Marko Petek

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, ...

SUSPHIRE aims to provide a sustainable, low-cost biomanufacturing platform for the commercial production of insect pheromones.

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.

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.

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.

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

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

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

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 ...

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

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

Investigation files _I_03_Omics

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

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

Investigation files _I_02_FieldTrials

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

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

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

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

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

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

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

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

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

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

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 ...

Investigation files _I_01_LabTrials

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 ...

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 ...

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

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

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 ...

Supplementary Information linked together

Files connected to investigation: _I_01_LabTrials

Files connected to study: _S_01_TargetSelect

Files connected to study: _S_02_dsRNAorder

Files connected to study: _S_03_dsRNAprod

Files connected to study: _S_04_Stages

Files connected to study: _S_05_jun2016

Files connected to study: _S_06_oct2016

Files connected to study: _S_07_dec2016

Files connected to study: _S_08_jan2017

Files connected to study: _S_09_jun2017

Files connected to study: _S_10_apr2018

Files connected to 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:

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:

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:

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:

_p_RNAinVAL/_I_01_LabTrials/_S_09_jun2017/_A_03_jun2017-qPCR/

_p_RNAinVAL/_I_01_LabTrials/_S_09_jun2017/_A_02_jun2017-RNAisol/

_p_RNAinVAL/_I_01_LabTrials/_S_07_dec2016/_A_03_dec2016-qPCR/

_p_RNAinVAL/_I_01_LabTrials/_S_07_dec2016/_A_02_dec2016-RNAisol/

_p_RNAinVAL/_I_01_LabTrials/_S_05_jun2016/_A_03_jun2016-qPCR/

_p_RNAinVAL/_I_01_LabTrials/_S_05_jun2016/_A_02_jun2016-RNAisol/

_p_RNAinVAL/_I_01_LabTrials/_S_04_Stages/_A_04_stages-qPCR/

_p_RNAinVAL/_I_01_LabTrials/_S_04_Stages/_A_03_stages-RNAisol/

_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/

_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/

_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/

_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/

_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/

_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/

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_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/

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_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/

_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/

_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/

_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/

_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/

_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/

_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/

_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/

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_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/

_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/

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_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/

_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/

_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/

_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/

_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/

_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/

_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/

_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/

_p_RNAinVAL/_I_03_Omics/_S_02_metagenome_resp/_A_06_extr_bact-assembly/