_S_P1_SxPv10vsSxP12

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Short Name: P1_SxPv10vsSxP12 Title: Comparison between SxPv1.0 and SxPv1.2 Description: Volatilome characterization of SxPv1.0 T3 plants, SxPv1.2 T1 plants and WT plants. Raw Data: pISA Study creation date: 2020-11-01 pISA Study creator: RMF Principal investigator: Diego Orzaez License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

SEEK ID: https://fairdomhub.org/studies/947

Investigation: _I_T21_SXPsysbio

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

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Creators and Submitter

Creator

Marko Petek

Submitter

Marko Petek

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Views: 1280

Created: 9th Apr 2022 at 18:39

Last updated: 21st Sep 2022 at 10:44

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People (1)
Programmes (1)
Projects (1)
Investigations (1)
Assays (4)
Data files (9)
Documents (3)

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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_P1_SxPv10vsSxP12-files

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

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Marko Petek

Files connected to study: _S_P1_SxPv10vsSxP12

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P1_SxPv10vsSxP12

Organisms: No organisms

SOPs: No SOPs

Data files: _STUDY_METADATA.TXT

Snapshots: No snapshots

Created: 9th Apr 2022 at 18:39, Last updated: 21st Sep 2022 at 10:45

_A_LeavesSxPv10vsv12-GCMS

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

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Marko Petek

Short Name: LeavesSxPv10vsv12-GCMS Assay Class: WET Assay Type: GCMS Title: Leaf volatilome of SxPv1.0, SxPv1.2 T1 and WT Description: The purpose of this assay is to define the volatilome of SxPv1.0, v1.2 and WT Nicotiana benthamiana plant leaves, focusing on the differences between them, by GC-MS. pISA Assay creation date: 2020-12-12 pISA Assay creator: RMF Lab manager: DO Sample collection protocol: Leaf samples were collected at 4 weeks after transplant for young stage and at 7 weeks for adult ...

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P1_SxPv10vsSxP12

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, output/SxPcomp_LEAVES_quantifications.xlsx

Snapshots: No snapshots

Created: 9th Apr 2022 at 18:44, Last updated: 21st Sep 2022 at 10:45

_A_RootsSxPv10vsv12-GCMS

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

All creators

Marko Petek

Short Name: RootsSxPv10vsv12-GCMS Assay Class: WET Assay Type: GCMS Title: Roots volatilome of SxPv1.0, SxPv1.2 T1 and WT Description: The purpose of this assay is to define the volatilome of SxPv1.0, v1.2 and WT Nicotiana benthamiana plant roots, focusing on the differences between them, by GC-MS. pISA Assay creation date: 2021-11-25 pISA Assay creator: RMF Lab manager: DO Sample collection protocol: Root samples were collected at 7 weeks, in a early flowering stage of plants. Samples were ...

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P1_SxPv10vsSxP12

Organisms: No organisms

SOPs: No SOPs

Data files: Metadata.txt, _ASSAY_METADATA.TXT, output/SxPcomp_ROOT_quantifications.xlsx

Snapshots: No snapshots

Created: 9th Apr 2022 at 18:44, Last updated: 21st Sep 2022 at 10:45

_A_SxPv10vsv12-phenotyping

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

All creators

Marko Petek

Short Name: SxPv10vsv12-phenotyping Assay Class: WET Assay Type: phenotyping Title: Images of phenotyping SxPv10, SxPv12 and WT for comparative study Description: Pictures taken of third generation of SPv10 plants, first generation of SxPv12 and WT before collecting samples pISA Assay creation date: 2021-11-25 pISA Assay creator: RMF Phenodata: ../../phenodata_20201212.txt Featuredata:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P1_SxPv10vsSxP12

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, output/images information.csv, output/raw/_A_SxPv10vsv12-phenotyping.output.ra...

Snapshots: No snapshots

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

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