output/MJU_24112021/perl_commands.txt Version 1
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA/
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Created: 11th Apr 2022 at 14:09
Last updated: 21st Sep 2022 at 10:46
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Version 1 (earliest) Created 11th Apr 2022 at 14:09 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_SxP12-newG-DE Title: Gene expression analysis of Sxp 1.2 Description: exp4 in phenodata 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_SxPv12_fastq-QC, _A_02_SxPv12_mapping-CLC, _A_03_SxPv12_limmavoom_DE-R, _A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA, _S_P4_SxP12-newG-DE-files
Short Name: 04_SxPv12_GeneSetEnrichment-RNAseg-GSEA Assay Class: DRY Assay Type: RNAseq-GSEA Title: GSEA of SxPv1.2 expression data Description: GSEA anaylysis with MapMan3 BINs as gene sets and SxPv1.2 logFC data. pISA Assay creation date: 2021-11-24 pISA Assay creator: Mojca Juteršek Phenodata: ../../phenodata_20191104.txt Featuredata: Data:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_T21_SXPsysbio
Study: _S_P4_SxP12-newG-DE
