input/Samples_phenodata.txt Version 1
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP10-newG-DE/_A_05_Phenotype_analysis-Stat/
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input/Samples_phenodata.txt
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SampleName PlantLine SamplingDay FreshWeight Height NumberOfLeaves al ol yl ProductionPhenotype 5_1_7_1 SP5_1_7 54 1.71 7.5 14 53045 5207373 2430 high_producer 5_1_7_3 SP5_1_7 54 1.83 7.5 13 44925 5559436 4011 high_producer 5_1_7_4 SP5_1_7 54 1.09 6.5 14 51014 7161429 4354 high_producer 5_1_7_7 SP5_1_7 54 0.46 7.5 13 18247 1139086 2204 high_producer 5_2_4_3 SP5_2_4 54 0.52 8 13 58660 4325612 7873 high_producer 5_2_4_4 SP5_2_4 54 1.06 7 12 89824 7804551 11432 high_producer 5_2_4_6 SP5_2_4 54 0.61 7 15 84332 3260543 6402 high_producer 5_2_4_7 SP5_2_4 54 0.42 7 13 55524 3643716 6155 high_producer 5_1_10_1 SP5_1_10 35 2.54 15.5 17 880 371596 2727 low_producer 5_1_10_2 SP5_1_10 35 2.13 17 16 1764 346570 1786 low_producer 5_1_10_3 SP5_1_10 35 1.78 14 16 1309 336052 1835 low_producer 5_1_10_4 SP5_1_10 35 1.83 14.5 15 1256 259820 1431 low_producer 5_2_5_4 SP5_2_5 35 2.16 20 17 4585 492560 3135 low_producer 5_2_5_5 SP5_2_5 35 2 19 17 6332 427628 2059 low_producer 5_2_5_6 SP5_2_5 35 2.02 19 16 2824 370640 2082 low_producer 5_2_5_8 SP5_2_5 35 2.21 20.5 16 5958 644989 2766 low_producer WT_1 WT 35 4.23 19 15 0 0 0 no_producer WT_2 WT 35 4.34 18.5 17 0 0 0 no_producer WT_4 WT 35 3.71 18 15 0 0 0 no_producer WT_5 WT 35 3.34 18.5 17 0 0 0 no_producer
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Created: 9th Apr 2022 at 22:06
Last updated: 21st Sep 2022 at 10:46
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Version 1 (earliest) Created 9th Apr 2022 at 22:06 by Marko Petek
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https://orcid.org/0000-0003-3644-7827PhD in Biotechnology, Research Associate at Department of Biotechnology and Systems Biology, National Institute of Biology
National Institute of Biology, Department of Biotechnology and Systems Biology projects
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, _p_RNAinVAL, tst, tst2, Playground
Web page: http://www.nib.si/eng/index.php/departments/department-of-biotechnology-and-systems-biology
SUSPHIRE aims to provide a sustainable, low-cost biomanufacturing platform for the commercial production of insect pheromones.
Synthetic biology data management spreadsheet: https://fairdomhub.org/data_files/6036
Programme: NIBSys
Public web page: http://susphire.info/susphireproject/
Start date: 1st Apr 2018
End date: 30th Sep 2021
Short Name: T21_SXPsysbio Title: Use a systems biology approach to identify regulatory bottlenecks in SxPv1 Description: Samples from SXPv1.0 plants as well as sister nulls (progeny from the original transgenic event in which the transgene has segregated) and wild type will be grown and leaf samples taken for RNA extraction and profiling of primary metabolites and volatiles (target pheromones as well as potential derivatives) (P1, P5). Phenotypic and GC-MS data will be obtained and analysed from ...
Submitter: Marko Petek
Studies: Investigation files, _S_P1_SPv10T0andT1, _S_P1_SPv10T2andT3, _S_P1_SPv1TransientExp, _S_P1_SxPAltAcTransferases, _S_P1_SxPv10vsSxP12, _S_P1_SxPv12T2, _S_P4_CoExpNetViz, _S_P4_DiNAR, _S_P4_GAtreat, _S_P4_SxP10-newG-DE, _S_P4_SxP10-oldG-DE, _S_P4_SxP1012-finalG, _S_P4_SxP12-newG-DE
Assays: _A_00_SxP_photos-phenotyping, _A_01_RNA1-RNAisol, _A_01_SxP_Data_Only-CoExp, _A_01_SxPv12_fastq-QC, _A_01_mapping-CLC, _A_01_toNewGenome-CLC-mapping, _A_02_FastQC-bioinfo, _A_02_Nb_datasets-CoExp, _A_02_SxPv12_mapping-CLC, _A_02_limmavoomDE-R, _A_02a_limmavoom-multim-R, _A_02a_limmavoomDEbylines-R, _A_02b_limmavoom-uniquem-R, _A_03_MapMan-visualisation, _A_03_NewGenome-MapMan, _A_03_SxPv12_limmavoom_DE-R, _A_03_mapping-CLC, _A_03a_mapping2-STAR, _A_04_GSEA-Stat, _A_04_MapManBINenrich-GSEA, _A_04_Mercator-bioinfo, _A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA, _A_05_DEstat-R, _A_05_Phenotype_analysis-Stat, _A_05_VOCcomp-Bioinfo, _A_05a_DEstat2-R, _A_05b_DElow-wt-R, _A_06_MapMan-bioinfo, _A_06_SxPv1-0_Illumina-Centrifuge, _A_07_NbAUSv1-0-InterPro, _A_07_transgenes-CLC, _A_CKN-DiNAR, _A_CKN_NbL35-DiNAR, _A_LeavesSxPv10vsv12-GCMS, _A_P4_v10v12-phenotyping, _A_PIS-DiNAR, _A_PIS-SxPv12-DiNAR, _A_PIS_NbL35-DiNAR, _A_RootsSxPv10vsv12-GCMS, _A_SP10T0Analysis-GCMS, _A_SP10T1Analysis-GCMS, _A_SPv10EaDActAnalysis-GCMS, _A_SPv10T2Analysis-GCMS, _A_SPv10T3Analysis-GCMS, _A_SPv10_phenotyping-Images, _A_SxPAlternativeAcetyltransferases-GCMS, _A_SxPv10vsv12-phenotyping, _A_SxPv12ScreeningT2-GCMS, _A_TransientSPv11andSPv12-GCMS, _I_T21_SXPsysbio-files, _S_P1_SPv10T0andT1-files, _S_P1_SPv10T2andT3-files, _S_P1_SPv1TransientExp-files, _S_P1_SxPAltAcTransferases-files, _S_P1_SxPv10vsSxP12-files, _S_P1_SxPv12T2-files, _S_P4_CoExpNetViz-files, _S_P4_DiNAR-files, _S_P4_GAtreat-files, _S_P4_SxP10-newG-DE-files, _S_P4_SxP10-oldG-DE-files, _S_P4_SxP1012-finalG-files, _S_P4_SxP12-newG-DE-files
Short Name: P4_SxP10-newG-DE Title: SxPv1.0 RNA-seq analysis using the new Nb genome Description: Analysis of RNA-seq data (Illumina short reads) of two lines of SexyPlants (SxP v1.0) utilising the not yet published now high quality genome of Nicotiana benthamiana from the Newcotiana project. Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_01_toNewGenome-CLC-mapping, _A_02_limmavoomDE-R, _A_02a_limmavoomDEbylines-R, _A_03_NewGenome-MapMan, _A_04_GSEA-Stat, _A_05_Phenotype_analysis-Stat, _A_06_SxPv1-0_Illumina-Centrifuge, _A_07_NbAUSv1-0-InterPro, _S_P4_SxP10-newG-DE-files
Short Name: 05_Phenotype_analysis-Stat Assay Class: DRY Assay Type: Stat Title: Analysis of SxP phenotype Description: Plotting determined parameters: height, pheromone content, transgene expression. pISA Assay creation date: 2020-02-12 pISA Assay creator: Mojca Juteršek Analyst: Mojca Juteršek Phenodata: ../../phenodata_20191104.xlsx Featuredata: Data:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_T21_SXPsysbio
Study: _S_P4_SxP10-newG-DE
