PhD in Biotechnology, Research Associate at Department of Biotechnology and Systems Biology, National Institute of Biology
SEEK ID: https://fairdomhub.org/people/1071
Location:
Slovenia
ORCID:
https://orcid.org/0000-0003-3644-7827
Joined: 5th Apr 2018




Project roles
Project administrator
- SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture
- _p_stRT
- _p_RNAinVAL
Asset gatekeeper
- SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture
- _p_stRT
- _p_RNAinVAL
Asset housekeeper

_p_RNAinVAL (National Institute of Biology)
pISA-tree (National Institute of Biology) ; SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture (National Institute of Biology) ; _p_stRT (National Institute of Biology) ; ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato (National Institute of Biology)
Related items
- Programmes (1)
- Projects (5)
- Institutions (1)
- Investigations (4+9)
- Studies (21+44)
- Assays (64+178)
- Data files (354+915)
- Publications (1)
- Presentations (1)
- Documents (1492+1108)
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
Web page: http://www.nib.si/eng/index.php/departments/department-of-biotechnology-and-systems-biology
project: _p_stRT Short Name: stRT Title: Solanum tuberosum Reference Transcriptomes Description: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato pISA projects path: ../pISA-Projects Local pISA-tree organisation: National Institute of Biology pISA project creation date: 2019-10-22 pISA project creator: Maja Zagorscak, Ziva Ramsak, Marko Petek Project funding code: This project was supported by the Slovenian Research Agency (grants P4-0165, J4-4165, J4-7636, ...
Programme: NIBSys
Public web page: http://www.nib.si/eng/index.php/systems-biology
Start date: 1st Dec 2017
End date: 1st Jan 2020
Organisms: Solanum tuberosum, Potato virus Y
SUSPHIRE aims to provide a sustainable, low-cost biomanufacturing platform for the commercial production of insect pheromones.
Programme: NIBSys
Public web page: http://susphire.info/susphireproject/
Start date: 1st Apr 2018
End date: 30th Sep 2021
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
In this project, the involved partners are trying to develop the knowledge base that will enable the breeding of new potato varieties, tolerant to multiple environmental stressors.
Programme: NIBSys
Public web page: https://adapt.univie.ac.at/
Start date: 1st Jul 2020
End date: 30th Jun 2024
Organisms: Solanum tuberosum
pISA-tree: Standard project directory tree (ISA compliant)
Development of support for standardization of directory trees to suport ISA framework of research organization. We are developing a set of batch/make files to enable creation of trees for storage of assets (data/presentations/protocols/scripts) and description files that hold associated metadata for Investigation / Study / Assay levels.
Programme: NIBSys
Public web page: http://ablejec.nib.si/doc
Organisms: Not specified
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
Short Name: 02_FieldTrials Title: Field trials Description: Field trials - spraying CPB larvae on potato field with the insecticidal dsRNA validated for effectiveness in the laboratory trials 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_2019, _S_02_2020
Assays: _A_01_jun19-wet, _A_01_jun20-wet, _I_02_FieldTrials-files, _S_01_2019-files, _S_02_2020-files
Snapshots: No snapshots
Short Name: 01_LabTrials Title: Laboratory trials Description: Selection of targets and their validation in trials performed in the laboratories and greenhouse at NIB Phenodata: ./phenodata_20210113.txt pISA Investigation creation date: 2021-01-13 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_TargetSelect, _S_02_dsRNAorder, _S_03_dsRNAprod, _S_04_Stages, _S_05_jun2016, _S_06_oct2016, _S_07_dec2016, _S_08_jan2017, _S_09_jun2017, _S_10_apr2018, _S_11_may2018
Assays: _A_00_Ecoli-dry, _A_00_jun2017_dsRNA_stabil-wet, _A_01_AgroRNA-wet, _A_01_LitData-dry, _A_01_dec2016-phenotyping, _A_01_jan2017-phenotyping, _A_01_jun2016-phenotyping, _A_01_jun2017-phenotyping, _A_01_jun2017-phenotyping, _A_01_may2018-phenotyping, _A_01_oct2016-phenotyping, _A_01_pIsol-wet, _A_02_UlrichTop100-BLAST, _A_02_dec2016-RNAisol, _A_02_jun2016-RNAisol, _A_02_jun2017-RNAisol, _A_02_plasmid-SangerSeq, _A_02_qPCR_ampl_test-wet, _A_03_RNaseItreat-wet, _A_03_dec2016-qPCR, _A_03_jun2016-qPCR, _A_03_jun2017-qPCR, _A_03_patentDB-BLAST, _A_03_stages-RNAisol, _A_04_ortho-BLAST, _A_04_prod-qPCR, _A_04_stages-qPCR, _A_05_CPB_gene-annot, _A_06_splitter_BLAST-dry, _A_07_MergeEvi-dry, _A_08_SelTargetsA-dry, _I_01_LabTrials-files, _S_01_TargetSelect-files, _S_02_dsRNAorder-files, _S_03_dsRNAprod-files, _S_04_Stages-files, _S_05_jun2016-files, _S_06_oct2016-files, _S_07_dec2016-files, _S_08_jan2017-files, _S_09_jun2017-files, _S_10_apr2018-files, _S_11_may2018-files
Snapshots: No snapshots
Investigation: _I_STRT Short Name: STRT Title: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato Description: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato Phenodata: ./phenodata_20191022.txt pISA Investigation creation date: 2019-10-22 pISA Investigation creator: Maja Zagorscak, Ziva Ramsak, Marko Petek Principal investigator: Kristina Gruden License: MIT Sharing permission: Public Upload to FAIRDOMHub: Yes
RELATED ...
Submitter: Maja Zagorscak
Studies: SupplementaryInformation, _S_01_sequences, _S_02_denovo, _S_03_stCuSTr, _S_04_stPanTr
Assays: Supplementary Information, _A_01_GC_content-count, _A_01_evigene, _A_02.1_BUSCO, _A_02.2_assembly-contribution-count, _A_02.3_InterProScan, _A_02.4_STAR, _A_02.5_STARlong_matchAnnot, _A_02.6_TransRate, _A_02.7_VecScreen, _A_02.8_DIAMOND, _A_02_cdhit_3cvs-GFFmerged, _A_03.1_filtering, _A_03.2_components, _A_03_components_3cvs-GFFmerged, _A_04_BUSCO_3cvs-GFFmerged, _A_04_TransRate, _A_05_BUSCO, _A_05_MSA_3cvs-GFFmerged, _A_06_tr_rep-transrate, _A_07_Desiree-mapping, _A_08_centrifuge_3cvs-GFFmerged, _A_09_annotation-GFFmerged
Snapshots: No snapshots
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
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
Investigation files _I_03_Omics
Snapshots: No snapshots
Short Name: 02_2020 Title: Field trial in the year 2020 Description: Field trial in the year 2020 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
Snapshots: No snapshots
Short Name: 01_2019 Title: Field trial in the year 2019 Description: Field trial in the year 2019 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
Snapshots: No snapshots
Investigation files _I_02_FieldTrials
Snapshots: No snapshots
Short Name: 11_may2018 Title: CPB egg spraying experiment (dsMESH only) may2018 Description: Colorado potato beetle dsRNA egg spraying trial performed in May 2018 Raw Data: pISA Study creation date: 2021-05-10 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_01_LabTrials
Snapshots: No snapshots
Short Name: 10_apr2018 Title: CPB feeding experiment apr2018 Description: Colorado potato beetle dsRNA feeding trial performed in April 2018 Raw Data: pISA Study creation date: 2021-05-10 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_01_LabTrials
Snapshots: No snapshots
Short Name: 09_jun2017 Title: CPB feeding experiment jun2017 Description: Colorado potato beetle dsRNA feeding trial performed in June 2017 Raw Data: pISA Study creation date: 2021-05-10 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_01_LabTrials
Assays: _A_00_jun2017_dsRNA_stabil-wet, _A_01_jun2017-phenotyping, _A_02_jun2017-RNAisol, _A_03_jun2017-qPCR, _S_09_jun2017-files
Snapshots: No snapshots
Short Name: 08_jan2017 Title: CPB feeding experiment jan2017 Description: Colorado potato beetle dsRNA feeding trial performed in January 2017 Raw Data: pISA Study creation date: 2021-05-10 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_01_LabTrials
Snapshots: No snapshots
Short Name: 07_dec2016 Title: CPB feeding experiment dec2016 Description: Colorado potato beetle dsRNA feeding trial performed in December 2016 Raw Data: pISA Study creation date: 2021-05-10 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_01_LabTrials
Assays: _A_01_dec2016-phenotyping, _A_02_dec2016-RNAisol, _A_03_dec2016-qPCR, _S_07_dec2016-files
Snapshots: No snapshots
Short Name: 06_oct2016 Title: CPB feeding experiment oct2016 Description: Colorado potato beetle dsRNA feeding trial performed in October 2016 Raw Data: pISA Study creation date: 2021-05-10 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_01_LabTrials
Snapshots: No snapshots
Short Name: 05_jun2016 Title: CPB feeding experiment jun2016 Description: Colorado potato beetle dsRNA feeding trial performed in June 2016 Raw Data: pISA Study creation date: 2021-05-10 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_01_LabTrials
Assays: _A_01_jun2016-phenotyping, _A_02_jun2016-RNAisol, _A_03_jun2016-qPCR, _S_05_jun2016-files
Snapshots: No snapshots
Short Name: 04_Stages Title: Expression of target genes in CPB developmental stages and body parts Description: Expression of target genes in CPB developmental stages and body parts Raw Data: pISA Study creation date: 2021-05-10 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_01_LabTrials
Assays: _A_02_qPCR_ampl_test-wet, _A_03_stages-RNAisol, _A_04_stages-qPCR, _S_04_Stages-files
Snapshots: No snapshots
Short Name: 03_dsRNAprod Title: Production of selected desigend dsRNAs in-vivo Description: We established the production of two selected designed dsRNAs in-vivo in bacterial cultures of E. coli TH115 (DE3), a strain that does not produce RNases and is thus suitable for production of long dsRNA Raw Data: pISA Study creation date: 2021-01-14 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_01_LabTrials
Assays: _A_00_Ecoli-dry, _A_01_pIsol-wet, _A_02_plasmid-SangerSeq, _A_03_RNaseItreat-wet, _A_04_prod-qPCR, _S_03_dsRNAprod-files
Snapshots: No snapshots
Short Name: 02_dsRNAorder Title: Ordering the production of dsRNA of selected target genes Description: In-vitro production of dsRNAs designed to silence selected CPB genes Raw Data: pISA Study creation date: 2021-01-14 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_01_LabTrials
Assays: _A_01_AgroRNA-wet, _S_02_dsRNAorder-files
Snapshots: No snapshots
Short Name: 01_TargetSelect Title: Search for genes that might be good targets for control using dsRNAs (RNAi pesticides) Description: We will examine the results of RNAi screening experiments in model organisms (e.g. Drosophila melanogaster, Tribolium castaneum) as well as employ our previous data and literature knowledge on CPB gene expression and physiology Raw Data: pISA Study creation date: 2021-01-13 pISA Study creator: Marko Petek Principal investigator: Marko Petek License: CC BY 4.0 ...
Submitter: Marko Petek
Investigation: _I_01_LabTrials
Assays: _A_01_LitData-dry, _A_02_UlrichTop100-BLAST, _A_03_patentDB-BLAST, _A_04_ortho-BLAST, _A_05_CPB_gene-annot, _A_06_splitter_BLAST-dry, _A_07_MergeEvi-dry, _A_08_SelTargetsA-dry, _S_01_TargetSelect-files
Snapshots: No snapshots
Investigation files _I_01_LabTrials
Snapshots: No snapshots
Study: _S_03_stCuSTr Short Name: 03_stCuSTr Title: Solanum tuberosum Cultivar-Specific Transcriptomes Description: Solanum tuberosum Cultivar-Specific Transcriptomes Raw Data: ../_S_01_sequences/, ../_S_02_denovo/ pISA Study creation date: 2019-10-22 pISA Study creator: Maja Zagorscak, Marko Petek, Ziva Ramsak Principal investigator: Kristina Gruden License: MIT Sharing permission: Public Upload to FAIRDOMHub: Yes
RELATED FILES: /reports/README.MD https://fairdomhub.org/documents/346 /_STUDY_METADATA.TXT ...
Submitter: Maja Zagorscak
Investigation: _I_STRT
Assays: _A_01_evigene, _A_02.1_BUSCO, _A_02.2_assembly-contribution-count, _A_02.3_InterProScan, _A_02.4_STAR, _A_02.5_STARlong_matchAnnot, _A_02.6_TransRate, _A_02.7_VecScreen, _A_02.8_DIAMOND, _A_03.1_filtering, _A_03.2_components, _A_04_TransRate, _A_05_BUSCO
Snapshots: No snapshots
Study: _S_02_denovo Short Name: 02_denovo Title: De novo assemblies Description: De novo assemblies for cration of potato reference transcriptomes Raw Data: ../_S_01_sequences/ pISA Study creation date: 2019-10-23 pISA Study creator: Maja Zagorscak, Marko Petek, Ziva Ramsak Principal investigator: Kristina Gruden License: MIT Sharing permission: Public Upload to FAIRDOMHub: Yes
RELATED FILES: /reports/README.MD https://fairdomhub.org/documents/343 /_STUDY_METADATA.TXT https://fairdomhub.org/documents/342 ...
Snapshots: Snapshot 1
Assay: _A_02.3_InterProScan Short Name: 02.3_InterProScan Assay Class: DRY Assay Type: InterProScan Title: InterProScan on tr2aacds output Description: InterProScan on tr2aacds output pISA Assay creation date: 2019-10-22 pISA Assay creator: Marko Petek Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt
Submitter: Maja Zagorscak
Biological problem addressed: Annotation
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum
Models: No Models
SOPs: No SOPs
Data files: /input/path_to_files.txt, /intermediate/intermediate.tar, /output/Desiree_IPS_filtered_aggregated_filtere..., /output/PW363_IPS_filtered_aggregated_filtered.tsv, /output/Rywal_IPS_filtered_aggregated_filtered.tsv, /reports/IPS_PowerQuery_PivotTable.xlsx, /scripts/01_potato_tr_evigene_IPS_commands.txt, /scripts/02_reshape_merge_aggregate_filter.Rmd
Snapshots: Snapshot 1
Assay: _A_02.4_STAR Short Name: 02.4_STAR Assay Class: DRY Assay Type: STAR Title: mapping reads back to evigene .tr output Description: mapping reads back to evigene .tr output using STAR to check the percentage of reads that map pISA Assay creation date: 2019-10-22 pISA Assay creator: Marko Petek Phenodata: None Featuredata: None Data: see ./input/path_to_files.txt
Submitter: Maja Zagorscak
Biological problem addressed: Validation
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum
Models: No Models
SOPs: No SOPs
Data files: /input/path_to_files.txt, /output/output_STAR_logs-n-SJ.tar.gz, /output/samtoolsCoverage.zip, /reports/summaryCounts&SJ.xlsx, /scripts/STAR_commands.txt
Snapshots: Snapshot 1
Assay: _A_02.5_STARlong_matchAnnot Short Name: 02.5_STARlong_matchAnnot Assay Class: DRY Assay Type: matchAnnot Title: potato transcriptome v2 (evigene) STARlong mapping of transcripts to reference genome and MatchAnnot to get transcript annotations Description: potato initial transcriptome (evigene) STARlong mapping of transcripts to reference genome and MatchAnnot to get transcript annotations pISA Assay creation date: 2019-10-22 pISA Assay creator: Marko Petek Phenodata: None Featuredata: None ...
Submitter: Maja Zagorscak
Biological problem addressed: Annotation
Investigation: _I_STRT
Study: _S_03_stCuSTr
Organisms: Solanum tuberosum
Models: No Models
SOPs: No SOPs
Data files: /input/path_to_files.txt, /output/output_1_STARlong-logs-n-SJ.tar.gz, /output/output_2_matchAnnot-parsed-txt.tar.gz, /scripts/STARlongMatchAnnot_commands_ENCODE_den...
Snapshots: Snapshot 1
Supplementary Information linked together
Submitter: Maja Zagorscak
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT
Study: SupplementaryInformation
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: /reports/SupplementaryFigure1.pdf, /reports/SupplementaryFigure2.pdf, /reports/SupplementaryFigure3.pdf, /reports/SupplementaryFigure4.pdf, /reports/SupplementaryFile2.html, /reports/SupplementaryFile3.html, /reports/SupplementaryTableS1, /reports/SupplementaryTableS2, /reports/SupplementaryTableS3, /reports/SupplementaryTableS4, /reports/SupplementaryTableS5, /reports/SupplementaryTableS6, /reports/SupplementaryTableS7, /reports/SupplementaryTableS8, SupplementaryFile1
Snapshots: Snapshot 1
Files connected to investigation: _I_01_LabTrials
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_01_LabTrials
Study: Investigation files
Organisms: No organisms
SOPs: No SOPs
Data files: _INVESTIGATION_METADATA.TXT, featuredata_02092021.txt, phenodata_20210113.txt, phenodata_20210113.xlsx, reports/literature_CPB_experimental_procedures...., reports/qPCR_silencing_effects_choose_experimen...
Snapshots: No snapshots
Files connected to study: _S_01_TargetSelect
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_01_LabTrials
Study: _S_01_TargetSelect
Files connected to study: _S_02_dsRNAorder
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_01_LabTrials
Study: _S_02_dsRNAorder
Files connected to study: _S_03_dsRNAprod
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_01_LabTrials
Study: _S_03_dsRNAprod
Files connected to study: _S_04_Stages
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_01_LabTrials
Study: _S_04_Stages
Files connected to study: _S_05_jun2016
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_01_LabTrials
Study: _S_05_jun2016
Files connected to study: _S_06_oct2016
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_01_LabTrials
Study: _S_06_oct2016
Files connected to study: _S_07_dec2016
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_01_LabTrials
Study: _S_07_dec2016
Organisms: No organisms
SOPs: No SOPs
Data files: _STUDY_METADATA.TXT, analytes.xlsx
Snapshots: No snapshots
Files connected to study: _S_08_jan2017
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_01_LabTrials
Study: _S_08_jan2017
Files connected to study: _S_09_jun2017
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_01_LabTrials
Study: _S_09_jun2017
Files connected to study: _S_10_apr2018
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_01_LabTrials
Study: _S_10_apr2018
Files connected to study: _S_11_may2018
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_01_LabTrials
Study: _S_11_may2018
Short Name: 01_LitData-dry Assay Class: DRY Assay Type: dry Title: Compiling literature data on RNAi screens in insects Description: Compiling articles and final results of insect RNAi screens in model organisms (e.g. Drosophila melanogaster, Tribolium castaneum) pISA Assay creation date: 2021-01-13 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_01_LabTrials
Study: _S_01_TargetSelect
Organisms: No organisms
SOPs: No SOPs
Data files: _ASSAY_METADATA.TXT, output/Dm_mart_export.xls, output/GenomeRNAi_v14_FrequentHitters/GenomeRNA..., output/GenomeRNAi_v14_FrequentHitters/GenomeRNA..., output/Schnorrer_2010_Dm/Dm_lethal phenotypes n..., output/Schnorrer_2010_Dm/publication_info.txt, output/Tc-Ld-rnai_targets based on Tribolum.txt, output/Tc_mart_export.xls, output/Tenerius_2011/Terenius 2011 mmc2.xls, output/Tenerius_2011/publication_info.txt, output/Ulrich_2015/biomart-Ulrich2015_top100Dm.xls, output/Ulrich_2015/publication_info.txt, output/Ulrich_2015/uniprot-Ulrich2015_top100Tc.xls, output/human proteome turnover 2012 mcp.M111.01..., output/iBeetle_Tc/iB2Tc.csv, output/iBeetle_Tc/iB2Tc.xlsx, output/iBeetle_Tc/iBeetle-Base_larva_80penetran..., output/publication_info.txt
Snapshots: No snapshots
Short Name: 02_UlrichTop100-BLAST Assay Class: DRY Assay Type: BLAST Title: BLAST Ulrich top100 hits from Tribolium against CPB Description: Analysis of BLAST results from a query of top100 differentially expressed genes of Tribolium castaneum against Colorado potato beetle transcripts pISA Assay creation date: 2021-01-13 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_01_LabTrials
Study: _S_01_TargetSelect
Organisms: No organisms
SOPs: No SOPs
Data files: _ASSAY_METADATA.TXT, output/Tctop100cds__CPB_genome_nucl.tsv, output/Tctop100cds__CPB_genome_nucl.xlsx, output/Tctop100cds__CPB_genome_prot.tsv, output/Tctop100cds__CPB_genome_prot.xlsx, output/Tctop100cds__Ld_nucl.tsv, output/Tctop100cds__Ld_nucl.xlsx, scripts/ablastplus_shell_execution.txt
Snapshots: No snapshots
Short Name: 03_patentDB-BLAST Assay Class: DRY Assay Type: BLAST Title: NCBI patent BLAST Description: This is to find CPB nucleotide and peptide sequences that are already protected by patents pISA Assay creation date: 2021-01-14 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_01_LabTrials
Study: _S_01_TargetSelect
Organisms: No organisms
SOPs: No SOPs
Data files: _ASSAY_METADATA.TXT, output/aa/160128-markop-741.tsv, output/nt/160128-markop-740.tsv
Snapshots: No snapshots
Short Name: 04_ortho-BLAST Assay Class: DRY Assay Type: BLAST Title: BLAST to determine orthologs to model organisms Description: BLAST against D melanogaster and T castaneum to identify putative orthologous genes of CPB pISA Assay creation date: 2021-01-14 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_01_LabTrials
Study: _S_01_TargetSelect
Organisms: No organisms
SOPs: No SOPs
Data files: _ASSAY_METADATA.TXT, output/LDEC_Dm_orthologs.tsv, output/LDEC_Tc_orthologs.tsv
Snapshots: No snapshots
_p_RNAinVAL/_I_01_LabTrials/_S_09_jun2017/_A_03_jun2017-qPCR/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_01_LabTrials/_S_09_jun2017/_A_02_jun2017-RNAisol/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_01_LabTrials/_S_07_dec2016/_A_03_dec2016-qPCR/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_01_LabTrials/_S_07_dec2016/_A_02_dec2016-RNAisol/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_01_LabTrials/_S_05_jun2016/_A_03_jun2016-qPCR/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_01_LabTrials/_S_05_jun2016/_A_02_jun2016-RNAisol/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_01_LabTrials/_S_04_Stages/_A_04_stages-qPCR/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_01_LabTrials/_S_04_Stages/_A_03_stages-RNAisol/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
Abstract (Expand)
Authors: Marko Petek, Maja Zagorščak, Živa Ramšak, Sheri Sanders, Elizabeth Tseng, Mohamed Zouine, Anna Coll, Kristina Gruden
Date Published: No date defined
Publication Type: Not specified
DOI: 10.1101/845818
Citation: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek
_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/
Creator: Marko Petek
Submitter: Marko Petek