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- Marko Petek
Ph.D. in Biotechnology
Research associate at Department of Biotechnology and Systems Biology, National Institute of Biology
SEEK ID: https://fairdomhub.org/people/1071
Location:
Slovenia
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
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
- Projects (4)
- Institutions (1)
- Investigations (1)
- Studies (3)
- Assays (4)
- Data files (3)
- Publications (1)
- Documents (7)
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
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
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
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: 31st Mar 2021
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
...
Snapshots: No snapshots
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
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
...
Person responsible: Maja Zagorscak
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
...
Investigation: _I_STRT
Assays: No Assays
Study: _S_01_sequences
Short Name: 01_sequences
Title: NGS sequences for de novo assembly
Description: NGS sequences for de novo assembly; input for Study 02_denovo
Raw Data: see: ./reports/SupplementaryTableS1-Input_sequences_information.xlsx
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
...
Investigation: _I_STRT
Assays: No Assays
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
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
Supplementary Information linked together
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
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
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
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
...
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...
Supplementary Table S1 - Detailed sample information table used to generate the de novo transcriptome assemblies.
Raw and processed reads summary.
Layer _p_stRT/_I_STRT/ _S_01_sequences/reports
Creators: Maja Zagorscak, Marko Petek
Submitter: Maja Zagorscak
Supplementary Table S2 - Detailed de novo assemblies information table.
Primary potato transcriptome assemblies summary listing parameters used for short-read de novo assembly generation.
Layer _p_stRT/_I_STRT/_S_02_denovo/reports/
Creators: Maja Zagorscak, Marko Petek
Submitter: Maja Zagorscak
_p_stRT/_I_STRT
pipeline
Creators: Maja Zagorscak, Marko Petek
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
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_stRT/_I_STRT/_S_01_sequences
Creators: Maja Zagorscak, Marko Petek
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT/_I_STRT/_S_01_sequences
Creators: Maja Zagorscak, Marko Petek
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT/_I_STRT/_S_02_denovo
Creators: Maja Zagorscak, Marko Petek
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT/_I_STRT/_S_02_denovo
Creators: Maja Zagorscak, Marko Petek
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT/_I_STRT/_S_02_denovo
Creators: Maja Zagorscak, Marko Petek
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT/_I_STRT/_S_01_sequences
Creators: Maja Zagorscak, Marko Petek
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
_p_stRT
Creators: Maja Zagorscak, Kristina Gruden, Marko Petek, Ziva Ramsak, Anna Coll Rius
Submitter: Maja Zagorscak
Investigations: No Investigations
Studies: No Studies
Assays: No Assays