input/phenodata_CPB_DNAseq.txt Version 1
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_04_DE_divers-R/
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input/phenodata_CPB_DNAseq.txt
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Sample_ID Sample_Name Treatment Species Tissue Time_of_preparation Total_DNA_Amount_(ng) Qubit_Conc._(ng/?L) Volume_(?L) RI0000 zymo_std NA CPB gut 15.12.2017 2387 68.2 35 RI0325 H2O_1 water CPB gut 15.12.2017 295 8.42 35 RI0326 H2O_2 water CPB gut 15.12.2017 246 7.04 35 RI0327 H2O_3 water CPB gut 15.12.2017 136 3.88 35 RI0328 vATP_1 dsvATPaseE CPB gut 15.12.2017 749 21.4 35 RI0329 vATP_2 dsvATPaseE CPB gut 15.12.2017 1134 32.4 35 RI0330 vATP_3 dsvATPaseE CPB gut 15.12.2017 371 10.6 35 RI0331 egfp_1 dsEGFP CPB gut 15.12.2017 77 2.2 35 RI0332 egfp_2 dsEGFP CPB gut 15.12.2017 413 11.8 35 RI0333 egfp_3 dsEGFP CPB gut 15.12.2017 473 13.5 35
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Created: 12th Nov 2021 at 22:53
Last updated: 12th Nov 2021 at 22:53
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Version 1 (earliest) Created 12th Nov 2021 at 22:53 by Marko Petek
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https://orcid.org/0000-0003-3644-7827PhD in Biotechnology, Research Associate at Department of Biotechnology and Systems Biology, National Institute of Biology
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
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
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
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
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
