_A_03-Centrifuge

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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/

SEEK ID: https://fairdomhub.org/assays/1600

Class: Experimental assay

Submitter: Marko Petek

Projects: _p_RNAinVAL

Investigation: _I_03_Omics

Study: _S_02_metagenome_resp

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Assay type: Experimental Assay Type

Technology type: Technology Type

Organisms: No organisms

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Creators and Submitter

Creator

Marko Petek

Submitter

Marko Petek

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Views: 648

Created: 12th Nov 2021 at 22:43

Last updated: 12th Nov 2021 at 23:14

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People (1)
Programmes (1)
Projects (1)
Investigations (1)
Studies (1)
Data files (15)
Documents (24)

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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

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Created: 12th Nov 2021 at 22:42

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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

Snapshots: No snapshots

Created: 12th Nov 2021 at 22:42

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output/pavian/RNAinVAL_CPB_gut_content_shotgun_viruses_classification_DNA_seq-180319.csv

_p_RNAinVAL

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Marko Petek

_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_03-Centrifuge/

Creator: Marko Petek

Submitter: Marko Petek

Relationship type: Not specified

Investigations: _I_03_Omics