_Assay_METADATA.TXT
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP10-oldG-DE/_A_01_RNA1-RNAisol/
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_Assay_METADATA.TXT
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Assay: _A_01_RNA1-RNAisol Short Name: RNA1-RNAisol Assay Class: WET Assay Type: RNAisol Title: RNA isolation from sexy plants Description: Isolation of RNA from SxPv1.0 plants. 4 biological replicates per every included line. pISA Assay creation date: 2018-12-13 pISA Assay creator: SpelaB Lab manager: Elena Phenodata: None Featuredata: Creation date: 2018-12-13 RNA ID: $_RNA Homogenisation protocol: fastPrep Date Homogenisation: 2018-12-13 Isolation Protocol: Rneasy_Plant Date Isolation: 2018-12-13 Storage RNA: CU0369 Dnase treatment protocol: * Dnase ID: $_DNase Date DNAse_treatment: 2018-12-13 Storage_DNAse_treated: CU0370 Operator: Elena cDNA ID: $_cDNA DateRT: 2018-12-13 Notes: Data:
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Created: 9th Apr 2022 at 18:51
Last updated: 21st Sep 2022 at 10:46
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Version 2 (latest) Created 9th Apr 2022 at 19:51 by Marko Petek
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Version 1 (earliest) Created 9th Apr 2022 at 18:51 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-oldG-DE Title: SxPv1.0 RNA-seq analysis using old Nb genome Description: Analysis of RNA-seq data (Illumina short reads) of two lines of SexyPlants (SxP v1.0) utilising the published (old) genome of Nicotiana benthamiana. Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: No
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_00_SxP_photos-phenotyping, _A_01_RNA1-RNAisol, _A_02_FastQC-bioinfo, _A_03_mapping-CLC, _A_03a_mapping2-STAR, _A_04_Mercator-bioinfo, _A_05_DEstat-R, _A_05a_DEstat2-R, _A_05b_DElow-wt-R, _A_06_MapMan-bioinfo, _A_07_transgenes-CLC, _S_P4_SxP10-oldG-DE-files
Assay: _A_01_RNA1-RNAisol Short Name: RNA1-RNAisol Assay Class: WET Assay Type: RNAisol Title: RNA isolation from sexy plants Description: Isolation of RNA from SxPv1.0 plants. 4 biological replicates per every included line. pISA Assay creation date: 2018-12-13 pISA Assay creator: SpelaB Lab manager: Elena Phenodata: None Featuredata: Creation date: 2018-12-13 RNA ID: $_RNA Homogenisation protocol: fastPrep Date Homogenisation: 2018-12-13 Isolation Protocol: Rneasy_Plant Date Isolation: 2018-12-13 ...
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_T21_SXPsysbio
Study: _S_P4_SxP10-oldG-DE
