[Data set] Co-action of COP1, SPA and cryptochrome in light signal transduction and photomorphogenesis of the moss Physcomitrium patens

Registered ARC content:

• root
  • isa.investigation.xlsx
  • workflows
    • SNP_pipe.sh
    • DEG_pipeline.R
    • 3D_PCA_plot.R
  • runs
    • RNA-Seq_analysis
      • Expression_profile_KOs.xlsx
      • DEGs
        • mapping_stats.xlsx
        • 31315.p.sort.rpkm
        • 31315.p.sort.wo_zero.counts
        • 31315.p.sort.counts
        • 31315.p.sort.wo_zero.rpkm
        • sample_annotation.xlsx
        • gene_expression
          • PCA_variance_RPKM_normalized.png
          • PCA_3D_legend.gif
          • HC_RPKM_normalized.png
          • PCA_2D_RPKM_normalized.png
          • 3D_PCA - movie032.png - movie019.png - movie035.png - movie050.png - movie043.png - movie027.png - movie033.png - movie031.png - movie042.png - movie039.png - movie028.png - movie023.png - movie021.png - movie016.png - movie009.png - movie011.png - movie012.png - movie018.png - movie046.png - movie007.png - movie001.png - movie041.png - movie003.png - movie004.png - movie008.png - movie030.png - movie020.png - movie010.png - movie002.png - movie049.png - movie029.png - movie026.png - movie005.png - movie022.png - movie024.png - movie017.png - movie037.png - movie013.png - movie006.png - movie034.png - movie040.png - movie014.png - movie045.png - movie047.png - movie000.png - movie038.png - movie048.png - movie044.png - movie025.png - movie036.png - movie015.png
        • DEGs_0.9
          • cop_L_spa_D - cop_L_vs.spa_D_intersection_three_methods_8261.tsv.filter-1_1.tsv - cop_L_vs.spa_D_intersection_four_methods_8228.tsv - cop_L_vs._spa_D_intersection_four_methods_8228.tsv.filter-1_1.tsv - DEGpipe_cop_L vs. spa_D.log - cop_L_vs._spa_D_intersection_three_methods_8261.tsv - NOISeq - cop_L vs. spa_D_8342_NOISeq_rpkm_prob.tsv - cop_L vs. spa_D_10536_NOISeqbio_tmm_prob_seed_12345.tsv - cop_L vs. spa_D_4625_NOISeq_nnorm_prob.tsv - cop_L vs. spa_D_10472_NOISeqbio_rpkm_prob_seed_12345.tsv - cop_L vs. spa_D_8389_NOISeq_tmm_prob.tsv - plots - cop_L vs. spa_D NOISeq - DE.nnorn_0.9 - cop_L vs. spa_D NOISeqbio - DE.rpkm_0.995 - cop_L vs. spa_D NOISeq - DE.rpkm_0.9_MD - cop_L vs. spa_D NOISeqbio - DE.nnorm_0.9 - cop_L vs. spa_D NOISeq - DE.tmm_0.9 - cop_L vs. spa_D NOISeqbio - DE.rpkm_0.9 - cop_L vs. spa_D NOISeq - DE.rpkm_0.9 - cop_L vs. spa_D NOISeq - noiseqbionnorm - cop_L vs. spa_D NOISeq - DE.nnorn_0.8 - cop_L vs. spa_D NOISeq - noiseqbiorpkm - cop_L vs. spa_D NOISeq - DE.rpkm_0.8 - cop_L vs. spa_D NOISeq - noiseqbiontmm - cop_L vs. spa_D NOISeq - DE.nnorm_0.9_MD - cop_L vs. spa_D NOISeqbio - DE.nnorm_0.995 - cop_L vs. spa_D NOISeq - DE.tmm_0.8 - edgeR - cop_L vs. spa_D_13966_edgeR_fdr.tsv - plots - cop_L vs. spa_D edgeR - plotBCV - cop_L vs. spa_D edgeR - plotMDS - cop_L vs. spa_D edgeR - plotBCV - GLM - cop_L vs. spa_D edgeR - plotSmear - DESeq2 - cop_L vs. spa_D_12189_DESeq2_fdr.tsv - plots - cop_L vs. spa_D DESeq2 - PCA - cop_L vs. spa_D DESeq2 - SdPlot.1 - cop_L vs. spa_D DESeq2 - SdPlot.3 - cop_L vs. spa_D DESeq2 - DispEsts - cop_L vs. spa_D DESeq2 - SdPlot.2
          • spa_D_WT_D - spa_D_vs.WT_D_intersection_four_methods_534.tsv.filter-1_1.tsv - spa_D_vs.WT_D_intersection_four_methods_534.tsv - DEGpipe_spa_D vs. WT_D.log - spa_D_vs._WT_D_intersection_three_methods_1129.tsv.filter-1_1.tsv - spa_D_vs._WT_D_intersection_three_methods_1129.tsv - NOISeq - spa_D vs. WT_D_761_NOISeqbio_rpkm_prob_seed_12345.tsv - spa_D vs. WT_D_775_NOISeqbio_tmm_prob_seed_12345.tsv - spa_D vs. WT_D_1214_NOISeq_tmm_prob.tsv - spa_D vs. WT_D_1218_NOISeq_rpkm_prob.tsv - spa_D vs. WT_D_245_NOISeq_nnorm_prob.tsv - plots - spa_D vs. WT_D NOISeq - DE.rpkm_0.8 - spa_D vs. WT_D NOISeq - DE.tmm_0.9 - spa_D vs. WT_D NOISeq - DE.rpkm_0.9 - spa_D vs. WT_D NOISeq - DE.rpkm_0.9_MD - spa_D vs. WT_D NOISeq - DE.nnorn_0.8 - spa_D vs. WT_D NOISeq - DE.tmm_0.8 - spa_D vs. WT_D NOISeq - DE.nnorn_0.9 - spa_D vs. WT_D NOISeq - DE.nnorm_0.9_MD - spa_D vs. WT_D NOISeqbio - DE.nnorm_0.9 - spa_D vs. WT_D NOISeq - noiseqbiontmm - spa_D vs. WT_D NOISeqbio - DE.nnorm_0.995 - spa_D vs. WT_D NOISeqbio - DE.rpkm_0.9 - spa_D vs. WT_D NOISeq - noiseqbionnorm - spa_D vs. WT_D NOISeq - noiseqbiorpkm - spa_D vs. WT_D NOISeqbio - DE.rpkm_0.995 - edgeR - spa_D vs. WT_D_3488_edgeR_fdr.tsv - plots - spa_D vs. WT_D edgeR - plotMDS - spa_D vs. WT_D edgeR - plotBCV - spa_D vs. WT_D edgeR - plotBCV - GLM - spa_D vs. WT_D edgeR - plotSmear - DESeq2 - spa_D vs. WT_D_2568_DESeq2_fdr.tsv - plots - spa_D vs. WT_D DESeq2 - SdPlot.2 - spa_D vs. WT_D DESeq2 - SdPlot.1 - spa_D vs. WT_D DESeq2 - SdPlot.3 - spa_D vs. WT_D DESeq2 - PCA - spa_D vs. WT_D DESeq2 - DispEsts
          • cop_D_cop_L - cop_D_vs.cop_L_intersection_three_methods_8578.tsv.filter-1_1.tsv - cop_D_vs.cop_L_intersection_four_methods_8440.tsv - cop_D_vs._cop_L_intersection_three_methods_8578.tsv - DEGpipe_cop_D vs. cop_L.log - cop_D_vs._cop_L_intersection_four_methods_8440.tsv.filter-1_1.tsv - NOISeq - cop_D vs. cop_L_8216_NOISeq_nnorm_prob.tsv - cop_D vs. cop_L_8602_NOISeq_tmm_prob.tsv - cop_D vs. cop_L_10103_NOISeqbio_tmm_prob_seed_12345.tsv - cop_D vs. cop_L_8635_NOISeq_rpkm_prob.tsv - cop_D vs. cop_L_10391_NOISeqbio_rpkm_prob_seed_12345.tsv - plots - cop_D vs. cop_L NOISeqbio - DE.nnorm_0.995 - cop_D vs. cop_L NOISeq - DE.rpkm_0.9_MD - cop_D vs. cop_L NOISeqbio - DE.rpkm_0.995 - cop_D vs. cop_L NOISeq - DE.nnorm_0.9_MD - cop_D vs. cop_L NOISeq - noiseqbiorpkm - cop_D vs. cop_L NOISeq - DE.rpkm_0.9 - cop_D vs. cop_L NOISeqbio - DE.rpkm_0.9 - cop_D vs. cop_L NOISeq - noiseqbiontmm - cop_D vs. cop_L NOISeq - DE.rpkm_0.8 - cop_D vs. cop_L NOISeq - DE.tmm_0.8 - cop_D vs. cop_L NOISeqbio - DE.nnorm_0.9 - cop_D vs. cop_L NOISeq - noiseqbionnorm - cop_D vs. cop_L NOISeq - DE.nnorn_0.8 - cop_D vs. cop_L NOISeq - DE.tmm_0.9 - cop_D vs. cop_L NOISeq - DE.nnorn_0.9 - edgeR - cop_D vs. cop_L_14109_edgeR_fdr.tsv - plots - cop_D vs. cop_L edgeR - plotSmear - cop_D vs. cop_L edgeR - plotBCV - cop_D vs. cop_L edgeR - plotBCV - GLM - cop_D vs. cop_L edgeR - plotMDS - DESeq2 - cop_D vs. cop_L_12443_DESeq2_fdr.tsv - plots - cop_D vs. cop_L DESeq2 - SdPlot.3 - cop_D vs. cop_L DESeq2 - PCA - cop_D vs. cop_L DESeq2 - DispEsts - cop_D vs. cop_L DESeq2 - SdPlot.1 - cop_D vs. cop_L DESeq2 - SdPlot.2
          • cop_D_spa_L - cop_D_vs.spa_L_intersection_three_methods_5666.tsv - cop_D_vs._spa_L_intersection_four_methods_5186.tsv - DEGpipe_cop_D vs. spa_L.log - cop_D_vs._spa_L_intersection_four_methods_5186.tsv.filter-1_1.tsv - cop_D_vs.spa_L_intersection_three_methods_5666.tsv.filter-1_1.tsv - NOISeq - cop_D vs. spa_L_5643_NOISeq_tmm_prob.tsv - cop_D vs. spa_L_5739_NOISeq_rpkm_prob.tsv - cop_D vs. spa_L_5630_NOISeq_nnorm_prob.tsv - cop_D vs. spa_L_6659_NOISeqbio_rpkm_prob_seed_12345.tsv - cop_D vs. spa_L_5912_NOISeqbio_tmm_prob_seed_12345.tsv - plots - cop_D vs. spa_L NOISeq - DE.tmm_0.9 - cop_D vs. spa_L NOISeqbio - DE.rpkm_0.9 - cop_D vs. spa_L NOISeq - DE.rpkm_0.9_MD - cop_D vs. spa_L NOISeqbio - DE.nnorm_0.9 - cop_D vs. spa_L NOISeq - noiseqbiorpkm - cop_D vs. spa_L NOISeq - DE.rpkm_0.8 - cop_D vs. spa_L NOISeq - DE.rpkm_0.9 - cop_D vs. spa_L NOISeq - noiseqbionnorm - cop_D vs. spa_L NOISeq - DE.tmm_0.8 - cop_D vs. spa_L NOISeq - DE.nnorm_0.9_MD - cop_D vs. spa_L NOISeq - DE.nnorn_0.8 - cop_D vs. spa_L NOISeqbio - DE.nnorm_0.995 - cop_D vs. spa_L NOISeq - noiseqbiontmm - cop_D vs. spa_L NOISeq - DE.nnorn_0.9 - cop_D vs. spa_L NOISeqbio - DE.rpkm_0.995 - edgeR - cop_D vs. spa_L_11120_edgeR_fdr.tsv - plots - cop_D vs. spa_L edgeR - plotBCV - cop_D vs. spa_L edgeR - plotMDS - cop_D vs. spa_L edgeR - plotBCV - GLM - cop_D vs. spa_L edgeR - plotSmear - DESeq2 - cop_D vs. spa_L_10520_DESeq2_fdr.tsv - plots - cop_D vs. spa_L DESeq2 - PCA - cop_D vs. spa_L DESeq2 - SdPlot.3 - cop_D vs. spa_L DESeq2 - SdPlot.2 - cop_D vs. spa_L DESeq2 - DispEsts - cop_D vs. spa_L DESeq2 - SdPlot.1
          • cop_L_spa_L - cop_L_vs.spa_L_intersection_four_methods_15.tsv.filter-1_1.tsv - cop_L_vs.spa_L_intersection_four_methods_15.tsv - cop_L_vs._spa_L_intersection_three_methods_95.tsv - cop_L_vs._spa_L_intersection_three_methods_95.tsv.filter-1_1.tsv - DEGpipe_cop_L vs. spa_L.log - NOISeq - cop_L vs. spa_L_216_NOISeq_nnorm_prob.tsv - cop_L vs. spa_L_42_NOISeqbio_tmm_prob_seed_12345.tsv - cop_L vs. spa_L_167_NOISeq_tmm_prob.tsv - cop_L vs. spa_L_32_NOISeqbio_rpkm_prob_seed_12345.tsv - cop_L vs. spa_L_171_NOISeq_rpkm_prob.tsv - plots - cop_L vs. spa_L NOISeq - DE.nnorn_0.8 - cop_L vs. spa_L NOISeq - DE.rpkm_0.9_MD - cop_L vs. spa_L NOISeqbio - DE.rpkm_0.9 - cop_L vs. spa_L NOISeq - DE.tmm_0.9 - cop_L vs. spa_L NOISeq - noiseqbionnorm - cop_L vs. spa_L NOISeq - DE.nnorn_0.9 - cop_L vs. spa_L NOISeqbio - DE.rpkm_0.995 - cop_L vs. spa_L NOISeq - DE.rpkm_0.8 - cop_L vs. spa_L NOISeq - DE.tmm_0.8 - cop_L vs. spa_L NOISeq - DE.nnorm_0.9_MD - cop_L vs. spa_L NOISeq - noiseqbiontmm - cop_L vs. spa_L NOISeq - DE.rpkm_0.9 - cop_L vs. spa_L NOISeqbio - DE.nnorm_0.995 - cop_L vs. spa_L NOISeqbio - DE.nnorm_0.9 - cop_L vs. spa_L NOISeq - noiseqbiorpkm - edgeR - cop_L vs. spa_L_287_edgeR_fdr.tsv - plots - cop_L vs. spa_L edgeR - plotBCV - GLM - cop_L vs. spa_L edgeR - plotMDS - cop_L vs. spa_L edgeR - plotBCV - cop_L vs. spa_L edgeR - plotSmear - DESeq2 - cop_L vs. spa_L_276_DESeq2_fdr.tsv - plots - cop_L vs. spa_L DESeq2 - PCA - cop_L vs. spa_L DESeq2 - SdPlot.3 - cop_L vs. spa_L DESeq2 - SdPlot.2 - cop_L vs. spa_L DESeq2 - DispEsts - cop_L vs. spa_L DESeq2 - SdPlot.1
          • spa_L_WT_L - spa_L_vs.WT_L_intersection_three_methods_360.tsv.filter-1_1.tsv - spa_L_vs.WT_L_intersection_three_methods_360.tsv - spa_L_vs._WT_L_intersection_four_methods_92.tsv.filter-1_1.tsv - spa_L_vs._WT_L_intersection_four_methods_92.tsv - DEGpipe_spa_L vs. WT_L.log - NOISeq - spa_L vs. WT_L_513_NOISeq_rpkm_prob.tsv - spa_L vs. WT_L_130_NOISeqbio_tmm_prob_seed_12345.tsv - spa_L vs. WT_L_259_NOISeq_nnorm_prob.tsv - spa_L vs. WT_L_533_NOISeq_tmm_prob.tsv - spa_L vs. WT_L_150_NOISeqbio_rpkm_prob_seed_12345.tsv - plots - spa_L vs. WT_L NOISeq - DE.rpkm_0.8 - spa_L vs. WT_L NOISeqbio - DE.nnorm_0.995 - spa_L vs. WT_L NOISeq - DE.rpkm_0.9_MD - spa_L vs. WT_L NOISeq - DE.tmm_0.8 - spa_L vs. WT_L NOISeq - DE.nnorn_0.8 - spa_L vs. WT_L NOISeq - DE.rpkm_0.9 - spa_L vs. WT_L NOISeq - DE.tmm_0.9 - spa_L vs. WT_L NOISeq - noiseqbiorpkm - spa_L vs. WT_L NOISeqbio - DE.nnorm_0.9 - spa_L vs. WT_L NOISeq - DE.nnorm_0.9_MD - spa_L vs. WT_L NOISeq - noiseqbionnorm - spa_L vs. WT_L NOISeq - DE.nnorn_0.9 - spa_L vs. WT_L NOISeqbio - DE.rpkm_0.995 - spa_L vs. WT_L NOISeq - noiseqbiontmm - spa_L vs. WT_L NOISeqbio - DE.rpkm_0.9 - edgeR - spa_L vs. WT_L_988_edgeR_fdr.tsv - plots - spa_L vs. WT_L edgeR - plotBCV - GLM - spa_L vs. WT_L edgeR - plotMDS - spa_L vs. WT_L edgeR - plotSmear - spa_L vs. WT_L edgeR - plotBCV - DESeq2 - spa_L vs. WT_L_1041_DESeq2_fdr.tsv - plots - spa_L vs. WT_L DESeq2 - SdPlot.3 - spa_L vs. WT_L DESeq2 - PCA - spa_L vs. WT_L DESeq2 - DispEsts - spa_L vs. WT_L DESeq2 - SdPlot.1 - spa_L vs. WT_L DESeq2 - SdPlot.2
          • cop_L_WT_L - cop_L_vs.WT_L_intersection_four_methods_1193.tsv.filter-1_1.tsv - DEGpipe_cop_L vs. WT_L.log - cop_L_vs.WT_L_intersection_three_methods_1748.tsv - cop_L_vs._WT_L_intersection_three_methods_1748.tsv.filter-1_1.tsv - cop_L_vs._WT_L_intersection_four_methods_1193.tsv - NOISeq - cop_L vs. WT_L_1704_NOISeqbio_rpkm_prob_seed_12345.tsv - cop_L vs. WT_L_1849_NOISeq_tmm_prob.tsv - cop_L vs. WT_L_1431_NOISeqbio_tmm_prob_seed_12345.tsv - cop_L vs. WT_L_634_NOISeq_nnorm_prob.tsv - cop_L vs. WT_L_1810_NOISeq_rpkm_prob.tsv - plots - cop_L vs. WT_L NOISeq - DE.tmm_0.8 - cop_L vs. WT_L NOISeq - DE.nnorm_0.9_MD - cop_L vs. WT_L NOISeq - DE.rpkm_0.9 - cop_L vs. WT_L NOISeq - DE.rpkm_0.8 - cop_L vs. WT_L NOISeq - noiseqbiontmm - cop_L vs. WT_L NOISeqbio - DE.rpkm_0.995 - cop_L vs. WT_L NOISeqbio - DE.nnorm_0.9 - cop_L vs. WT_L NOISeq - DE.nnorn_0.8 - cop_L vs. WT_L NOISeqbio - DE.nnorm_0.995 - cop_L vs. WT_L NOISeq - noiseqbiorpkm - cop_L vs. WT_L NOISeq - DE.nnorn_0.9 - cop_L vs. WT_L NOISeq - DE.rpkm_0.9_MD - cop_L vs. WT_L NOISeq - DE.tmm_0.9 - cop_L vs. WT_L NOISeqbio - DE.rpkm_0.9 - cop_L vs. WT_L NOISeq - noiseqbionnorm - edgeR - cop_L vs. WT_L_5829_edgeR_fdr.tsv - plots - cop_L vs. WT_L edgeR - plotBCV - cop_L vs. WT_L edgeR - plotMDS - cop_L vs. WT_L edgeR - plotSmear - cop_L vs. WT_L edgeR - plotBCV - GLM - DESeq2 - cop_L vs. WT_L_4265_DESeq2_fdr.tsv - plots - cop_L vs. WT_L DESeq2 - SdPlot.3 - cop_L vs. WT_L DESeq2 - SdPlot.2 - cop_L vs. WT_L DESeq2 - SdPlot.1 - cop_L vs. WT_L DESeq2 - PCA - cop_L vs. WT_L DESeq2 - DispEsts
          • cop_L_WT_D - cop_L_vs.WT_D_intersection_three_methods_9360.tsv - cop_L_vs._WT_D_intersection_four_methods_9089.tsv - cop_L_vs._WT_D_intersection_four_methods_9089.tsv.filter-1_1.tsv - cop_L_vs.WT_D_intersection_three_methods_9360.tsv.filter-1_1.tsv - DEGpipe_cop_L vs. WT_D.log - NOISeq - cop_L vs. WT_D_7200_NOISeq_nnorm_prob.tsv - cop_L vs. WT_D_10749_NOISeqbio_rpkm_prob_seed_12345.tsv - cop_L vs. WT_D_9361_NOISeq_tmm_prob.tsv - cop_L vs. WT_D_9419_NOISeq_rpkm_prob.tsv - cop_L vs. WT_D_10789_NOISeqbio_tmm_prob_seed_12345.tsv - plots - cop_L vs. WT_D NOISeq - DE.rpkm_0.9 - cop_L vs. WT_D NOISeq - DE.rpkm_0.8 - cop_L vs. WT_D NOISeq - noiseqbionnorm - cop_L vs. WT_D NOISeq - DE.rpkm_0.9_MD - cop_L vs. WT_D NOISeqbio - DE.nnorm_0.995 - cop_L vs. WT_D NOISeq - DE.nnorn_0.9 - cop_L vs. WT_D NOISeq - DE.tmm_0.9 - cop_L vs. WT_D NOISeq - noiseqbiorpkm - cop_L vs. WT_D NOISeqbio - DE.rpkm_0.9 - cop_L vs. WT_D NOISeqbio - DE.rpkm_0.995 - cop_L vs. WT_D NOISeq - noiseqbiontmm - cop_L vs. WT_D NOISeqbio - DE.nnorm_0.9 - cop_L vs. WT_D NOISeq - DE.nnorm_0.9_MD - cop_L vs. WT_D NOISeq - DE.tmm_0.8 - cop_L vs. WT_D NOISeq - DE.nnorn_0.8 - edgeR - cop_L vs. WT_D_14938_edgeR_fdr.tsv - plots - cop_L vs. WT_D edgeR - plotBCV - GLM - cop_L vs. WT_D edgeR - plotMDS - cop_L vs. WT_D edgeR - plotBCV - cop_L vs. WT_D edgeR - plotSmear - DESeq2 - cop_L vs. WT_D_13221_DESeq2_fdr.tsv - plots - cop_L vs. WT_D DESeq2 - SdPlot.3 - cop_L vs. WT_D DESeq2 - SdPlot.2 - cop_L vs. WT_D DESeq2 - SdPlot.1 - cop_L vs. WT_D DESeq2 - DispEsts - cop_L vs. WT_D DESeq2 - PCA
          • spa_D_spa_L - spa_D_vs.spa_L_intersection_three_methods_5429.tsv - spa_D_vs._spa_L_intersection_four_methods_5162.tsv.filter-1_1.tsv - spa_D_vs.spa_L_intersection_three_methods_5429.tsv.filter-1_1.tsv - spa_D_vs._spa_L_intersection_four_methods_5162.tsv - DEGpipe_spa_D vs. spa_L.log - NOISeq - spa_D vs. spa_L_5975_NOISeqbio_tmm_prob_seed_12345.tsv - spa_D vs. spa_L_3651_NOISeq_nnorm_prob.tsv - spa_D vs. spa_L_6749_NOISeqbio_rpkm_prob_seed_12345.tsv - spa_D vs. spa_L_5519_NOISeq_rpkm_prob.tsv - spa_D vs. spa_L_5501_NOISeq_tmm_prob.tsv - plots - spa_D vs. spa_L NOISeq - DE.nnorm_0.9_MD - spa_D vs. spa_L NOISeq - DE.rpkm_0.9 - spa_D vs. spa_L NOISeq - noiseqbiontmm - spa_D vs. spa_L NOISeq - DE.nnorn_0.9 - spa_D vs. spa_L NOISeq - noiseqbiorpkm - spa_D vs. spa_L NOISeq - DE.rpkm_0.9_MD - spa_D vs. spa_L NOISeqbio - DE.nnorm_0.9 - spa_D vs. spa_L NOISeq - DE.nnorn_0.8 - spa_D vs. spa_L NOISeq - noiseqbionnorm - spa_D vs. spa_L NOISeq - DE.tmm_0.8 - spa_D vs. spa_L NOISeqbio - DE.rpkm_0.995 - spa_D vs. spa_L NOISeq - DE.rpkm_0.8 - spa_D vs. spa_L NOISeqbio - DE.nnorm_0.995 - spa_D vs. spa_L NOISeqbio - DE.rpkm_0.9 - spa_D vs. spa_L NOISeq - DE.tmm_0.9 - edgeR - spa_D vs. spa_L_10894_edgeR_fdr.tsv - plots - spa_D vs. spa_L edgeR - plotMDS - spa_D vs. spa_L edgeR - plotSmear - spa_D vs. spa_L edgeR - plotBCV - GLM - spa_D vs. spa_L edgeR - plotBCV - DESeq2 - spa_D vs. spa_L_10293_DESeq2_fdr.tsv - plots - spa_D vs. spa_L DESeq2 - DispEsts - spa_D vs. spa_L DESeq2 - SdPlot.3 - spa_D vs. spa_L DESeq2 - SdPlot.2 - spa_D vs. spa_L DESeq2 - PCA - spa_D vs. spa_L DESeq2 - SdPlot.1
          • cop_D_WT_D - DEGpipe_cop_D vs. WT_D.log - cop_D_vs.WT_D_intersection_three_methods_1418.tsv.filter-1_1.tsv - cop_D_vs.WT_D_intersection_four_methods_933.tsv - cop_D_vs._WT_D_intersection_four_methods_933.tsv.filter-1_1.tsv - cop_D_vs._WT_D_intersection_three_methods_1418.tsv - NOISeq - cop_D vs. WT_D_1505_NOISeq_tmm_prob.tsv - cop_D vs. WT_D_1466_NOISeqbio_rpkm_prob_seed_12345.tsv - cop_D vs. WT_D_1497_NOISeq_rpkm_prob.tsv - cop_D vs. WT_D_1494_NOISeqbio_tmm_prob_seed_12345.tsv - cop_D vs. WT_D_895_NOISeq_nnorm_prob.tsv - plots - cop_D vs. WT_D NOISeqbio - DE.nnorm_0.9 - cop_D vs. WT_D NOISeqbio - DE.rpkm_0.9 - cop_D vs. WT_D NOISeq - noiseqbiontmm - cop_D vs. WT_D NOISeq - DE.nnorn_0.8 - cop_D vs. WT_D NOISeq - DE.tmm_0.8 - cop_D vs. WT_D NOISeq - DE.rpkm_0.8 - cop_D vs. WT_D NOISeq - noiseqbiorpkm - cop_D vs. WT_D NOISeq - DE.rpkm_0.9 - cop_D vs. WT_D NOISeq - DE.rpkm_0.9_MD - cop_D vs. WT_D NOISeq - noiseqbionnorm - cop_D vs. WT_D NOISeq - DE.nnorn_0.9 - cop_D vs. WT_D NOISeqbio - DE.rpkm_0.995 - cop_D vs. WT_D NOISeq - DE.tmm_0.9 - cop_D vs. WT_D NOISeq - DE.nnorm_0.9_MD - cop_D vs. WT_D NOISeqbio - DE.nnorm_0.995 - edgeR - cop_D vs. WT_D_4524_edgeR_fdr.tsv - plots - cop_D vs. WT_D edgeR - plotMDS - cop_D vs. WT_D edgeR - plotBCV - GLM - cop_D vs. WT_D edgeR - plotBCV - cop_D vs. WT_D edgeR - plotSmear - DESeq2 - cop_D vs. WT_D_3324_DESeq2_fdr.tsv - plots - cop_D vs. WT_D DESeq2 - SdPlot.3 - cop_D vs. WT_D DESeq2 - SdPlot.1 - cop_D vs. WT_D DESeq2 - SdPlot.2 - cop_D vs. WT_D DESeq2 - PCA - cop_D vs. WT_D DESeq2 - DispEsts
          • spa_L_WT_D - DEGpipe_spa_L vs. WT_D.log - spa_L_vs.WT_D_intersection_four_methods_5944.tsv.filter-1_1.tsv - spa_L_vs.WT_D_intersection_three_methods_6384.tsv.filter-1_1.tsv - spa_L_vs._WT_D_intersection_four_methods_5944.tsv - spa_L_vs._WT_D_intersection_three_methods_6384.tsv - NOISeq - spa_L vs. WT_D_7564_NOISeqbio_rpkm_prob_seed_12345.tsv - spa_L vs. WT_D_6403_NOISeq_tmm_prob.tsv - spa_L vs. WT_D_5146_NOISeq_nnorm_prob.tsv - spa_L vs. WT_D_6445_NOISeq_rpkm_prob.tsv - spa_L vs. WT_D_7759_NOISeqbio_tmm_prob_seed_12345.tsv - plots - spa_L vs. WT_D NOISeqbio - DE.rpkm_0.995 - spa_L vs. WT_D NOISeq - DE.tmm_0.9 - spa_L vs. WT_D NOISeq - noiseqbiorpkm - spa_L vs. WT_D NOISeq - DE.rpkm_0.9_MD - spa_L vs. WT_D NOISeq - DE.nnorn_0.9 - spa_L vs. WT_D NOISeqbio - DE.nnorm_0.9 - spa_L vs. WT_D NOISeq - noiseqbionnorm - spa_L vs. WT_D NOISeq - DE.nnorn_0.8 - spa_L vs. WT_D NOISeq - noiseqbiontmm - spa_L vs. WT_D NOISeq - DE.nnorm_0.9_MD - spa_L vs. WT_D NOISeq - DE.tmm_0.8 - spa_L vs. WT_D NOISeqbio - DE.nnorm_0.995 - spa_L vs. WT_D NOISeq - DE.rpkm_0.8 - spa_L vs. WT_D NOISeq - DE.rpkm_0.9 - spa_L vs. WT_D NOISeqbio - DE.rpkm_0.9 - edgeR - spa_L vs. WT_D_12077_edgeR_fdr.tsv - plots - spa_L vs. WT_D edgeR - plotSmear - spa_L vs. WT_D edgeR - plotBCV - spa_L vs. WT_D edgeR - plotBCV - GLM - spa_L vs. WT_D edgeR - plotMDS - DESeq2 - spa_L vs. WT_D_11520_DESeq2_fdr.tsv - plots - spa_L vs. WT_D DESeq2 - SdPlot.3 - spa_L vs. WT_D DESeq2 - PCA - spa_L vs. WT_D DESeq2 - SdPlot.1 - spa_L vs. WT_D DESeq2 - SdPlot.2 - spa_L vs. WT_D DESeq2 - DispEsts
          • spa_D_WT_L - spa_D_vs.WT_L_intersection_three_methods_6610.tsv - DEGpipe_spa_D vs. WT_L.log - spa_D_vs._WT_L_intersection_three_methods_6610.tsv.filter-1_1.tsv - spa_D_vs.WT_L_intersection_four_methods_6407.tsv - spa_D_vs._WT_L_intersection_four_methods_6407.tsv.filter-1_1.tsv - NOISeq - spa_D vs. WT_L_6665_NOISeq_rpkm_prob.tsv - spa_D vs. WT_L_8111_NOISeqbio_rpkm_prob_seed_12345.tsv - spa_D vs. WT_L_7650_NOISeqbio_tmm_prob_seed_12345.tsv - spa_D vs. WT_L_2775_NOISeq_nnorm_prob.tsv - spa_D vs. WT_L_6698_NOISeq_tmm_prob.tsv - plots - spa_D vs. WT_L NOISeqbio - DE.rpkm_0.995 - spa_D vs. WT_L NOISeq - DE.nnorm_0.9_MD - spa_D vs. WT_L NOISeq - DE.rpkm_0.9 - spa_D vs. WT_L NOISeq - DE.tmm_0.9 - spa_D vs. WT_L NOISeq - noiseqbiorpkm - spa_D vs. WT_L NOISeqbio - DE.nnorm_0.995 - spa_D vs. WT_L NOISeq - noiseqbionnorm - spa_D vs. WT_L NOISeqbio - DE.nnorm_0.9 - spa_D vs. WT_L NOISeq - DE.rpkm_0.8 - spa_D vs. WT_L NOISeq - noiseqbiontmm - spa_D vs. WT_L NOISeq - DE.tmm_0.8 - spa_D vs. WT_L NOISeq - DE.nnorn_0.8 - spa_D vs. WT_L NOISeq - DE.rpkm_0.9_MD - spa_D vs. WT_L NOISeq - DE.nnorn_0.9 - spa_D vs. WT_L NOISeqbio - DE.rpkm_0.9 - edgeR - spa_D vs. WT_L_12398_edgeR_fdr.tsv - plots - spa_D vs. WT_L edgeR - plotSmear - spa_D vs. WT_L edgeR - plotBCV - GLM - spa_D vs. WT_L edgeR - plotMDS - spa_D vs. WT_L edgeR - plotBCV - DESeq2 - spa_D vs. WT_L_10676_DESeq2_fdr.tsv - plots - spa_D vs. WT_L DESeq2 - SdPlot.3 - spa_D vs. WT_L DESeq2 - SdPlot.2 - spa_D vs. WT_L DESeq2 - PCA - spa_D vs. WT_L DESeq2 - SdPlot.1 - spa_D vs. WT_L DESeq2 - DispEsts
          • cop_D_WT_L - cop_D_vs.WT_L_intersection_four_methods_6271.tsv - cop_D_vs._WT_L_intersection_four_methods_6271.tsv.filter-1_1.tsv - cop_D_vs.WT_L_intersection_three_methods_6925.tsv.filter-1_1.tsv - cop_D_vs._WT_L_intersection_three_methods_6925.tsv - DEGpipe_cop_D vs. WT_L.log - NOISeq - cop_D vs. WT_L_6972_NOISeq_tmm_prob.tsv - cop_D vs. WT_L_7723_NOISeqbio_rpkm_prob_seed_12345.tsv - cop_D vs. WT_L_7716_NOISeqbio_tmm_prob_seed_12345.tsv - cop_D vs. WT_L_4314_NOISeq_nnorm_prob.tsv - cop_D vs. WT_L_6976_NOISeq_rpkm_prob.tsv - plots - cop_D vs. WT_L NOISeq - DE.tmm_0.8 - cop_D vs. WT_L NOISeq - noiseqbiontmm - cop_D vs. WT_L NOISeq - noiseqbiorpkm - cop_D vs. WT_L NOISeq - DE.tmm_0.9 - cop_D vs. WT_L NOISeq - DE.nnorn_0.9 - cop_D vs. WT_L NOISeq - DE.rpkm_0.8 - cop_D vs. WT_L NOISeq - DE.nnorn_0.8 - cop_D vs. WT_L NOISeqbio - DE.rpkm_0.9 - cop_D vs. WT_L NOISeq - DE.rpkm_0.9_MD - cop_D vs. WT_L NOISeq - DE.nnorm_0.9_MD - cop_D vs. WT_L NOISeqbio - DE.rpkm_0.995 - cop_D vs. WT_L NOISeqbio - DE.nnorm_0.9 - cop_D vs. WT_L NOISeqbio - DE.nnorm_0.995 - cop_D vs. WT_L NOISeq - DE.rpkm_0.9 - cop_D vs. WT_L NOISeq - noiseqbionnorm - edgeR - cop_D vs. WT_L_12738_edgeR_fdr.tsv - plots - cop_D vs. WT_L edgeR - plotMDS - cop_D vs. WT_L edgeR - plotSmear - cop_D vs. WT_L edgeR - plotBCV - GLM - cop_D vs. WT_L edgeR - plotBCV - DESeq2 - cop_D vs. WT_L_11155_DESeq2_fdr.tsv - plots - cop_D vs. WT_L DESeq2 - PCA - cop_D vs. WT_L DESeq2 - DispEsts - cop_D vs. WT_L DESeq2 - SdPlot.2 - cop_D vs. WT_L DESeq2 - SdPlot.1 - cop_D vs. WT_L DESeq2 - SdPlot.3
          • cop_D_spa_D - DEGpipe_cop_D vs. spa_D.log - cop_D_vs.spa_D_intersection_three_methods_203.tsv - cop_D_vs._spa_D_intersection_four_methods_40.tsv - cop_D_vs._spa_D_intersection_four_methods_40.tsv.filter-1_1.tsv - cop_D_vs.spa_D_intersection_three_methods_203.tsv.filter-1_1.tsv - NOISeq - cop_D vs. spa_D_62_NOISeqbio_tmm_prob_seed_12345.tsv - cop_D vs. spa_D_60_NOISeqbio_rpkm_prob_seed_12345.tsv - cop_D vs. spa_D_277_NOISeq_tmm_prob.tsv - cop_D vs. spa_D_29_NOISeq_nnorm_prob.tsv - cop_D vs. spa_D_270_NOISeq_rpkm_prob.tsv - plots - cop_D vs. spa_D NOISeq - noiseqbiorpkm - cop_D vs. spa_D NOISeq - DE.tmm_0.8 - cop_D vs. spa_D NOISeq - DE.tmm_0.9 - cop_D vs. spa_D NOISeqbio - DE.nnorm_0.995 - cop_D vs. spa_D NOISeq - DE.rpkm_0.9 - cop_D vs. spa_D NOISeqbio - DE.rpkm_0.995 - cop_D vs. spa_D NOISeq - DE.nnorm_0.9_MD - cop_D vs. spa_D NOISeq - DE.nnorn_0.8 - cop_D vs. spa_D NOISeq - DE.rpkm_0.9_MD - cop_D vs. spa_D NOISeqbio - DE.rpkm_0.9 - cop_D vs. spa_D NOISeqbio - DE.nnorm_0.9 - cop_D vs. spa_D NOISeq - DE.nnorn_0.9 - cop_D vs. spa_D NOISeq - DE.rpkm_0.8 - cop_D vs. spa_D NOISeq - noiseqbionnorm - cop_D vs. spa_D NOISeq - noiseqbiontmm - edgeR - cop_D vs. spa_D_791_edgeR_fdr.tsv - plots - cop_D vs. spa_D edgeR - plotSmear - cop_D vs. spa_D edgeR - plotBCV - GLM - cop_D vs. spa_D edgeR - plotMDS - cop_D vs. spa_D edgeR - plotBCV - DESeq2 - cop_D vs. spa_D_459_DESeq2_fdr.tsv - plots - cop_D vs. spa_D DESeq2 - SdPlot.3 - cop_D vs. spa_D DESeq2 - PCA - cop_D vs. spa_D DESeq2 - SdPlot.2 - cop_D vs. spa_D DESeq2 - SdPlot.1 - cop_D vs. spa_D DESeq2 - DispEsts
          • WT_D_WT_L - WT_D_vs.WT_L_intersection_four_methods_7377.tsv - WT_D_vs._WT_L_intersection_four_methods_7377.tsv.filter-1_1.tsv - WT_D_vs.WT_L_intersection_three_methods_7726.tsv - DEGpipe_WT_D vs. WT_L.log - WT_D_vs._WT_L_intersection_three_methods_7726.tsv.filter-1_1.tsv - NOISeq - WT_D vs. WT_L_4189_NOISeq_nnorm_prob.tsv - WT_D vs. WT_L_7801_NOISeq_tmm_prob.tsv - WT_D vs. WT_L_8967_NOISeqbio_rpkm_prob_seed_12345.tsv - WT_D vs. WT_L_9187_NOISeqbio_tmm_prob_seed_12345.tsv - WT_D vs. WT_L_7773_NOISeq_rpkm_prob.tsv - plots - WT_D vs. WT_L NOISeq - DE.rpkm_0.8 - WT_D vs. WT_L NOISeq - DE.nnorm_0.9_MD - WT_D vs. WT_L NOISeq - noiseqbiontmm - WT_D vs. WT_L NOISeq - DE.tmm_0.9 - WT_D vs. WT_L NOISeq - DE.rpkm_0.9 - WT_D vs. WT_L NOISeq - noiseqbiorpkm - WT_D vs. WT_L NOISeq - DE.nnorn_0.8 - WT_D vs. WT_L NOISeqbio - DE.nnorm_0.9 - WT_D vs. WT_L NOISeq - DE.tmm_0.8 - WT_D vs. WT_L NOISeqbio - DE.rpkm_0.9 - WT_D vs. WT_L NOISeq - DE.rpkm_0.9_MD - WT_D vs. WT_L NOISeqbio - DE.rpkm_0.995 - WT_D vs. WT_L NOISeq - DE.nnorn_0.9 - WT_D vs. WT_L NOISeq - noiseqbionnorm - WT_D vs. WT_L NOISeqbio - DE.nnorm_0.995 - edgeR - WT_D vs. WT_L_13555_edgeR_fdr.tsv - plots - WT_D vs. WT_L edgeR - plotSmear - WT_D vs. WT_L edgeR - plotBCV - WT_D vs. WT_L edgeR - plotMDS - WT_D vs. WT_L edgeR - plotBCV - GLM - DESeq2 - WT_D vs. WT_L_11922_DESeq2_fdr.tsv - plots - WT_D vs. WT_L DESeq2 - SdPlot.3 - WT_D vs. WT_L DESeq2 - PCA - WT_D vs. WT_L DESeq2 - SdPlot.2 - WT_D vs. WT_L DESeq2 - DispEsts - WT_D vs. WT_L DESeq2 - SdPlot.1
  • assays
    • Nanodrop
      • isa.assay.xlsx
      • README.md
    • Bioanalyzer
      • isa.assay.xlsx
      • README.md
    • RNASeq
      • isa.assay.xlsx
      • README.md
      • dataset
        • R2
          • R2_1.fq.gz
          • R2_2.fq.gz
        • R11
          • R11_1.fq.gz
          • R11_2.fq.gz
        • R8
          • R8_2.fq.gz
          • R8_1.fq.gz
        • R28
          • R28_2.fq.gz
          • R28_1.fq.gz
        • R1
          • R1_1.fq.gz
          • R1_2.fq.gz
        • R9
          • R9_1.fq.gz
        • R19
          • R19_1.fq.gz
          • R19_2.fq.gz
        • R7
          • R7_1.fq.gz
          • R7_2.fq.gz
        • R27
          • R27_1.fq.gz
          • R27_2.fq.gz
        • R13
          • R13_2.fq.gz
          • R13_1.fq.gz
        • R26
          • R26_1.fq.gz
          • R26_2.fq.gz
        • R20
          • R20_1.fq.gz
          • R20_2.fq.gz
        • R4
          • R4_1.fq.gz
          • R4_2.fq.gz
        • R16
          • R16_1.fq.gz
          • R16_2.fq.gz
        • R14
          • R14_1.fq.gz
          • R14_2.fq.gz
        • R21
          • R21_1.fq.gz
          • R21_2.fq.gz
        • R22
          • R22_2.fq.gz
          • R22_1.fq.gz
        • R24
          • R24_2.fq.gz
          • R24_1.fq.gz
  • studies
    • Ppatens
      • README.md
      • isa.study.xlsx