_S_01_ns-dsRNA_trans

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Short Name: 01_ns-dsRNA_trans Title: CPB transcriptome response to non-specific dsRNA feeding Description: Global transcriptome response of CPB gut tissue to non-specific dsRNA (dsEGFP) feeding Raw Data: pISA Study creation date: 2021-01-15 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

SEEK ID: https://fairdomhub.org/studies/907

Investigation: _I_03_Omics

Projects: _p_RNAinVAL

Study position:

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Creators and Submitter

Creator

Marko Petek

Submitter

Marko Petek

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Views: 809

Created: 12th Nov 2021 at 22:42

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People (1)
Programmes (1)
Projects (1)
Investigations (1)
Assays (3)
Data files (9)
Documents (20)

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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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_p_RNAinVAL

This project’s main objective was to identify novel Colorado potato beetle gene targets for the development of specific RNAi insecticides and further validate prospective targets using transcriptomics. The work included gene selection, establishment of double-stranded RNA (dsRNA) production methodology and the evaluation of dsRNAs’ insecticidal potential in CPB feeding laboratory and field trials.

Programme: NIBSys

Public web page: http://projects.nib.si/rnainval/

Start date: 1st Nov 2014

End date: 31st Oct 2017

Organisms: Leptinotarsa decemlineata

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_I_03_Omics

_p_RNAinVAL

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Marko Petek

Short Name: 03_Omics Title: Omics analysis of RNAi response in CPB Description: Transcriptomics and metagenome changes upon feeding CPB larvae with dsRNA Phenodata: ./phenodata_20210115.txt pISA Investigation creation date: 2021-01-15 pISA Investigation creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

Submitter: Marko Petek

Studies: Investigation files, _S_01_ns-dsRNA_trans, _S_02_metagenome_resp

Assays: _A_01-DNAisol, _A_01_RNA-Seq_dsEGFP-NGS, _A_02-DNASeq, _A_02_CLC-RNASeq, _A_03-Centrifuge, _A_04_DE_divers-R, _A_05_extr_reads-rcf, _A_06_extr_bact-assembly, _A_07_allReads_meta-assembly, _I_03_Omics-files, _S_01_ns-dsRNA_trans-files, _S_02_metagenome_resp-files

Snapshots: No snapshots

Created: 12th Nov 2021 at 22:42

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_S_01_ns-dsRNA_trans-files

_p_RNAinVAL

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Marko Petek

Files connected to study: _S_01_ns-dsRNA_trans

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_03_Omics

Study: _S_01_ns-dsRNA_trans

Organisms: No organisms

SOPs: No SOPs

Data files: _STUDY_METADATA.TXT

Snapshots: No snapshots

Created: 12th Nov 2021 at 22:42, Last updated: 12th Nov 2021 at 22:42

_A_01_RNA-Seq_dsEGFP-NGS

_p_RNAinVAL

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Marko Petek

Short Name: 01_RNA-Seq_dsEGFP-NGS Assay Class: WET Assay Type: NGS Title: Treatment of dsEGFP and water treated samples before sending for RNA-Seq Description: RNA-Seq DNase and cleanup of dsEGFP and water treated CPB larval samples from the june2017 experiment to determine non-specific response of dsRNA consumption pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_03_Omics

Study: _S_01_ns-dsRNA_trans

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, output/24112017_totRNA_DNase_treated_for_RNAseq...

Snapshots: No snapshots

Created: 12th Nov 2021 at 22:42, Last updated: 12th Nov 2021 at 22:44

_A_02_CLC-RNASeq

_p_RNAinVAL

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Marko Petek

Short Name: 02_CLC-RNASeq Assay Class: DRY Assay Type: RNASeq Title: CLC RNA-Seq data analysis dsEGFP vs water treatment Description: CLC RNA-Seq data analysis dsEGFP vs water treatment pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_03_Omics

Study: _S_01_ns-dsRNA_trans

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, input/Ldec.genome.10062013.xlsx, input/Ldec.genome.10062013__mRNA.xlsx, output/Expression Browser.xlsx, reports/CLC.xlsx, reports/FlyBaseIDs_DE_for_PaintOmics.xlsx

Snapshots: No snapshots

Created: 12th Nov 2021 at 22:43, Last updated: 12th Nov 2021 at 22:46

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