyrB-heme-2",
"name": "WT-gyrB-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PgyrB-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PgyrB-venus",
"annotationValue": "C. glutamicum WT + pJC1-PgyrB-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_8",
"name": "Biolector-NCgl2776-gyrB-wzy_8",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C2",
"annotationValue": "C2"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_0_\u00b5M_FeSO4_+_4_\u00b5M_hemin",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 0 \u00b5M FeSO4 + 4 \u00b5M hemin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
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"@id": "EFO:0001702",
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"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
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"parameterName": {
"@id": "PATO:0015009",
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"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
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"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
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"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
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"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
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}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
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}
},
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
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}
},
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"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
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}
],
"inputs": [
{
"@id": "#Sample_WT-gyrB-heme-3",
"name": "WT-gyrB-heme-3",
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PgyrB-venus",
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"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PgyrB-venus",
"annotationValue": "C. glutamicum WT + pJC1-PgyrB-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_9",
"name": "Biolector-NCgl2776-gyrB-wzy_9",
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{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
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"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
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"annotationValue": "D2"
}
},
{
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}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_100_\u00b5M_FeSO4_",
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}
},
{
"category": {
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}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
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}
},
{
"category": {
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"parameterName": {
"@id": "DPBO:0000101",
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}
},
"value": {
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}
},
{
"category": {
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}
},
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}
},
{
"category": {
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}
},
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"@id": "#UserTerm_Flower_Plate_(48-well)",
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}
},
{
"category": {
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"parameterName": {
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"annotationValue": "filterset"
}
},
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"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
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}
},
{
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}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
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},
{
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}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
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},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
"@id": "#UserTerm_not_applicable",
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}
},
{
"category": {
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"@id": "#UserTerm_shaker_frequency",
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}
},
"value": {
"@id": "#UserTerm_1200_rpm",
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},
{
"category": {
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"@id": "#UserTerm_cycle_time",
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},
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}
},
{
"category": {
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},
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}
],
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{
"@id": "#Sample_WT-gyrB-iron-1",
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PgyrB-venus",
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},
"value": {
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}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
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}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_10",
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}
},
"value": {
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}
},
{
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},
"value": {
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}
},
{
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}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
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},
{
"category": {
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"parameterName": {
"@id": "DPBO:0000101",
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}
},
"value": {
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}
},
{
"category": {
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}
},
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}
},
{
"category": {
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"@id": "MS:1001938",
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}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
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"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
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}
},
{
"category": {
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}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
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},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-gyrB-iron-2",
"name": "WT-gyrB-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PgyrB-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PgyrB-venus",
"annotationValue": "C. glutamicum WT + pJC1-PgyrB-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_11",
"name": "Biolector-NCgl2776-gyrB-wzy_11",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F2",
"annotationValue": "F2"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_100_\u00b5M_FeSO4_",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 100 \u00b5M FeSO4 "
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-gyrB-iron-3",
"name": "WT-gyrB-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PgyrB-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PgyrB-venus",
"annotationValue": "C. glutamicum WT + pJC1-PgyrB-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_12",
"name": "Biolector-NCgl2776-gyrB-wzy_12",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A3",
"annotationValue": "A3"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_0_\u00b5M_FeSO4_+_4_\u00b5M_hemin",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 0 \u00b5M FeSO4 + 4 \u00b5M hemin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-ssuD1-heme-1",
"name": "WT-ssuD1-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PssuD1-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PssuD1-venus",
"annotationValue": "C. glutamicum WT + pJC1-PssuD1-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_13",
"name": "Biolector-NCgl2776-gyrB-wzy_13",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B3",
"annotationValue": "B3"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_0_\u00b5M_FeSO4_+_4_\u00b5M_hemin",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 0 \u00b5M FeSO4 + 4 \u00b5M hemin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-ssuD1-heme-2",
"name": "WT-ssuD1-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PssuD1-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PssuD1-venus",
"annotationValue": "C. glutamicum WT + pJC1-PssuD1-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_14",
"name": "Biolector-NCgl2776-gyrB-wzy_14",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C3",
"annotationValue": "C3"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_0_\u00b5M_FeSO4_+_4_\u00b5M_hemin",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 0 \u00b5M FeSO4 + 4 \u00b5M hemin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-ssuD1-heme-3",
"name": "WT-ssuD1-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PssuD1-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PssuD1-venus",
"annotationValue": "C. glutamicum WT + pJC1-PssuD1-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_15",
"name": "Biolector-NCgl2776-gyrB-wzy_15",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D3",
"annotationValue": "D3"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_100_\u00b5M_FeSO4_",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 100 \u00b5M FeSO4 "
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-ssuD1-iron-1",
"name": "WT-ssuD1-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PssuD1-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PssuD1-venus",
"annotationValue": "C. glutamicum WT + pJC1-PssuD1-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_16",
"name": "Biolector-NCgl2776-gyrB-wzy_16",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E3",
"annotationValue": "E3"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_100_\u00b5M_FeSO4_",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 100 \u00b5M FeSO4 "
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
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"@id": "EFO:0001702",
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"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
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"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-ssuD1-iron-2",
"name": "WT-ssuD1-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PssuD1-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PssuD1-venus",
"annotationValue": "C. glutamicum WT + pJC1-PssuD1-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_17",
"name": "Biolector-NCgl2776-gyrB-wzy_17",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F3",
"annotationValue": "F3"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_100_\u00b5M_FeSO4_",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 100 \u00b5M FeSO4 "
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-ssuD1-iron-3",
"name": "WT-ssuD1-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-PssuD1-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-PssuD1-venus",
"annotationValue": "C. glutamicum WT + pJC1-PssuD1-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_18",
"name": "Biolector-NCgl2776-gyrB-wzy_18",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A4",
"annotationValue": "A4"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_0_\u00b5M_FeSO4_+_4_\u00b5M_hemin",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 0 \u00b5M FeSO4 + 4 \u00b5M hemin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-wzy-heme-1",
"name": "WT-wzy-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pwzy-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_19",
"name": "Biolector-NCgl2776-gyrB-wzy_19",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B4",
"annotationValue": "B4"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_0_\u00b5M_FeSO4_+_4_\u00b5M_hemin",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 0 \u00b5M FeSO4 + 4 \u00b5M hemin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-wzy-heme-2",
"name": "WT-wzy-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pwzy-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_20",
"name": "Biolector-NCgl2776-gyrB-wzy_20",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C4",
"annotationValue": "C4"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_0_\u00b5M_FeSO4_+_4_\u00b5M_hemin",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 0 \u00b5M FeSO4 + 4 \u00b5M hemin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
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"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
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}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
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"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
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}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
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"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-wzy-heme-3",
"name": "WT-wzy-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pwzy-venus",
"category": {
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"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pwzy-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_21",
"name": "Biolector-NCgl2776-gyrB-wzy_21",
"parameterValues": [
{
"category": {
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"parameterName": {
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"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D4",
"annotationValue": "D4"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
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"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_100_\u00b5M_FeSO4_",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 100 \u00b5M FeSO4 "
}
},
{
"category": {
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"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-wzy-iron-1",
"name": "WT-wzy-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pwzy-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_22",
"name": "Biolector-NCgl2776-gyrB-wzy_22",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E4",
"annotationValue": "E4"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_100_\u00b5M_FeSO4_",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 100 \u00b5M FeSO4 "
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-wzy-iron-2",
"name": "WT-wzy-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pwzy-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_23",
"name": "Biolector-NCgl2776-gyrB-wzy_23",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F4",
"annotationValue": "F4"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_100_\u00b5M_FeSO4_",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 100 \u00b5M FeSO4 "
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_WT-wzy-iron-3",
"name": "WT-wzy-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum WT + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_WT_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum WT + pJC1-Pwzy-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_24",
"name": "Biolector-NCgl2776-gyrB-wzy_24",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A5",
"annotationValue": "A5"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_0_\u00b5M_FeSO4_+_4_\u00b5M_hemin",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 0 \u00b5M FeSO4 + 4 \u00b5M hemin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-NCgl2776-heme-1",
"name": "DdtxR-NCgl2776-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl2776-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl2776-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl2776-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_25",
"name": "Biolector-NCgl2776-gyrB-wzy_25",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
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"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B5",
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},
{
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},
"value": {
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},
{
"category": {
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"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
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},
"value": {
"@id": "#UserTerm_3",
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}
},
{
"category": {
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"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
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},
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"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
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},
{
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},
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},
{
"category": {
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"termAccession": "PATO:0015009"
}
},
"value": {
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}
},
{
"category": {
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},
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},
{
"category": {
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},
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}
},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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},
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},
{
"category": {
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{
"category": {
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},
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"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
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}
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{
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl2776-venus",
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},
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}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
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}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_26",
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{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
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"termAccession": "NFDI4PSO:1000101"
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},
"value": {
"@id": "#UserTerm_C5",
"annotationValue": "C5"
}
},
{
"category": {
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},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_0_\u00b5M_FeSO4_+_4_\u00b5M_hemin",
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},
{
"category": {
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"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
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},
{
"category": {
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},
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},
{
"category": {
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},
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"@id": "#UserTerm_Biolector_I",
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}
},
{
"category": {
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},
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"@id": "#UserTerm_Flower_Plate_(48-well)",
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},
{
"category": {
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}
},
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},
{
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},
"value": {
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},
{
"category": {
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}
},
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}
},
{
"category": {
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}
},
"value": {
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},
{
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},
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}
},
{
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},
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}
},
{
"category": {
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},
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{
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},
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}
]
}
],
"outputs": [
{
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]
},
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},
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},
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},
{
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},
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},
{
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},
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},
{
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},
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},
{
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},
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},
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},
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},
{
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},
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},
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},
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},
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},
{
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},
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},
{
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}
}
]
}
],
"outputs": [
{
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]
},
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},
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},
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},
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},
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},
{
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},
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},
{
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},
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},
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},
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},
{
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},
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},
{
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},
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},
{
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},
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},
{
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},
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{
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"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
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"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
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}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
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{
"@id": "#Sample_DdtxR-NCgl2776-iron-2",
"name": "DdtxR-NCgl2776-iron-2",
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl2776-venus",
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"@id": "#MaterialAttribute/MIAPPE:0041",
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"termAccession": "MIAPPE:0041"
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},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PNCgl2776-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PNCgl2776-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_29",
"name": "Biolector-NCgl2776-gyrB-wzy_29",
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{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
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"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F5",
"annotationValue": "F5"
}
},
{
"category": {
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"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_100_\u00b5M_FeSO4_",
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},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
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"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
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"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
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},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
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"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
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"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
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},
{
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}
},
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},
{
"category": {
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},
"value": {
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}
},
{
"category": {
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}
},
"value": {
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}
},
{
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},
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}
},
{
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}
},
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}
},
{
"category": {
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}
},
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},
{
"category": {
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},
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{
"category": {
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},
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}
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{
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PNCgl2776-venus",
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}
},
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}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
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}
]
},
{
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{
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"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
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},
{
"category": {
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"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
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},
"value": {
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}
},
{
"category": {
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}
},
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}
},
{
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},
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},
{
"category": {
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},
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{
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},
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{
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{
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},
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},
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{
"category": {
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},
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},
{
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},
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}
]
}
],
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{
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"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
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]
},
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},
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},
{
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},
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},
{
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}
},
"value": {
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},
{
"category": {
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},
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},
{
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},
{
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},
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},
{
"category": {
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}
},
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},
{
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}
},
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},
{
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}
},
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},
{
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},
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{
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},
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}
},
{
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}
},
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}
},
{
"category": {
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}
},
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},
{
"category": {
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},
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},
{
"category": {
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},
"value": {
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}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
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}
]
},
{
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},
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},
{
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},
"value": {
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"annotationValue": "CGXII + 2% glucose + Kanamycin + 0 \u00b5M FeSO4 + 4 \u00b5M hemin"
}
},
{
"category": {
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"@id": "DPBO:1000155",
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"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
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"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
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"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
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"@id": "MS:1001938",
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"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
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}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
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}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
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"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
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}
},
"value": {
"@id": "#UserTerm_20,95%",
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}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
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"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
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}
},
{
"category": {
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"parameterName": {
"@id": "UO:0000196",
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"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
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}
},
"value": {
"@id": "#UserTerm_30_min",
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},
{
"category": {
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},
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"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
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}
],
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{
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"name": "DdtxR-gyrB-heme-3",
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PgyrB-venus",
"category": {
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"annotationValue": "Organism",
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PgyrB-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PgyrB-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_33",
"name": "Biolector-NCgl2776-gyrB-wzy_33",
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{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
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"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D6",
"annotationValue": "D6"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
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"@id": "NCIT:C85504",
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"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_100_\u00b5M_FeSO4_",
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}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
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"@id": "DPBO:1000155",
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"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
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"termAccession": "DPBO:0000101"
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},
"value": {
"@id": "#UserTerm_3",
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}
},
{
"category": {
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}
},
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"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
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"@id": "MS:1001938",
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}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
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}
},
{
"category": {
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"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
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},
{
"category": {
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}
},
"value": {
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},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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}
},
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}
},
{
"category": {
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}
},
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},
{
"category": {
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"category": {
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},
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}
],
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{
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}
},
"value": {
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}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
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}
]
},
{
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}
},
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},
{
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},
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},
{
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},
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},
{
"category": {
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},
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},
{
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},
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},
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},
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},
{
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}
},
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},
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},
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},
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},
{
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},
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},
{
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},
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}
},
{
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}
},
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}
},
{
"category": {
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},
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},
{
"category": {
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{
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},
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}
]
}
],
"outputs": [
{
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}
]
},
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},
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},
{
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},
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},
{
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},
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},
{
"category": {
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},
"value": {
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}
},
{
"category": {
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},
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},
{
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},
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},
{
"category": {
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}
},
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},
{
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},
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},
{
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},
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}
},
{
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}
},
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}
},
{
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},
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}
},
{
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}
},
"value": {
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-gyrB-iron-3",
"name": "DdtxR-gyrB-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PgyrB-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PgyrB-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PgyrB-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_36",
"name": "Biolector-NCgl2776-gyrB-wzy_36",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_A7",
"annotationValue": "A7"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_0_\u00b5M_FeSO4_+_4_\u00b5M_hemin",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 0 \u00b5M FeSO4 + 4 \u00b5M hemin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-ssuD1-heme-1",
"name": "DdtxR-ssuD1-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PssuD1-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PssuD1-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PssuD1-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_37",
"name": "Biolector-NCgl2776-gyrB-wzy_37",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B7",
"annotationValue": "B7"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_0_\u00b5M_FeSO4_+_4_\u00b5M_hemin",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 0 \u00b5M FeSO4 + 4 \u00b5M hemin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
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"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
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"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-ssuD1-heme-2",
"name": "DdtxR-ssuD1-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PssuD1-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PssuD1-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PssuD1-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_38",
"name": "Biolector-NCgl2776-gyrB-wzy_38",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C7",
"annotationValue": "C7"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_0_\u00b5M_FeSO4_+_4_\u00b5M_hemin",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 0 \u00b5M FeSO4 + 4 \u00b5M hemin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-ssuD1-heme-3",
"name": "DdtxR-ssuD1-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PssuD1-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PssuD1-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PssuD1-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_39",
"name": "Biolector-NCgl2776-gyrB-wzy_39",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D7",
"annotationValue": "D7"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_100_\u00b5M_FeSO4_",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 100 \u00b5M FeSO4 "
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
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}
},
"value": {
"@id": "#UserTerm_30_min",
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-ssuD1-iron-1",
"name": "DdtxR-ssuD1-iron-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PssuD1-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PssuD1-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PssuD1-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_40",
"name": "Biolector-NCgl2776-gyrB-wzy_40",
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{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E7",
"annotationValue": "E7"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_100_\u00b5M_FeSO4_",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 100 \u00b5M FeSO4 "
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
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}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
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"@id": "EFO:0001702",
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"termSource": "EFO",
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}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
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"@id": "PATO:0015009",
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"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
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"parameterName": {
"@id": "NCIT:C722",
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}
},
"value": {
"@id": "#UserTerm_20,95%",
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}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
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}
},
"value": {
"@id": "#UserTerm_0%",
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}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
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"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
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}
},
"value": {
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}
},
{
"category": {
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"@id": "#UserTerm_cycle_time",
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},
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}
},
{
"category": {
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}
},
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}
],
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{
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"name": "DdtxR-ssuD1-iron-2",
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{
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"characteristicType": {
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"annotationValue": "Organism",
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}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-PssuD1-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-PssuD1-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
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"name": "Biolector-NCgl2776-gyrB-wzy_41",
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{
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"parameterName": {
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"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
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"annotationValue": "F7"
}
},
{
"category": {
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}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_100_\u00b5M_FeSO4_",
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}
},
{
"category": {
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"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
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}
},
{
"category": {
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}
},
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}
},
{
"category": {
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}
},
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}
},
{
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}
},
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},
{
"category": {
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"parameterName": {
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}
},
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},
{
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},
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},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
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},
{
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},
"value": {
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}
},
{
"category": {
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}
},
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}
},
{
"category": {
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}
},
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},
{
"category": {
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},
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},
{
"category": {
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},
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-PssuD1-venus",
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},
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}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
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]
},
{
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},
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}
},
{
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},
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},
{
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}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
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},
{
"category": {
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},
"value": {
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}
},
{
"category": {
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}
},
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}
},
{
"category": {
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}
},
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}
},
{
"category": {
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}
},
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}
},
{
"category": {
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},
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},
{
"category": {
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}
},
"value": {
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}
},
{
"category": {
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}
},
"value": {
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}
},
{
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},
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}
},
{
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}
},
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}
},
{
"category": {
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}
},
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},
{
"category": {
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}
},
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}
},
{
"category": {
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},
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}
],
"inputs": [
{
"@id": "#Sample_DdtxR-wzy-heme-1",
"name": "DdtxR-wzy-heme-1",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-Pwzy-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_43",
"name": "Biolector-NCgl2776-gyrB-wzy_43",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_B8",
"annotationValue": "B8"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_0_\u00b5M_FeSO4_+_4_\u00b5M_hemin",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 0 \u00b5M FeSO4 + 4 \u00b5M hemin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-wzy-heme-2",
"name": "DdtxR-wzy-heme-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-Pwzy-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_44",
"name": "Biolector-NCgl2776-gyrB-wzy_44",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_C8",
"annotationValue": "C8"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_0_\u00b5M_FeSO4_+_4_\u00b5M_hemin",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 0 \u00b5M FeSO4 + 4 \u00b5M hemin"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
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"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
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}
},
"value": {
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
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"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-wzy-heme-3",
"name": "DdtxR-wzy-heme-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-Pwzy-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_45",
"name": "Biolector-NCgl2776-gyrB-wzy_45",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
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"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_D8",
"annotationValue": "D8"
}
},
{
"category": {
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"parameterName": {
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"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_100_\u00b5M_FeSO4_",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 100 \u00b5M FeSO4 "
}
},
{
"category": {
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"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
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"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
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"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
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"parameterName": {
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"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
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}
},
"value": {
"@id": "#UserTerm_20,95%",
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}
},
{
"category": {
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"parameterName": {
"@id": "NCIT:C65288",
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"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
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}
},
{
"category": {
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"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
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}
},
"value": {
"@id": "#UserTerm_30_min",
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}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
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}
},
"value": {
"@id": "#UserTerm_23.06143",
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}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-wzy-iron-1",
"name": "DdtxR-wzy-iron-1",
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{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pwzy-venus",
"category": {
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"characteristicType": {
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"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-Pwzy-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_46",
"name": "Biolector-NCgl2776-gyrB-wzy_46",
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{
"category": {
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"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_E8",
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}
},
{
"category": {
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"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_100_\u00b5M_FeSO4_",
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}
},
{
"category": {
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"@id": "DPBO:1000155",
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"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
"@id": "#ProtocolParameter/UO:0000196",
"parameterName": {
"@id": "UO:0000196",
"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cycle_time",
"parameterName": {
"@id": "#UserTerm_cycle_time",
"annotationValue": "cycle time"
}
},
"value": {
"@id": "#UserTerm_30_min",
"annotationValue": "30 min"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": {
"@id": "#UserTerm_23.06143",
"annotationValue": "23.06143"
}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-wzy-iron-2",
"name": "DdtxR-wzy-iron-2",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pwzy-venus",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_C._glutamicum_DdtxR_+_pJC1-Pwzy-venus",
"annotationValue": "C. glutamicum DdtxR + pJC1-Pwzy-venus"
}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Biolector-NCgl2776-gyrB-wzy_47",
"name": "Biolector-NCgl2776-gyrB-wzy_47",
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/NFDI4PSO:1000101",
"parameterName": {
"@id": "NFDI4PSO:1000101",
"annotationValue": "Well",
"termSource": "NFDI4PSO",
"termAccession": "NFDI4PSO:1000101"
}
},
"value": {
"@id": "#UserTerm_F8",
"annotationValue": "F8"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CGXII_+_2%_glucose_+_Kanamycin_+_100_\u00b5M_FeSO4_",
"annotationValue": "CGXII + 2% glucose + Kanamycin + 100 \u00b5M FeSO4 "
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": {
"@id": "#UserTerm_750_\u00b5l",
"annotationValue": "750 \u00b5l"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
"value": {
"@id": "#UserTerm_3",
"annotationValue": "3"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_cultivation_device",
"parameterName": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
},
"value": {
"@id": "#UserTerm_Biolector_I",
"annotationValue": "Biolector I"
}
},
{
"category": {
"@id": "#ProtocolParameter/MS:1001938",
"parameterName": {
"@id": "MS:1001938",
"annotationValue": "sample plate type",
"termSource": "MS",
"termAccession": "MS:1001938"
}
},
"value": {
"@id": "#UserTerm_Flower_Plate_(48-well)",
"annotationValue": "Flower Plate (48-well)"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_filterset",
"parameterName": {
"@id": "#UserTerm_filterset",
"annotationValue": "filterset"
}
},
"value": {
"@id": "#UserTerm_backscatter_(gain_20);_YFP_(gain_80)",
"annotationValue": "backscatter (gain 20); YFP (gain 80)"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": {
"@id": "#UserTerm_30\u00b0C",
"annotationValue": "30\u00b0C"
}
},
{
"category": {
"@id": "#ProtocolParameter/PATO:0015009",
"parameterName": {
"@id": "PATO:0015009",
"annotationValue": "humidity",
"termSource": "PATO",
"termAccession": "PATO:0015009"
}
},
"value": {
"@id": "#UserTerm_85%",
"annotationValue": "85%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C722",
"parameterName": {
"@id": "NCIT:C722",
"annotationValue": "Oxygen",
"termSource": "NCIT",
"termAccession": "NCIT:C722"
}
},
"value": {
"@id": "#UserTerm_20,95%",
"annotationValue": "20,95%"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C65288",
"parameterName": {
"@id": "NCIT:C65288",
"annotationValue": "Carbon Dioxide",
"termSource": "NCIT",
"termAccession": "NCIT:C65288"
}
},
"value": {
"@id": "#UserTerm_0%",
"annotationValue": "0%"
}
},
{
"category": {
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"parameterName": {
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"annotationValue": "pH",
"termSource": "UO",
"termAccession": "UO:0000196"
}
},
"value": {
"@id": "#UserTerm_not_applicable",
"annotationValue": "not applicable"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
"value": {
"@id": "#UserTerm_1200_rpm",
"annotationValue": "1200 rpm"
}
},
{
"category": {
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"parameterName": {
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}
},
"value": {
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}
},
{
"category": {
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}
},
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}
}
],
"inputs": [
{
"@id": "#Sample_DdtxR-wzy-iron-3",
"name": "DdtxR-wzy-iron-3",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=C. glutamicum DdtxR + pJC1-Pwzy-venus",
"category": {
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"characteristicType": {
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"termSource": "MIAPPE",
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}
},
"value": {
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}
}
]
}
],
"outputs": [
{
"@id": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
"name": "assays/3_ReporterAssays/dataset/NCgl2776_gyrB_wzy/20240214_BiolectorAK115_Raw.csv",
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}
]
}
]
}
]
}
]
}