_I_03_Omics

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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

SEEK ID: https://fairdomhub.org/investigations/497

Projects: _p_RNAinVAL

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Creators and Submitter

Creator

Marko Petek

Submitter

Marko Petek

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Views: 708

Created: 12th Nov 2021 at 22:42

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People (1)
Programmes (1)
Projects (1)
Studies (3)
Assays (12)
Data files (105)
Documents (228)

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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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_S_02_metagenome_resp

_p_RNAinVAL

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Marko Petek

Short Name: 02_metagenome_resp Title: CPB gut microbiome response to dsRNA feeding Description: Response of CPB gut microbiome to dsRNA feeding on the level of microbe abundance 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

Submitter: Marko Petek

Investigation: _I_03_Omics

Assays: _A_01-DNAisol, _A_02-DNASeq, _A_03-Centrifuge, _A_04_DE_divers-R, _A_05_extr_reads-rcf, _A_06_extr_bact-assembly, _A_07_allReads_meta-assembly, _S_02_metagenome_resp-files

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Created: 12th Nov 2021 at 22:42

_S_01_ns-dsRNA_trans

_p_RNAinVAL

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Marko Petek

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

Submitter: Marko Petek

Investigation: _I_03_Omics

Assays: _A_01_RNA-Seq_dsEGFP-NGS, _A_02_CLC-RNASeq, _S_01_ns-dsRNA_trans-files

Snapshots: No snapshots

Created: 12th Nov 2021 at 22:42

Investigation files

_p_RNAinVAL

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Marko Petek

Investigation files _I_03_Omics

Submitter: Marko Petek

Investigation: _I_03_Omics

Assays: _I_03_Omics-files

Snapshots: No snapshots

Created: 12th Nov 2021 at 22:42

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_I_03_Omics-files

_p_RNAinVAL

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Marko Petek

Files connected to investigation: _I_03_Omics

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_03_Omics

Study: Investigation files

Organisms: No organisms

SOPs: No SOPs

Data files: _INVESTIGATION_METADATA.TXT, featuredata_02092021.txt, phenodata_20210115.txt

Snapshots: No snapshots

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

_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

_S_02_metagenome_resp-files

_p_RNAinVAL

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Marko Petek

Files connected to study: _S_02_metagenome_resp

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_03_Omics

Study: _S_02_metagenome_resp

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

_A_01-DNAisol

_p_RNAinVAL

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Marko Petek

Short Name: 01-DNAisol Assay Class: WET Assay Type: DNAisol Title: Isolation of gDNA from CPB gut content Description: Isolation of gDNA from CPB gut content pISA Assay creation date: 2021-01-15 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_02_metagenome_resp

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, other/phenodata_CPB_DNAseq.xlsx, other/testing_MoBI DNA isolation kit-bad/MoBIO_..., other/testing_MoBI DNA isolation kit-bad/MoBIO_..., other/testing_ZymoBIOMICS DNA Mini kit/zymoBIOM..., output/Nanodrop_11122017.xlsx, output/QubitData_14-12-2017_18-01-57.csv, output/QubitData_14-12-2017_18-01-57.xlsx, output/raw/Nanodrop_11122017.txt

Snapshots: No snapshots

Created: 12th Nov 2021 at 22:43, Last updated: 12th Nov 2021 at 23:11

_A_02-DNASeq

_p_RNAinVAL

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Marko Petek

Short Name: 02-DNASeq Assay Class: WET Assay Type: DNASeq Title: Shotgun CPB gut microbiome DNA-Seq Description: Sequencing of CPB gut microbiome genomic DNA to determine the offect of dsRNA feeding on the microbial flora pISA Assay creation date: 2021-01-15 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_02_metagenome_resp

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT

Snapshots: No snapshots

Created: 12th Nov 2021 at 22:43, Last updated: 12th Nov 2021 at 23:11

_A_03-Centrifuge

_p_RNAinVAL

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Marko Petek

Short Name: 03-Centrifuge Assay Class: DRY Assay Type: Centrifuge Title: Centrifuge classification of DNA reads Description: Taxonomic classification of shotgun gDNA Illumina reads from CPB gut microbiome and visualization using pavian pISA Assay creation date: 2021-01-15 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata: Data: http://stork/dirindex/fitostorage/fitostorageA/datarepo/ngs_omics/NGS_lde_dna-seq_2018_mpe_CPB-gut-metagenome/data/

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_03_Omics

Study: _S_02_metagenome_resp

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, output/DNA_seq_combined_mpa.txt, output/DNA_seq_combined_mpa_OTU.txt, output/DNA_seq_combined_mpa_TAX.txt, output/README.txt, output/centrifuge_sample_reports.txt.zip, output/pavian/RNAinVAL_CPB_gut_content_shotgun_..., output/pavian/RNAinVAL_CPB_gut_content_shotgun_..., output/pavian/RNAinVAL_CPB_gut_content_shotgun_..., output/pavian/RNAinVAL_CPB_gut_content_shotgun_..., output/pavian/RNAinVAL_CPB_gut_content_shotgun_..., output/pavian/RNAinVAL_CPB_gut_content_shotgun_..., reports/centrifuge_kreport_ANALYSIS_all_to_H2O...., reports/pavian_table_summary_for_article.xlsx, scripts/Centrifuge_ibis2_commands.txt

Snapshots: No snapshots

Created: 12th Nov 2021 at 22:43, Last updated: 12th Nov 2021 at 23:14

_A_04_DE_divers-R

_p_RNAinVAL

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Marko Petek

Short Name: 04_DE_divers-R Assay Class: DRY Assay Type: R Title: Diversity analysis and differential abundance Description: Metagenomic diversity analyisis using kraken data in R and differential abundance using phyloseq and DESeq R packages. pISA Assay creation date: 2021-01-15 pISA Assay creator: Marko Petek Analyst: 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_02_metagenome_resp

Organisms: No organisms

SOPs: No SOPs

Snapshots: No snapshots

Created: 12th Nov 2021 at 22:43, Last updated: 12th Nov 2021 at 23:00

_A_05_extr_reads-rcf

_p_RNAinVAL

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Marko Petek

Short Name: 05_extr_reads-rcf Assay Class: DRY Assay Type: rcf Title: Extract reads for specific taxa using recentrifuge (rcf) Description: Extract reads for specific bacterial taxa using recentrifuge for further use in de novo genome assembly pISA Assay creation date: 2021-01-16 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_02_metagenome_resp

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, output/CPB-DNAseq_RI0000asCTRL.rcf.xlsx, output/CPB-DNAseq_RI0000asCTRL_cut75.rcf.xlsx, output/CPB-DNAseq_noCTRL.rcf.xlsx, output/CPB-DNAseq_noCTRL_cut75.rcf.xlsx, output/fq/README.txt, reports/RI000_centrifuge_kreport--ZYMO_metageno..., scripts/Centrifuge_rextract_commands.txt

Snapshots: No snapshots

Created: 12th Nov 2021 at 22:43, Last updated: 12th Nov 2021 at 23:14

_A_06_extr_bact-assembly

_p_RNAinVAL

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Marko Petek

Short Name: 06_extr_bact-assembly Assay Class: DRY Assay Type: assembly Title: De novo genome assembly of bacteria Description: De novo genome assembly of bacteria from rcf-extracted shotgun metagenomics reads pISA Assay creation date: 2021-01-16 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_02_metagenome_resp

Organisms: No organisms

SOPs: No SOPs

Snapshots: No snapshots

Created: 12th Nov 2021 at 22:44, Last updated: 12th Nov 2021 at 23:36

_A_07_allReads_meta-assembly

_p_RNAinVAL

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Marko Petek

Short Name: 07_allReads_meta-assembly Assay Class: DRY Assay Type: assembly Title: De novo assembly of metagenome using metaSPAdes Description: De novo assembly of microbes present in the metagenome using metaSPAdes using all reads without selection but with rigorous filtering and read correction pISA Assay creation date: 2021-01-16 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_02_metagenome_resp

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, input/log.txt, output/params.txt, scripts/metaSpades_command.txt

Snapshots: No snapshots

Created: 12th Nov 2021 at 22:44, Last updated: 12th Nov 2021 at 23:07

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