_S_P4_SxP10-newG-DE

Actions

Order Assays

Overview
Related items

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

SEEK ID: https://fairdomhub.org/studies/952

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: 1240

Created: 9th Apr 2022 at 18:40

Last updated: 21st Sep 2022 at 10:44

Related items

People (1)
Programmes (1)
Projects (1)
Investigations (1)
Assays (9)
Data files (50)
Documents (41)

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-newG-DE-files

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

All creators

Marko Petek

Files connected to study: _S_P4_SxP10-newG-DE

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-newG-DE

Organisms: No organisms

SOPs: No SOPs

Data files: _STUDY_METADATA.TXT

Snapshots: No snapshots

Created: 9th Apr 2022 at 18:40, Last updated: 21st Sep 2022 at 10:45

_A_01_toNewGenome-CLC-mapping

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

All creators

Marko Petek

Short Name: toNewGenome-CLC-mapping Assay Class: DRY Assay Type: CLC-mapping Title: Mapping of SxP RNA-seq to the new Nb genome Description: Data; SxPv1.0 RNA-Seq, genome: NbV1 pISA Assay creation date: 2020-01-31 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-newG-DE

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT, output/Expression_browser_10_12_2019.txt

Snapshots: No snapshots

Created: 9th Apr 2022 at 18:49, Last updated: 21st Sep 2022 at 10:45

_A_02_limmavoomDE-R

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

All creators

Marko Petek

Short Name: limmavoomDE-R Assay Class: DRY Assay Type: R Title: Differential expression analysis of SxP mapping to the new genome Description: Data: total counts from mapping of SxPv1.0 erads to the NbV1 genome. Contrasting high-low, high-wt, low-wt pISA Assay creation date: 2020-01-31 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-newG-DE

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT, input/ExpBrows_limmavoom.txt, input/ExpBrows_limmavoom.xlsx, output/Results_logFC_padj.xlsx, output/results_logFC_padj_with_norm_counts1.txt

Snapshots: No snapshots

Created: 9th Apr 2022 at 18:50, Last updated: 21st Sep 2022 at 10:45

_A_02a_limmavoomDEbylines-R

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

All creators

Marko Petek

Short Name: 02a_limmavoomDEbylines-R Assay Class: DRY Assay Type: R Title: DE of SxP RNA-seq data by lines Description: Data: total counts from mapping of SxPv1.0 reads to NbV1 genome; contrasting lines (low1-wt, low2-wt, high1-wt, high2-wt). pISA Assay creation date: 2020-02-12 pISA Assay creator: Mojca JuterĹˇek Analyst: Mojca JuterĹˇek 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

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT, input/ExpBrows_limmavoom.txt, output/DEbyBINs.xlsx, output/DEbylines.xlsx

Snapshots: No snapshots

Created: 9th Apr 2022 at 18:50, Last updated: 21st Sep 2022 at 10:45

_A_03_NewGenome-MapMan

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

All creators

Marko Petek

Short Name: 03_NewGenome-MapMan Assay Class: DRY Assay Type: MapMan Title: MapMan visualisation of mapping SxP data to the new Nb genome Description: Data: logFC values of DE genes in SxPv1.0, MapMan3 mapping of NbV1 genome pISA Assay creation date: 2020-01-31 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-newG-DE

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT, input/MapMan4_annotation.xlsx, input/MapMan4_mapping.txt, input/alldata_for_MapMan_filtered0.05.txt, input/byLinesForMapMan.txt, input/l1-wt_forMapMan.xlsx, input/l2-wt_for_MapMan_filtered0.05.txt, input/nbe_AUS-AUGUSTUS_genes_2019-12-02_mapping...

Snapshots: No snapshots

Created: 9th Apr 2022 at 18:50, Last updated: 21st Sep 2022 at 10:45

_A_04_GSEA-Stat

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

All creators

Marko Petek

Short Name: 04_GSEA-Stat Assay Class: DRY Assay Type: Stat Title: GSEA analysis of SxP data Description: Gene sets: MapMan3 BINs from mapping of NbV1 genome, Data: TMM-normalized total counts of mapping SxPv1.0 data to NbV1 genome. pISA Assay creation date: 2020-01-31 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-newG-DE

Organisms: No organisms

SOPs: No SOPs

Snapshots: No snapshots

Created: 9th Apr 2022 at 18:50, Last updated: 21st Sep 2022 at 10:45

_A_05_Phenotype_analysis-Stat

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

All creators

Marko Petek

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 JuterĹˇek Analyst: Mojca JuterĹˇek 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

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT, input/Samples_phenodata.txt, input/TEMP.txt, input/byTransgenes.txt

Snapshots: No snapshots

Created: 9th Apr 2022 at 18:50, Last updated: 21st Sep 2022 at 10:45

_A_06_SxPv1-0_Illumina-Centrifuge

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

All creators

Marko Petek

Short Name: 06_SxPv1-0_Illumina-Centrifuge Assay Class: DRY Assay Type: Centrifuge Title: centrifuge analysis of reads from SxPv1.0 samples Description: Centrifuge analysis of fastq files from SxPv1.0 samples to determine potential contaminations with pathogenic fungi, bacteria, that could potentially be behind the stress response observed in difeferntial expression analysis. pISA Assay creation date: 2021-10-21 pISA Assay creator: Mojca JuterĹˇek Phenodata: ../../phenodata_20191104.txt Featuredata: ...

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP10-newG-DE

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, scripts/Centrifuge_script.txt

Snapshots: No snapshots

Created: 9th Apr 2022 at 18:50, Last updated: 21st Sep 2022 at 10:45

_A_07_NbAUSv1-0-InterPro

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

All creators

Marko Petek

Short Name: 07_NbAUSv1-0-InterPro Assay Class: DRY Assay Type: InterPro Title: InterProScan annotation of the new Nb genome - NbAUSv1.0 Description: * pISA Assay creation date: 2021-10-21 pISA Assay creator: * 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_SxP10-newG-DE

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, output/ProteinFastaNoDots.fa.tsv, scripts/IPRScript.txt, scripts/gffreadScript.txt

Snapshots: No snapshots

Created: 9th Apr 2022 at 18:51, 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