_S_P4_SxP10-oldG-DE

Actions

Order Assays

Overview
Related items

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

SEEK ID: https://fairdomhub.org/studies/953

Investigation: _I_T21_SXPsysbio

Projects: SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Contr...

Study position:

Help

Tree Split Graph

Export PNG

Click below to download a copy of the image

Download

Creators and Submitter

Creator

Marko Petek

Submitter

Marko Petek

Activity

Views: 1822

Created: 9th Apr 2022 at 18:41

Last updated: 21st Sep 2022 at 10:44

Related items

People (1)
Programmes (1)
Projects (1)
Investigations (1)
Assays (12)
Data files (50)
Documents (179)

Advanced People list for this Study with search and filtering

Marko Petek

Projects: pISA-tree, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, _p_RNAinVAL

Institutions: National Institute of Biology

https://orcid.org/0000-0003-3644-7827

Expertise: Molecular Biology, Transcriptomics, Solanum tuberosum, Plant biology, plant pathways, plant metabolism, Systems Biology

Tools: Molecular biology techniques (RNA/DNA/Protein), Microarray analysis, Bioinformatics, R, RNAseq, RNA interference, metabolic network visualization, metagenomics

PhD in Biotechnology, Research Associate at Department of Biotechnology and Systems Biology, National Institute of Biology

Advanced Programmes list for this Study with search and filtering

NIBSys

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

Advanced Projects list for this Study with search and filtering

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

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

Organisms: Planococcus citri, Nicotiana benthamiana, Penicillium chrysogenum

Advanced Investigations list for this Study with search and filtering

_I_T21_SXPsysbio

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

All creators

Marko Petek

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

Snapshots: No snapshots

Created: 9th Apr 2022 at 18:38, Last updated: 21st Sep 2022 at 10:44

Advanced Assays list for this Study with search and filtering

_S_P4_SxP10-oldG-DE-files

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

All creators

Marko Petek

Files connected to study: _S_P4_SxP10-oldG-DE

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-oldG-DE

Organisms: No organisms

SOPs: No SOPs

Data files: _STUDY_METADATA.TXT

Snapshots: No snapshots

Created: 9th Apr 2022 at 18:41, Last updated: 21st Sep 2022 at 10:45

_A_00_SxP_photos-phenotyping

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

All creators

Marko Petek

Short Name: 00_SxP_photos-phenotyping Assay Class: WET Assay Type: phenotyping Description: Photos of SxPv1.0 plants grown in greenhouse in Valencia (IBMCP) for RNA-Seq sampling. pISA Assay creation date: 2018-11-09 pISA Assay creator: Mojca JuterĹˇek Phenodata: ../../phenodata_20181212.xlsx Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-oldG-DE

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT, reports/growth.xls, reports/growthbyline.xls

Snapshots: No snapshots

Created: 9th Apr 2022 at 18:51, Last updated: 21st Sep 2022 at 10:45

_A_01_RNA1-RNAisol

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

All creators

Marko Petek

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

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT

Snapshots: No snapshots

Created: 9th Apr 2022 at 18:51, Last updated: 21st Sep 2022 at 10:45

_A_02_FastQC-bioinfo

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

All creators

Marko Petek

Assay: A02FastQC-bioinfo Short Name: 02FastQC-bioinfo Assay Class: DRY Assay Type: bioinfo Title: QC of raw reads Description: FastQ analysis of raw reads from SxPv1.0 RNA-Seq samples. pISA Assay creation date: 2019-03-20 pISA Assay creator: Mojca Juteršek Phenodata: ../../phenodata20181212.xlsx Featuredata: Data: __

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-oldG-DE

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT

Snapshots: No snapshots

Created: 9th Apr 2022 at 18:51, Last updated: 21st Sep 2022 at 10:45

_A_03_mapping-CLC

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

All creators

Marko Petek

Short Name: 03_mapping-CLC Assay Class: DRY Assay Type: CLC Title: 03_CLCmapping Description: Mapping of SxPv1.0 reads to the Kourelis 2019 Nb genome with CLC Genomics Workbench. pISA Assay creation date: 2019-26-03 pISA Assay creator: Mojca JuterĹˇek Phenodata: ../../phenodata_20181212.xlsx Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-oldG-DE

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT, output/Expression Browser.txt, output/ExpressionBrowser_cleaned.txt

Snapshots: No snapshots

Created: 9th Apr 2022 at 18:51, Last updated: 21st Sep 2022 at 10:45

_A_03a_mapping2-STAR

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

All creators

Marko Petek

Short Name: 03a_mapping2-STAR Assay Class: DRY Assay Type: STAR Title: Mapping of SxP reads with STAR Description: Mapping of SxPv1.0 reads to the Kourelis 2019 Nb genome with STAR. pISA Assay creation date: 2019-04-19 pISA Assay creator: Mojca JuterĹˇek Phenodata: ../../phenodata_20181212.xlsx Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-oldG-DE

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT, output/SexyPlant_counts_STAR_bothStr.txt, output/SexyPlant_counts_STAR_bothStr.xlsx, output/SexyPlant_counts_STAR_bothStr_Fto5.txt, output/SexyPlant_counts_STAR_bothStr_manualLogF..., scripts/STAR_commands.txt

Snapshots: No snapshots

Created: 9th Apr 2022 at 18:51, Last updated: 21st Sep 2022 at 10:45

_A_04_Mercator-bioinfo

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

All creators

Marko Petek

Short Name: 04_Mercator-bioinfo Assay Class: DRY Assay Type: bioinfo Title: Mercator annotation of Nbenthamiana fasta file Description: Mercator3 annotation of Kourelis 2019 Nb genome pISA Assay creation date: 2019-04-09 pISA Assay creator: Mojca JuterĹˇek Phenodata: ../../phenodata_20181212.xlsx Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-oldG-DE

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT, output/mercator.results.txt, output/mercator_mapping.xlsx

Snapshots: No snapshots

Created: 9th Apr 2022 at 18:52, Last updated: 21st Sep 2022 at 10:45

_A_05_DEstat-R

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

All creators

Marko Petek

Assay: A05DEstat-R Short Name: 05DEstat-R Assay Class: DRY Assay Type: R Title: Analysis of DE genes in R limma voom Description: DE analysis of SxPv1.0 count data with total counts determined from mapping with CLC. pISA Assay creation date: 2019-03-27 pISA Assay creator: Mojca Juteršek Analyst: Mojca Juteršek Phenodata: ../../phenodata20181212.xlsx Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-oldG-DE

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT, input/ExpressionBrowser_cleaned.txt, output/CLC_allcomparisons.xlsx, output/CLCresults_logFC_padj_with_norm_counts.txt, output/CLCresults_logFC_padj_with_norm_counts.xlsx, output/low_wt/low-wt.xlsx, output/low_wt/results_logFC_padj_with_norm_coun..., output/rawCLCresults_logFC_padj_with_norm_count...

Snapshots: No snapshots

Created: 9th Apr 2022 at 18:52, Last updated: 21st Sep 2022 at 10:45

_A_05a_DEstat2-R

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

All creators

Marko Petek

Short Name: 05a_DEstat2-R Assay Class: DRY Assay Type: R Title: DE analysis in R with count data from STAR Description: DE analysis of SxPv1.0 count data with total counts determined from mapping with STAR. pISA Assay creation date: 2019-04-19 pISA Assay creator: Mojca JuterĹˇek Analyst: Marko Petek Phenodata: ../../phenodata_20181212.xlsx Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-oldG-DE

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT, input/SexyPlant_counts_STAR_bothStr.txt, input/SexyPlant_counts_STAR_bothStr.xlsx, input/SexyPlant_counts_STAR_bothStr_Fto5.txt, input/SexyPlant_counts_STAR_bothStr_manualLogFC..., output/Copy of results_logFC_padj_with_norm_cou..., output/results_logFC_padj_with_norm_counts.txt, output/results_logFC_padj_with_norm_counts.xlsx, output/results_logFC_padj_with_norm_counts_MJU...., output/results_logFC_padj_with_norm_counts_gibb...

Snapshots: No snapshots

Created: 9th Apr 2022 at 18:52, Last updated: 21st Sep 2022 at 10:45

_A_05b_DElow-wt-R

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

All creators

Marko Petek

Short Name: 05b_DElow-wt-R Assay Class: DRY Assay Type: R Title: DE analysis in R using low-wt contrast Description: DE with total counts from mapping with CLC, contrasting low producers to wt. pISA Assay creation date: 2019-09-18 pISA Assay creator: Mojca JuterĹˇek Analyst: Mojca JuterĹˇek Phenodata: ../../phenodata_20181212.xlsx Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-oldG-DE

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT, output/low-wt.xlsx

Snapshots: No snapshots

Created: 9th Apr 2022 at 18:52, Last updated: 21st Sep 2022 at 10:45

_A_06_MapMan-bioinfo

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

All creators

Marko Petek

Short Name: 06_MapMan-bioinfo Assay Class: DRY Assay Type: bioinfo Title: MapMan visualisation of DE genes in SxP Description: LogFCs from DE analysis of total counts after mapping with CLC and Mercator3 mapping as inputs. pISA Assay creation date: 2019-03-27 pISA Assay creator: Mojca JuterĹˇek Phenodata: ../../phenodata_20181212.xlsx Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-oldG-DE

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT, input/MapMan_SexyPlant_experimental_ds.txt, input/MapMan_SexyPlant_experimental_ds.xlsx, input/MapMan_SexyPlant_experimental_ds_notfilte..., input/MapMan_SexyPlant_experimental_ds_notfilte..., input/mercator.results.txt, output/Wilcoxon_Rank_Sum_MapMan.xls, output/notfiltered/Wilcoxon_Rank_Sum_MapMan.xls

Snapshots: No snapshots

Created: 9th Apr 2022 at 18:52, Last updated: 21st Sep 2022 at 10:45

_A_07_transgenes-CLC

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

All creators

Marko Petek

Short Name: 08_transgenes-CLC Assay Class: DRY Assay Type: CLC Title: Mapping of RNA-seq data from SxP to transgenes Description: Mapping SxPv1.0 RNA-Seq reads to seqeunces of the three transgenes to determine transgene expression. pISA Assay creation date: 2019-07-09 pISA Assay creator: Mojca JuterĹˇek Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-oldG-DE

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT, output/Expression Browser-SxP_transgenes.txt, output/Expression Browser.txt, output/SxP_transgenes.xlsx

Snapshots: No snapshots

Created: 9th Apr 2022 at 18:53, Last updated: 21st Sep 2022 at 10:45

Showing 20 out of a possible 50 Data files Advanced Data files list for this Study with search and filtering