_S_P4_SxP12-newG-DE

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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

SEEK ID: https://fairdomhub.org/studies/955

Investigation: _I_T21_SXPsysbio

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

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Creator

Marko Petek

Submitter

Marko Petek

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Views: 1620

Created: 9th Apr 2022 at 18:41

Last updated: 21st Sep 2022 at 10:44

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People (1)
Programmes (1)
Projects (1)
Investigations (1)
Assays (5)
Data files (23)
Documents (61)

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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

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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

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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

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_I_T21_SXPsysbio

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

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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

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

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_S_P4_SxP12-newG-DE-files

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

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Marko Petek

Files connected to study: _S_P4_SxP12-newG-DE

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_SxP12-newG-DE

Organisms: No organisms

SOPs: No SOPs

Data files: _STUDY_METADATA.TXT, dinar_comparison_line41-wt.txt, dinar_comparison_line43-wt.txt, forMapMan_Padj0.05.txt

Snapshots: No snapshots

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

_A_01_SxPv12_fastq-QC

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

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Marko Petek

Short Name: SxPv1-2_fastq-QC Assay Class: DRY Assay Type: QC Title: Qulaity control of SxPv1-2 raw Illumina reads Description: FastQC of SxPv1.2 Illumina reads pISA Assay creation date: 2021-11-08 pISA Assay creator: Mojca JuterĹˇek 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

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT

Snapshots: No snapshots

Created: 9th Apr 2022 at 20:10, Last updated: 21st Sep 2022 at 10:45

_A_02_SxPv12_mapping-CLC

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

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Marko Petek

Short Name: SxPv12_mapping-CLC Assay Class: DRY Assay Type: CLC Title: CLC mapping of SxPv1.2 reads Description: Mapping SxPv1.2 Illumina reads to NbV1 genome in CLC Genomics Workbench pISA Assay creation date: 2021-11-10 pISA Assay creator: Mojca JuterĹˇek 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

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, output/Reverse_strand_mapping/ReverseStrand_Exp...

Snapshots: No snapshots

Created: 9th Apr 2022 at 20:11, Last updated: 21st Sep 2022 at 10:45

_A_03_SxPv12_limmavoom_DE-R

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

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Marko Petek

Assay: ASxPv12limmavoomDE-R Short Name: SxPv12limmavoomDE-R Assay Class: DRY Assay Type: R Title: Differential expression analysis of SxPv1.2 data in R Description: Difefrential expression analysis with limma-voom sript in R of total counts from mapping of SxPv1.2 reads to the NbV1 genome. pISA Assay creation date: 2021-11-10 pISA Assay creator: Mojca JuterÅ¡ek Analyst: Mojca JuterÅ¡ek Phenodata: ../../phenodata20191104.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

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, input/SXP12_CLC_totalcounts.txt, output/SXP12_logFC-pAdj.txt, output/SxP_v12_logFC.xlsx, output/comparison_v10to12.xlsx, output/v10notv12.txt, output/v12_v_v10_byBINs.xlsx, output/v12notv10.txt

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Created: 9th Apr 2022 at 20:11, Last updated: 21st Sep 2022 at 10:45

_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA

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

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Marko Petek

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 JuterĹˇek 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

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, input/NormCounts.txt, input/NormLogCounts.txt, input/SXP12_CLC_totalcounts.txt, output/GSEA_v12_parsedResults.xlsx, output/MJU_24112021/MJU_24112021_1_Data/4-1_vs_..., output/MJU_24112021/MJU_24112021_1_Data/4-1_vs_..., output/MJU_24112021/perl_commands.txt

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Created: 9th Apr 2022 at 20:11, Last updated: 21st Sep 2022 at 10:45

Showing 20 out of a possible 23 Data files Advanced Data files list for this Study with search and filtering