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"@id": "./",
"filename": "isa.investigation.xlsx",
"identifier": "Muentjes_et_al-2025",
"title": "In vivo online monitoring of intracellular lipid accumulation in Ustilago maydis ",
"description": "Single cell oils produced in microorganisms constitute appealing alternatives to plant oils. Oleaginous fungi accumulate triacylglycerols in lipid droplets (LD). Their biosynthesis is typically induced under nitrogen limitation. We exploit the fungal model Ustilago maydis for oil production. The stain BODIPY can be used to track LD formation during cultivation but this expensive compound is only affordable at small-scale. Therefore, mutant screening for optimization of oil production and composition would benefit from an inexpensive online monitoring system. Accordingly, we aimed at developing an intrinsic reporter that is suitable to track oil formation even in larger cultures. From three tested candidates, the potential delta(24)-sterol C-methyltransferase Erg6 turned out as the best reporter. Fluorescence microscopy confirmed its localization at the LD membrane. After optimization, Erg6 fused to mKate2 expressed from a promoter derived from glycolipid biosynthesis showed a good correlation of fluorescence with oil accumulation. Time course experiments in micro-cultivators demonstrated that the fluorescence read-out can be used to track oil formation starting at the onset of nitrogen limitation to approximate the LD amount. In essence, our study introduces a biosensor for oil monitoring, that can easily be transferred to other oleaginous yeasts. ",
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"firstName": "Michael",
"lastName": "Feldbr\u00fcgge",
"email": "feldbrue@hhu.de",
"affiliation": "Heinrich Heine University D\u00fcsseldorf, Biology",
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"firstName": "Kira",
"lastName": "M\u00fcntjes",
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"affiliation": "Heinrich Heine University D\u00fcsseldorf, Microbiology",
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"firstName": "Marcel",
"lastName": "Mann",
"email": "Marcel.Mann@avt.rwth-aachen.de",
"affiliation": "RWTH Aachen University",
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{
"@id": "0009-0005-1904-7479",
"firstName": "Paul",
"lastName": "Richter",
"email": "Paul.Richter@avt.rwth-aachen.de",
"affiliation": "RWTH Aachen University, ",
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{
"@id": "0000-0001-7217-1691",
"firstName": "Magnus",
"lastName": "Philipp",
"email": "magnus.philipp@ntnu.no",
"affiliation": "Norwegian University of Science and Technology, IBT;Heinrich Heine University D\u00fcsseldorf, Insitute for Microbiology;Heinrich-Heine-Universit\u00e4t D\u00fcsseldorf, Institute for Microbiology",
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"@id": "Lesley.Pluecker@uni-duesseldorf.de",
"firstName": "Lesley",
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"email": "Lesley.Pluecker@uni-duesseldorf.de",
"affiliation": "Heinrich Heine University D\u00fcsseldorf, Microbiology"
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}
]
},
{
"@id": "#Process_Strains",
"name": "Strains",
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},
"inputs": [
{
"@id": "#Sample_pUX0080",
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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": "#MaterialAttribute/#UserTerm_strain_collection_number",
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}
},
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}
},
{
"@id": "#MaterialAttributeValue/Genotype=MB215\u0394cyp1\u0394emt1/Pmtt1Per1-Gfp",
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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_pUX0081",
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{
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}
},
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"annotationValue": "Ux54"
}
},
{
"@id": "#MaterialAttributeValue/Genotype=MB215\u0394cyp1\u0394emt1/Pmtt1Erg6-Gfp",
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}
},
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}
},
{
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"category": {
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}
},
"value": {
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}
}
]
},
{
"@id": "#Sample_UMa2112",
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{
"@id": "#MaterialAttributeValue/strain collection number=UMa2112",
"category": {
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"characteristicType": {
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}
},
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"@id": "#UserTerm_UMa2112",
"annotationValue": "UMa2112"
}
},
{
"@id": "#MaterialAttributeValue/Genotype=MB215\u0394cyp1\u0394emt1\t\t",
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},
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}
},
{
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"category": {
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}
},
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}
}
]
},
{
"@id": "#Sample_UMa2112",
"name": "UMa2112",
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{
"@id": "#MaterialAttributeValue/strain collection number=UMa2112",
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}
},
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}
},
{
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},
{
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},
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"annotationValue": "./studies/S1_Identification of a LD reporter candidate/resources/Strain_sequences_modified_locus"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_Sei1-Gfp",
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},
{
"@id": "#Sample_Sei1-Gfp",
"name": "Sei1-Gfp"
},
{
"@id": "#Sample_Per1-Gfp",
"name": "Per1-Gfp"
},
{
"@id": "#Sample_Per1-Gfp",
"name": "Per1-Gfp"
},
{
"@id": "#Sample_Erg6-Gfp",
"name": "Erg6-Gfp"
},
{
"@id": "#Sample_Erg6-Gfp",
"name": "Erg6-Gfp"
},
{
"@id": "#Sample_WT",
"name": "WT"
}
]
},
{
"@id": "#Process_Cultivation_preculture",
"name": "Cultivation_preculture",
"executesProtocol": {
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"parameters": [
{
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}
},
{
"@id": "#ProtocolParameter/NCIT:C62103",
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}
},
{
"@id": "#ProtocolParameter/DPBO:1000155",
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"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_starting_material",
"parameterName": {
"@id": "#UserTerm_starting_material",
"annotationValue": "starting material"
}
},
{
"@id": "#ProtocolParameter/EFO:0001702",
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"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
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"annotationValue": "experiment time"
}
}
],
"components": [
{
"componentName": "wheel (ENVO:03501261)",
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"annotationValue": "cultivation device"
}
}
]
},
"parameterValues": [
{
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}
},
"value": {
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}
},
{
"category": {
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"termAccession": "NCIT:C62103"
}
},
"value": {
"@id": "#UserTerm_glass_tube",
"annotationValue": "glass tube"
}
},
{
"category": {
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"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": "3-5",
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"annotationValue": "milliliter",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000098"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_starting_material",
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"annotationValue": "starting material"
}
},
"value": {
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"annotationValue": "material from plate"
}
},
{
"category": {
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"parameterName": {
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"termSource": "EFO",
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}
},
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"unit": {
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"annotationValue": "Degree Celsius",
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}
},
{
"category": {
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"annotationValue": "experiment time"
}
},
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"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
],
"inputs": [
{
"@id": "#Sample_Per1-Gfp",
"name": "Per1-Gfp",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Ustilago maydis",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_Ustilago_maydis",
"annotationValue": "Ustilago maydis"
}
}
]
},
{
"@id": "#Sample_Sei1-Gfp",
"name": "Sei1-Gfp",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Ustilago maydis",
"category": {
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"characteristicType": {
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"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
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"annotationValue": "Ustilago maydis"
}
}
]
},
{
"@id": "#Sample_Erg6-Gfp",
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{
"@id": "#MaterialAttributeValue/Organism=Ustilago maydis",
"category": {
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"termSource": "MIAPPE",
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}
},
"value": {
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}
}
]
},
{
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{
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"category": {
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"characteristicType": {
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"termSource": "MIAPPE",
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}
},
"value": {
"@id": "#UserTerm_Ustilago_maydis",
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}
}
]
}
],
"outputs": [
{
"@id": "Per1-Gfp_preculture",
"name": "Per1-Gfp_preculture",
"type": "Raw Data File"
},
{
"@id": "Sai1-Gfp_preculture",
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},
{
"@id": "Erg6-Gfp_preculture",
"name": "Erg6-Gfp_preculture",
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},
{
"@id": "WT_preculture",
"name": "WT_preculture",
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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": "EFO",
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}
},
{
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
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}
},
{
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}
}
],
"components": [
{
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}
}
]
},
"parameterValues": [
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"parameterName": {
"@id": "#UserTerm_device",
"annotationValue": "device"
}
},
"value": {
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"annotationValue": "shake flask",
"termSource": "DPBO",
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}
},
{
"category": {
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"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
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"annotationValue": "Verdyn"
}
},
{
"category": {
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}
},
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}
},
{
"category": {
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},
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"termSource": "DPBO",
"termAccession": "DPBO:1000113"
}
},
"value": {
"@id": "#UserTerm_488",
"annotationValue": "488"
}
}
],
"inputs": [
{
"@id": "#Sample_Erg6-Kat2x_main_culture",
"name": "Erg6-Kat2x_main_culture"
},
{
"@id": "#Sample_Erg6-Kat2x_main_culture",
"name": "Erg6-Kat2x_main_culture"
},
{
"@id": "#Sample_Erg6-Kat2x_main_culture",
"name": "Erg6-Kat2x_main_culture"
},
{
"@id": "#Sample_Erg6-Kat2x_main_culture",
"name": "Erg6-Kat2x_main_culture"
},
{
"@id": "#Sample_Erg6-Kat2x_main_culture",
"name": "Erg6-Kat2x_main_culture"
},
{
"@id": "#Sample_Erg6-Kat2x_main_culture",
"name": "Erg6-Kat2x_main_culture"
},
{
"@id": "#Sample_Erg6-Katmx_main_culture",
"name": "Erg6-Katmx_main_culture"
},
{
"@id": "#Sample_Erg6-Katmx_main_culture",
"name": "Erg6-Katmx_main_culture"
},
{
"@id": "#Sample_Erg6-Katmx_main_culture",
"name": "Erg6-Katmx_main_culture"
},
{
"@id": "#Sample_Erg6-Katmx_main_culture",
"name": "Erg6-Katmx_main_culture"
},
{
"@id": "#Sample_Erg6-Katmx_main_culture",
"name": "Erg6-Katmx_main_culture"
},
{
"@id": "#Sample_Erg6-Katmx_main_culture",
"name": "Erg6-Katmx_main_culture"
},
{
"@id": "#Sample_Erg6-Kat_main_culture",
"name": "Erg6-Kat_main_culture"
},
{
"@id": "#Sample_Erg6-Kat_main_culture",
"name": "Erg6-Kat_main_culture"
},
{
"@id": "#Sample_Erg6-Kat_main_culture",
"name": "Erg6-Kat_main_culture"
},
{
"@id": "#Sample_Erg6-Kat_main_culture",
"name": "Erg6-Kat_main_culture"
},
{
"@id": "#Sample_Erg6-Kat_main_culture",
"name": "Erg6-Kat_main_culture"
},
{
"@id": "#Sample_Erg6-Kat_main_culture",
"name": "Erg6-Kat_main_culture"
},
{
"@id": "#Sample_WT_main_culture",
"name": "WT_main_culture"
},
{
"@id": "#Sample_WT_main_culture",
"name": "WT_main_culture"
},
{
"@id": "#Sample_WT_main_culture",
"name": "WT_main_culture"
},
{
"@id": "#Sample_WT_main_culture",
"name": "WT_main_culture"
},
{
"@id": "#Sample_WT_main_culture",
"name": "WT_main_culture"
},
{
"@id": "#Sample_WT_main_culture",
"name": "WT_main_culture"
}
],
"outputs": [
{
"@id": "./assays/A4_Erg6-Kat_protein_localization/dataset/Rawdata/Data_Erg6-Kat2x_microscopy/Day1_N_limitation_Ux143_2x_Laser488-5.tif",
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"type": "Raw Data File"
},
{
"@id": "#Sample_./assays/A4_Erg6-Kat_protein_localization/dataset/Rawdata/Data_Erg6-Kat2x_microscopy/Day1_N_limitation_Ux143_2x_Laser488-5.tif",
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"factorValues": [
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},
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},
{
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},
{
"@id": "#Sample_./assays/A4_Erg6-Kat_protein_localization/dataset/Rawdata/Data_Erg6-Kat2x_microscopy/Day2_N_limitation_UX143_2x_Laser488-10.tif",
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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": "#Process_Fluorescence_microscopy_2",
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"executesProtocol": {
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"name": "./assays/A4_Erg6-Kat protein localization/protocols/Microscopy/Fluorescence_microscopy.md",
"parameters": [
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}
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}
},
"value": {
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}
],
"inputs": [
{
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"name": "Erg6-Kat2x_main_culture"
},
{
"@id": "#Sample_Erg6-Kat2x_main_culture",
"name": "Erg6-Kat2x_main_culture"
},
{
"@id": "#Sample_Erg6-Kat2x_main_culture",
"name": "Erg6-Kat2x_main_culture"
},
{
"@id": "#Sample_Erg6-Kat2x_main_culture",
"name": "Erg6-Kat2x_main_culture"
},
{
"@id": "#Sample_Erg6-Kat2x_main_culture",
"name": "Erg6-Kat2x_main_culture"
},
{
"@id": "#Sample_Erg6-Kat2x_main_culture",
"name": "Erg6-Kat2x_main_culture"
},
{
"@id": "#Sample_Erg6-Katmx_main_culture",
"name": "Erg6-Katmx_main_culture"
},
{
"@id": "#Sample_Erg6-Katmx_main_culture",
"name": "Erg6-Katmx_main_culture"
},
{
"@id": "#Sample_Erg6-Katmx_main_culture",
"name": "Erg6-Katmx_main_culture"
},
{
"@id": "#Sample_Erg6-Katmx_main_culture",
"name": "Erg6-Katmx_main_culture"
},
{
"@id": "#Sample_Erg6-Katmx_main_culture",
"name": "Erg6-Katmx_main_culture"
},
{
"@id": "#Sample_Erg6-Katmx_main_culture",
"name": "Erg6-Katmx_main_culture"
},
{
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"name": "Erg6-Kat_main_culture"
},
{
"@id": "#Sample_Erg6-Kat_main_culture",
"name": "Erg6-Kat_main_culture"
},
{
"@id": "#Sample_Erg6-Kat_main_culture",
"name": "Erg6-Kat_main_culture"
},
{
"@id": "#Sample_Erg6-Kat_main_culture",
"name": "Erg6-Kat_main_culture"
},
{
"@id": "#Sample_Erg6-Kat_main_culture",
"name": "Erg6-Kat_main_culture"
},
{
"@id": "#Sample_Erg6-Kat_main_culture",
"name": "Erg6-Kat_main_culture"
},
{
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"name": "WT_main_culture"
},
{
"@id": "#Sample_WT_main_culture",
"name": "WT_main_culture"
}
],
"outputs": [
{
"@id": "./assays/A4_Erg6-Kat_protein_localization/dataset/Rawdata/Data_Erg6-Kat2x_microscopy/Day1_N_limitation_Ux143_2x_Laser561-5.tif",
"name": "./assays/A4_Erg6-Kat protein localization/dataset/Rawdata/Data_Erg6-Kat2x_microscopy/Day1_N limitation_Ux143_2x_Laser561-5.tif",
"type": "Raw Data File"
},
{
"@id": "#Sample_./assays/A4_Erg6-Kat_protein_localization/dataset/Rawdata/Data_Erg6-Kat2x_microscopy/Day1_N_limitation_Ux143_2x_Laser561-5.tif",
"name": "./assays/A4_Erg6-Kat protein localization/dataset/Rawdata/Data_Erg6-Kat2x_microscopy/Day1_N limitation_Ux143_2x_Laser561-5.tif",
"factorValues": [
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"category": {
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},
"value": 1,
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]
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"annotationValue": "Pemt1_promoter"
}
},
{
"@id": "#MaterialAttributeValue/reporter=egfp",
"category": {
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"characteristicType": {
"@id": "#UserTerm_reporter",
"annotationValue": "reporter"
}
},
"value": {
"@id": "#UserTerm_egfp",
"annotationValue": "egfp"
}
},
{
"@id": "#MaterialAttributeValue/recombinant plasmid=p123_ Pemt1_erg6-egfp_cbxR ",
"category": {
"@id": "#MaterialAttribute/OBI:0000410",
"characteristicType": {
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"annotationValue": "recombinant plasmid",
"termSource": "OBI",
"termAccession": "OBI:0000410"
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},
"value": {
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"annotationValue": "p123_ Pemt1_erg6-egfp_cbxR "
}
}
]
},
{
"@id": "#Sample_Erg6_gene",
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"category": {
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}
},
"value": {
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"annotationValue": "p123"
}
},
{
"@id": "#MaterialAttributeValue/Promoter=Pemt1_promoter",
"category": {
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"annotationValue": "Promoter",
"termSource": "NCIT",
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}
},
"value": {
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}
},
{
"@id": "#MaterialAttributeValue/reporter=mKate2",
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"characteristicType": {
"@id": "#UserTerm_reporter",
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}
},
"value": {
"@id": "#UserTerm_mKate2",
"annotationValue": "mKate2"
}
},
{
"@id": "#MaterialAttributeValue/recombinant plasmid=p123_ Pemt1_Erg6-mKate2_cbxR",
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},
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"annotationValue": "p123_ Pemt1_Erg6-mKate2_cbxR"
}
}
]
},
{
"@id": "#Sample_pUX0082",
"name": "pUX0082"
},
{
"@id": "#Sample_pUX120",
"name": "pUX120"
},
{
"@id": "#Sample_pUX121",
"name": "pUX121"
},
{
"@id": "#Sample_pUX195",
"name": "pUX195"
},
{
"@id": "#Sample_pUX0082",
"name": "pUX0082",
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"@id": "#MaterialAttributeValue/strain collection number=Ux81",
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}
},
"value": {
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}
},
{
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"characteristicType": {
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}
}
}
]
},
{
"@id": "#Sample_UMa2112",
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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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}
}
]
}
]
},
"processSequence": [
{
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"executesProtocol": {
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"name": "./studies/S1_Identification of a LD reporter candidate/protocols/Plasmid generation .md"
},
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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": "#MaterialAttributeValue/recombinant plasmid=p123_ Pcyp2_erg6-egfp_cbxR ",
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}
},
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}
}
]
},
{
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}
},
"value": {
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}
},
{
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}
},
"value": {
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}
},
{
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}
},
"value": {
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}
},
{
"@id": "#MaterialAttributeValue/recombinant plasmid=p123_ Pemt1_erg6-egfp_cbxR ",
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},
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}
}
]
},
{
"@id": "#Sample_Erg6_gene",
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}
},
"value": {
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}
},
{
"@id": "#MaterialAttributeValue/Promoter=Pemt1_promoter",
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}
},
"value": {
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}
},
{
"@id": "#MaterialAttributeValue/reporter=mKate2",
"category": {
"@id": "#MaterialAttribute/#UserTerm_reporter",
"characteristicType": {
"@id": "#UserTerm_reporter",
"annotationValue": "reporter"
}
},
"value": {
"@id": "#UserTerm_mKate2",
"annotationValue": "mKate2"
}
},
{
"@id": "#MaterialAttributeValue/recombinant plasmid=p123_ Pemt1_Erg6-mKate2_cbxR",
"category": {
"@id": "#MaterialAttribute/OBI:0000410",
"characteristicType": {
"@id": "OBI:0000410",
"annotationValue": "recombinant plasmid",
"termSource": "OBI",
"termAccession": "OBI:0000410"
}
},
"value": {
"@id": "#UserTerm_p123__Pemt1_Erg6-mKate2_cbxR",
"annotationValue": "p123_ Pemt1_Erg6-mKate2_cbxR"
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_pUX0082",
"name": "pUX0082"
},
{
"@id": "#Sample_pUX120",
"name": "pUX120"
},
{
"@id": "#Sample_pUX121",
"name": "pUX121"
},
{
"@id": "#Sample_pUX195",
"name": "pUX195"
}
]
},
{
"@id": "#Process_Strains",
"name": "Strains",
"executesProtocol": {
"@id": "#Protocol_./studies/S1_Identification_of_a_LD_reporter_candidate/protocols/Plasmid_generation_.md",
"name": "./studies/S1_Identification of a LD reporter candidate/protocols/Plasmid generation .md"
},
"inputs": [
{
"@id": "#Sample_pUX0082",
"name": "pUX0082",
"characteristics": [
{
"@id": "#MaterialAttributeValue/strain collection number=Ux81",
"category": {
"@id": "#MaterialAttribute/#UserTerm_strain_collection_number",
"characteristicType": {
"@id": "#UserTerm_strain_collection_number",
"annotationValue": "strain collection number"
}
},
"value": {
"@id": "#UserTerm_Ux81",
"annotationValue": "Ux81"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/#UserTerm_expression_unit_copy_number",
"characteristicType": {
"@id": "#UserTerm_expression_unit_copy_number",
"annotationValue": "expression unit copy number"
}
}
}
]
},
{
"@id": "#Sample_UMa2112",
"name": "UMa2112",
"characteristics": [
{
"@id": "#MaterialAttributeValue/strain collection number=UMa2112",
"category": {
"@id": "#MaterialAttribute/#UserTerm_strain_collection_number",
"characteristicType": {
"@id": "#UserTerm_strain_collection_number",
"annotationValue": "strain collection number"
}
},
"value": {
"@id": "#UserTerm_UMa2112",
"annotationValue": "UMa2112"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/#UserTerm_expression_unit_copy_number",
"characteristicType": {
"@id": "#UserTerm_expression_unit_copy_number",
"annotationValue": "expression unit copy number"
}
}
}
]
},
{
"@id": "#Sample_pUX120",
"name": "pUX120",
"characteristics": [
{
"@id": "#MaterialAttributeValue/strain collection number=Ux82",
"category": {
"@id": "#MaterialAttribute/#UserTerm_strain_collection_number",
"characteristicType": {
"@id": "#UserTerm_strain_collection_number",
"annotationValue": "strain collection number"
}
},
"value": {
"@id": "#UserTerm_Ux82",
"annotationValue": "Ux82"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/#UserTerm_expression_unit_copy_number",
"characteristicType": {
"@id": "#UserTerm_expression_unit_copy_number",
"annotationValue": "expression unit copy number"
}
}
}
]
},
{
"@id": "#Sample_UMa2112",
"name": "UMa2112",
"characteristics": [
{
"@id": "#MaterialAttributeValue/strain collection number=UMa2112",
"category": {
"@id": "#MaterialAttribute/#UserTerm_strain_collection_number",
"characteristicType": {
"@id": "#UserTerm_strain_collection_number",
"annotationValue": "strain collection number"
}
},
"value": {
"@id": "#UserTerm_UMa2112",
"annotationValue": "UMa2112"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/#UserTerm_expression_unit_copy_number",
"characteristicType": {
"@id": "#UserTerm_expression_unit_copy_number",
"annotationValue": "expression unit copy number"
}
}
}
]
},
{
"@id": "#Sample_pUX121",
"name": "pUX121",
"characteristics": [
{
"@id": "#MaterialAttributeValue/strain collection number=Ux83",
"category": {
"@id": "#MaterialAttribute/#UserTerm_strain_collection_number",
"characteristicType": {
"@id": "#UserTerm_strain_collection_number",
"annotationValue": "strain collection number"
}
},
"value": {
"@id": "#UserTerm_Ux83",
"annotationValue": "Ux83"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/#UserTerm_expression_unit_copy_number",
"characteristicType": {
"@id": "#UserTerm_expression_unit_copy_number",
"annotationValue": "expression unit copy number"
}
}
}
]
},
{
"@id": "#Sample_UMa2112",
"name": "UMa2112",
"characteristics": [
{
"@id": "#MaterialAttributeValue/strain collection number=UMa2112",
"category": {
"@id": "#MaterialAttribute/#UserTerm_strain_collection_number",
"characteristicType": {
"@id": "#UserTerm_strain_collection_number",
"annotationValue": "strain collection number"
}
},
"value": {
"@id": "#UserTerm_UMa2112",
"annotationValue": "UMa2112"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/#UserTerm_expression_unit_copy_number",
"characteristicType": {
"@id": "#UserTerm_expression_unit_copy_number",
"annotationValue": "expression unit copy number"
}
}
}
]
},
{
"@id": "#Sample_pUX195",
"name": "pUX195",
"characteristics": [
{
"@id": "#MaterialAttributeValue/strain collection number=Ux143",
"category": {
"@id": "#MaterialAttribute/#UserTerm_strain_collection_number",
"characteristicType": {
"@id": "#UserTerm_strain_collection_number",
"annotationValue": "strain collection number"
}
},
"value": {
"@id": "#UserTerm_Ux143",
"annotationValue": "Ux143"
}
},
{
"@id": "#MaterialAttributeValue/expression unit copy number=1",
"category": {
"@id": "#MaterialAttribute/#UserTerm_expression_unit_copy_number",
"characteristicType": {
"@id": "#UserTerm_expression_unit_copy_number",
"annotationValue": "expression unit copy number"
}
},
"value": {
"@id": "#UserTerm_1",
"annotationValue": "1"
}
}
]
},
{
"@id": "#Sample_UMa2112",
"name": "UMa2112",
"characteristics": [
{
"@id": "#MaterialAttributeValue/strain collection number=UMa2112",
"category": {
"@id": "#MaterialAttribute/#UserTerm_strain_collection_number",
"characteristicType": {
"@id": "#UserTerm_strain_collection_number",
"annotationValue": "strain collection number"
}
},
"value": {
"@id": "#UserTerm_UMa2112",
"annotationValue": "UMa2112"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/#UserTerm_expression_unit_copy_number",
"characteristicType": {
"@id": "#UserTerm_expression_unit_copy_number",
"annotationValue": "expression unit copy number"
}
}
}
]
},
{
"@id": "#Sample_pUX195",
"name": "pUX195",
"characteristics": [
{
"@id": "#MaterialAttributeValue/strain collection number=Ux143",
"category": {
"@id": "#MaterialAttribute/#UserTerm_strain_collection_number",
"characteristicType": {
"@id": "#UserTerm_strain_collection_number",
"annotationValue": "strain collection number"
}
},
"value": {
"@id": "#UserTerm_Ux143",
"annotationValue": "Ux143"
}
},
{
"@id": "#MaterialAttributeValue/expression unit copy number=2",
"category": {
"@id": "#MaterialAttribute/#UserTerm_expression_unit_copy_number",
"characteristicType": {
"@id": "#UserTerm_expression_unit_copy_number",
"annotationValue": "expression unit copy number"
}
},
"value": {
"@id": "#UserTerm_2",
"annotationValue": "2"
}
}
]
},
{
"@id": "#Sample_UMa2112",
"name": "UMa2112",
"characteristics": [
{
"@id": "#MaterialAttributeValue/strain collection number=UMa2112",
"category": {
"@id": "#MaterialAttribute/#UserTerm_strain_collection_number",
"characteristicType": {
"@id": "#UserTerm_strain_collection_number",
"annotationValue": "strain collection number"
}
},
"value": {
"@id": "#UserTerm_UMa2112",
"annotationValue": "UMa2112"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/#UserTerm_expression_unit_copy_number",
"characteristicType": {
"@id": "#UserTerm_expression_unit_copy_number",
"annotationValue": "expression unit copy number"
}
}
}
]
},
{
"@id": "#Sample_pUX195",
"name": "pUX195",
"characteristics": [
{
"@id": "#MaterialAttributeValue/strain collection number=Ux143",
"category": {
"@id": "#MaterialAttribute/#UserTerm_strain_collection_number",
"characteristicType": {
"@id": "#UserTerm_strain_collection_number",
"annotationValue": "strain collection number"
}
},
"value": {
"@id": "#UserTerm_Ux143",
"annotationValue": "Ux143"
}
},
{
"@id": "#MaterialAttributeValue/expression unit copy number=m",
"category": {
"@id": "#MaterialAttribute/#UserTerm_expression_unit_copy_number",
"characteristicType": {
"@id": "#UserTerm_expression_unit_copy_number",
"annotationValue": "expression unit copy number"
}
},
"value": {
"@id": "#UserTerm_m",
"annotationValue": "m"
}
}
]
},
{
"@id": "#Sample_UMa2112",
"name": "UMa2112",
"characteristics": [
{
"@id": "#MaterialAttributeValue/strain collection number=UMa2112",
"category": {
"@id": "#MaterialAttribute/#UserTerm_strain_collection_number",
"characteristicType": {
"@id": "#UserTerm_strain_collection_number",
"annotationValue": "strain collection number"
}
},
"value": {
"@id": "#UserTerm_UMa2112",
"annotationValue": "UMa2112"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/#UserTerm_expression_unit_copy_number",
"characteristicType": {
"@id": "#UserTerm_expression_unit_copy_number",
"annotationValue": "expression unit copy number"
}
}
}
]
},
{
"@id": "#Sample_UMa2112",
"name": "UMa2112",
"characteristics": [
{
"@id": "#MaterialAttributeValue/strain collection number=UMa2112",
"category": {
"@id": "#MaterialAttribute/#UserTerm_strain_collection_number",
"characteristicType": {
"@id": "#UserTerm_strain_collection_number",
"annotationValue": "strain collection number"
}
},
"value": {
"@id": "#UserTerm_UMa2112",
"annotationValue": "UMa2112"
}
},
{
"@id": "#EmptyMaterialAttributeValue",
"category": {
"@id": "#MaterialAttribute/#UserTerm_expression_unit_copy_number",
"characteristicType": {
"@id": "#UserTerm_expression_unit_copy_number",
"annotationValue": "expression unit copy number"
}
}
}
]
}
],
"outputs": [
{
"@id": "#Sample_Pcyp1_Erg6-Gfp",
"name": "Pcyp1_Erg6-Gfp"
},
{
"@id": "#Sample_Pcyp1_Erg6-Gfp",
"name": "Pcyp1_Erg6-Gfp"
},
{
"@id": "#Sample_Pcyp2_Erg6-Gfp",
"name": "Pcyp2_Erg6-Gfp"
},
{
"@id": "#Sample_Pcyp2_Erg6-Gfp",
"name": "Pcyp2_Erg6-Gfp"
},
{
"@id": "#Sample_Pemt1_Erg6-Gfp",
"name": "Pemt1_Erg6-Gfp"
},
{
"@id": "#Sample_Pemt1_Erg6-Gfp",
"name": "Pemt1_Erg6-Gfp"
},
{
"@id": "#Sample_Erg6-Kat",
"name": "Erg6-Kat"
},
{
"@id": "#Sample_Erg6-Kat",
"name": "Erg6-Kat"
},
{
"@id": "#Sample_Erg6-Kat2x",
"name": "Erg6-Kat2x"
},
{
"@id": "#Sample_Erg6-Kat2x",
"name": "Erg6-Kat2x"
},
{
"@id": "#Sample_Erg6-Katmx",
"name": "Erg6-Katmx"
},
{
"@id": "#Sample_Erg6-Katmx",
"name": "Erg6-Katmx"
},
{
"@id": "#Sample_WT",
"name": "WT"
}
]
},
{
"@id": "#Process_Cultivation_preculture",
"name": "Cultivation_preculture",
"executesProtocol": {
"@id": "#Protocol_S2_Erg6_biosensor_optimization_Cultivation_preculture",
"parameters": [
{
"@id": "#ProtocolParameter/#UserTerm_Device",
"parameterName": {
"@id": "#UserTerm_Device",
"annotationValue": "Device"
}
},
{
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
{
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_start_material",
"parameterName": {
"@id": "#UserTerm_start_material",
"annotationValue": "start material"
}
},
{
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
}
],
"components": [
{
"componentName": "wheel (ENVO:03501261)",
"componentType": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Device",
"parameterName": {
"@id": "#UserTerm_Device",
"annotationValue": "Device"
}
},
"value": {
"@id": "#UserTerm_glass_tube",
"annotationValue": "glass tube"
}
},
{
"category": {
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
"value": {
"@id": "#UserTerm_CM-glc",
"annotationValue": "CM-glc"
}
},
{
"category": {
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
"value": "3-5",
"unit": {
"@id": "https://bioregistry.io/UO:0000098",
"annotationValue": "milliliter",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000098"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_start_material",
"parameterName": {
"@id": "#UserTerm_start_material",
"annotationValue": "start material"
}
},
"value": {
"@id": "#UserTerm_cell_material_from_fresh_plate",
"annotationValue": "cell material from fresh plate"
}
},
{
"category": {
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
"value": 28,
"unit": {
"@id": "https://bioregistry.io/NCIT:C42559",
"annotationValue": "Degree Celsius",
"termSource": "NCIT",
"termAccession": "https://bioregistry.io/NCIT:C42559"
}
},
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
},
"value": "12-16",
"unit": {
"@id": "https://bioregistry.io/UO:0000032",
"annotationValue": "hour",
"termSource": "UO",
"termAccession": "https://bioregistry.io/UO:0000032"
}
}
],
"inputs": [
{
"@id": "#Sample_Pcyp1_Erg6-Gfp",
"name": "Pcyp1_Erg6-Gfp",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Ustilago maydis",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_Ustilago_maydis",
"annotationValue": "Ustilago maydis"
}
}
]
},
{
"@id": "#Sample_Pcyp2_Erg6-Gfp",
"name": "Pcyp2_Erg6-Gfp",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Ustilago maydis",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_Ustilago_maydis",
"annotationValue": "Ustilago maydis"
}
}
]
},
{
"@id": "#Sample_Pemt1_Erg6-Gfp",
"name": "Pemt1_Erg6-Gfp",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Ustilago maydis",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_Ustilago_maydis",
"annotationValue": "Ustilago maydis"
}
}
]
},
{
"@id": "#Sample_Erg6-Kat",
"name": "Erg6-Kat",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Ustilago maydis",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_Ustilago_maydis",
"annotationValue": "Ustilago maydis"
}
}
]
},
{
"@id": "#Sample_Erg6-Kat2x",
"name": "Erg6-Kat2x",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Ustilago maydis",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_Ustilago_maydis",
"annotationValue": "Ustilago maydis"
}
}
]
},
{
"@id": "#Sample_Erg6-Katmx",
"name": "Erg6-Katmx",
"characteristics": [
{
"@id": "#MaterialAttributeValue/Organism=Ustilago maydis",
"category": {
"@id": "#MaterialAttribute/MIAPPE:0041",
"characteristicType": {
"@id": "MIAPPE:0041",
"annotationValue": "Organism",
"termSource": "MIAPPE",
"termAccession": "MIAPPE:0041"
}
},
"value": {
"@id": "#UserTerm_Ustilago_maydis",
"annotationValue": "Ustilago maydis"
}
}
]
}
],
"outputs": [
{
"@id": "Pcyp1_Erg6-Gfp_preculture",
"name": "Pcyp1_Erg6-Gfp_preculture",
"type": "Raw Data File"
},
{
"@id": "Pcyp2_Erg6-Gfp_preculture",
"name": "Pcyp2_Erg6-Gfp_preculture",
"type": "Raw Data File"
},
{
"@id": "Pemt_Erg6-Gfp_preculture",
"name": "Pemt_Erg6-Gfp_preculture",
"type": "Raw Data File"
},
{
"@id": "Erg6-Kat_preculture",
"name": "Erg6-Kat_preculture",
"type": "Raw Data File"
},
{
"@id": "Erg6-Kat2x_preculture",
"name": "Erg6-Kat2x_preculture",
"type": "Raw Data File"
},
{
"@id": "Erg6-Katmx_preculture",
"name": "Erg6-Katmx_preculture",
"type": "Raw Data File"
}
]
},
{
"@id": "#Process_Cultivation_main_culture",
"name": "Cultivation_main_culture",
"executesProtocol": {
"@id": "#Protocol_S2_Erg6_biosensor_optimization_Cultivation_main_culture",
"parameters": [
{
"@id": "#ProtocolParameter/#UserTerm_Device",
"parameterName": {
"@id": "#UserTerm_Device",
"annotationValue": "Device"
}
},
{
"@id": "#ProtocolParameter/NCIT:C85504",
"parameterName": {
"@id": "NCIT:C85504",
"annotationValue": "Growth Medium",
"termSource": "NCIT",
"termAccession": "NCIT:C85504"
}
},
{
"@id": "#ProtocolParameter/DPBO:1000155",
"parameterName": {
"@id": "DPBO:1000155",
"annotationValue": "culture medium volume",
"termSource": "DPBO",
"termAccession": "DPBO:1000155"
}
},
{
"@id": "#ProtocolParameter/DPBO:0000101",
"parameterName": {
"@id": "DPBO:0000101",
"annotationValue": "start OD600",
"termSource": "DPBO",
"termAccession": "DPBO:0000101"
}
},
{
"@id": "#ProtocolParameter/EFO:0001702",
"parameterName": {
"@id": "EFO:0001702",
"annotationValue": "temperature",
"termSource": "EFO",
"termAccession": "EFO:0001702"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_shaker_frequency",
"parameterName": {
"@id": "#UserTerm_shaker_frequency",
"annotationValue": "shaker frequency"
}
},
{
"@id": "#ProtocolParameter/#UserTerm_experiment_time",
"parameterName": {
"@id": "#UserTerm_experiment_time",
"annotationValue": "experiment time"
}
}
],
"components": [
{
"componentName": "orbital shaker ()",
"componentType": {
"@id": "#UserTerm_cultivation_device",
"annotationValue": "cultivation device"
}
}
]
},
"parameterValues": [
{
"category": {
"@id": "#ProtocolParameter/#UserTerm_Device",
"parameterName": {
"@id": "#UserTerm_Device",
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"@id": "#Process_Quantification",
"name": "Quantification",
"executesProtocol": {
"@id": "#Protocol_./assays/A5_Quantification_of_LD_numbers_in_Erg6-Kat_overexpression/protocols/Protocol_quantification.md",
"name": "./assays/A5_Quantification of LD numbers in Erg6-Kat overexpression/protocols/Protocol_quantification.md"
},
"inputs": [
{
"@id": "./assays/A5_Quantification_of_LD_numbers_in_Erg6-Kat_overexpression/dataset/Rawdata/Erg6-Kat2x_pictures_quantif/Day3_N_limitation_UX143_2x_BF-DIC-1.tif",
"name": "./assays/A5_Quantification of LD numbers in Erg6-Kat overexpression/dataset/Rawdata/Erg6-Kat2x_pictures_quantif/Day3_N limitation_UX143_2x_BF-DIC-1.tif",
"type": "Raw Data File"
},
{
"@id": "./assays/A5_Quantification_of_LD_numbers_in_Erg6-Kat_overexpression/dataset/Rawdata/Erg6-Katmx_pictures_quantif/Day3_N_limitation_UX143_3x_BF-DIC-4.tif",
"name": "./assays/A5_Quantification of LD numbers in Erg6-Kat overexpression/dataset/Rawdata/Erg6-Katmx_pictures_quantif/Day3_N limitation_UX143_3x_BF-DIC-4.tif",
"type": "Raw Data File"
},
{
"@id": "./assays/A5_Quantification_of_LD_numbers_in_Erg6-Kat_overexpression/dataset/Rawdata/Erg6-Kat_pictures_quantif/Day3_N_limitation_UX143_1x_BF-DIC-3.tif",
"name": "./assays/A5_Quantification of LD numbers in Erg6-Kat overexpression/dataset/Rawdata/Erg6-Kat_pictures_quantif/Day3_N limitation_UX143_1x_BF-DIC-3.tif",
"type": "Raw Data File"
},
{
"@id": "./assays/A5_Quantification_of_LD_numbers_in_Erg6-Kat_overexpression/dataset/Rawdata/WT_picutures_quantif/Day3_N_limitation_UMa2112_BF-DIC-2.tif",
"name": "./assays/A5_Quantification of LD numbers in Erg6-Kat overexpression/dataset/Rawdata/WT_picutures_quantif/Day3_N limitation_UMa2112_BF-DIC-2.tif",
"type": "Raw Data File"
}
],
"outputs": [
{
"@id": "./assays/A5_Quantification_of_LD_numbers_in_Erg6-Kat_overexpression/dataset/Rawdata/LD_quantification_raw.xlsx",
"name": "./assays/A5_Quantification of LD numbers in Erg6-Kat overexpression/dataset/Rawdata/LD_quantification_raw.xlsx",
"type": "Raw Data File"
},
{
"@id": "./assays/A5_Quantification_of_LD_numbers_in_Erg6-Kat_overexpression/dataset/Rawdata/LD_quantification_raw.xlsx",
"name": "./assays/A5_Quantification of LD numbers in Erg6-Kat overexpression/dataset/Rawdata/LD_quantification_raw.xlsx",
"type": "Raw Data File"
},
{
"@id": "./assays/A5_Quantification_of_LD_numbers_in_Erg6-Kat_overexpression/dataset/Rawdata/LD_quantification_raw.xlsx",
"name": "./assays/A5_Quantification of LD numbers in Erg6-Kat overexpression/dataset/Rawdata/LD_quantification_raw.xlsx",
"type": "Raw Data File"
},
{
"@id": "./assays/A5_Quantification_of_LD_numbers_in_Erg6-Kat_overexpression/dataset/Rawdata/LD_quantification_raw.xlsx",
"name": "./assays/A5_Quantification of LD numbers in Erg6-Kat overexpression/dataset/Rawdata/LD_quantification_raw.xlsx",
"type": "Raw Data File"
}
]
}
]
}
]
}
]
}