Marko Petek
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
Roles
Project administrator
- SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture
- _p_stRT
- _p_RNAinVAL
Asset housekeeper
- 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
Programme administrator
Their tagsRelated items
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
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
WARNING: THIS IS A TEST PROJECT CREATED FOR TESTING THE UPLOAD TO FAIRDOMHUB USING seekr AND SEEK API
pISA-tree: Standard project directory tree
A set of batch files is used to create standard directory tree for research projects. Batch files are provided to make standardized nested directories in accordance with the ISA Abstract Model levels (Investigation/Study/Assay).
https://github.com/NIB-SI/pISA-tree
Linked resources:
- R support for pISA-tree DOI ...
Programme: NIBSys
Public web page: http://ablejec.nib.si/doc
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
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
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
Short Name: T21_SXPsysbio Title: Use a systems biology approach to identify regulatory bottlenecks in SxPv1 Description: Samples from SXPv1.0 plants as well as sister nulls (progeny from the original transgenic event in which the transgene has segregated) and wild type will be grown and leaf samples taken for RNA extraction and profiling of primary metabolites and volatiles (target pheromones as well as potential derivatives) (P1, P5). Phenotypic and GC-MS data will be obtained and analysed from ...
Submitter: Marko Petek
Studies: Investigation files, _S_P1_SPv10T0andT1, _S_P1_SPv10T2andT3, _S_P1_SPv1TransientExp, _S_P1_SxPAltAcTransferases, _S_P1_SxPv10vsSxP12, _S_P1_SxPv12T2, _S_P4_CoExpNetViz, _S_P4_DiNAR, _S_P4_GAtreat, _S_P4_SxP10-newG-DE, _S_P4_SxP10-oldG-DE, _S_P4_SxP1012-finalG, _S_P4_SxP12-newG-DE
Assays: _A_00_SxP_photos-phenotyping, _A_01_RNA1-RNAisol, _A_01_SxP_Data_Only-CoExp, _A_01_SxPv12_fastq-QC, _A_01_mapping-CLC, _A_01_toNewGenome-CLC-mapping, _A_02_FastQC-bioinfo, _A_02_Nb_datasets-CoExp, _A_02_SxPv12_mapping-CLC, _A_02_limmavoomDE-R, _A_02a_limmavoom-multim-R, _A_02a_limmavoomDEbylines-R, _A_02b_limmavoom-uniquem-R, _A_03_MapMan-visualisation, _A_03_NewGenome-MapMan, _A_03_SxPv12_limmavoom_DE-R, _A_03_mapping-CLC, _A_03a_mapping2-STAR, _A_04_GSEA-Stat, _A_04_MapManBINenrich-GSEA, _A_04_Mercator-bioinfo, _A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA, _A_05_DEstat-R, _A_05_Phenotype_analysis-Stat, _A_05_VOCcomp-Bioinfo, _A_05a_DEstat2-R, _A_05b_DElow-wt-R, _A_06_MapMan-bioinfo, _A_06_SxPv1-0_Illumina-Centrifuge, _A_07_NbAUSv1-0-InterPro, _A_07_transgenes-CLC, _A_CKN-DiNAR, _A_CKN_NbL35-DiNAR, _A_LeavesSxPv10vsv12-GCMS, _A_P4_v10v12-phenotyping, _A_PIS-DiNAR, _A_PIS-SxPv12-DiNAR, _A_PIS_NbL35-DiNAR, _A_RootsSxPv10vsv12-GCMS, _A_SP10T0Analysis-GCMS, _A_SP10T1Analysis-GCMS, _A_SPv10EaDActAnalysis-GCMS, _A_SPv10T2Analysis-GCMS, _A_SPv10T3Analysis-GCMS, _A_SPv10_phenotyping-Images, _A_SxPAlternativeAcetyltransferases-GCMS, _A_SxPv10vsv12-phenotyping, _A_SxPv12ScreeningT2-GCMS, _A_TransientSPv11andSPv12-GCMS, _I_T21_SXPsysbio-files, _S_P1_SPv10T0andT1-files, _S_P1_SPv10T2andT3-files, _S_P1_SPv1TransientExp-files, _S_P1_SxPAltAcTransferases-files, _S_P1_SxPv10vsSxP12-files, _S_P1_SxPv12T2-files, _S_P4_CoExpNetViz-files, _S_P4_DiNAR-files, _S_P4_GAtreat-files, _S_P4_SxP10-newG-DE-files, _S_P4_SxP10-oldG-DE-files, _S_P4_SxP1012-finalG-files, _S_P4_SxP12-newG-DE-files
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_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
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
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
Short Name: DiNAR Title: DiNAR analyses of SxP DE data Description: DiNAR visualisation of SxPv1.0 and SxPv1.2 expressoin data in either PIS or CKN networks. Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_CKN-DiNAR, _A_CKN_NbL35-DiNAR, _A_PIS-DiNAR, _A_PIS-SxPv12-DiNAR, _A_PIS_NbL35-DiNAR, _S_P4_DiNAR-files
Short Name: Gibberelin_treatment Title: GA3 treatment of SxPs Description: SxP lines were treated with 3 different GA3 concentrations (1, 10 and 100 micromolar) and control solution. WT Nb plants were used for control. From v1.0 T3, low producing line 5_2_5 and high producing line 5_1_7 were used and from v1.2 T2 lines 4_1 and 4_3. Treatment was done for 5 consecutive weeks, once per week with spraying the leaves. Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution ...
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Short Name: P4_SxP10-newG-DE Title: SxPv1.0 RNA-seq analysis using the new Nb genome Description: Analysis of RNA-seq data (Illumina short reads) of two lines of SexyPlants (SxP v1.0) utilising the not yet published now high quality genome of Nicotiana benthamiana from the Newcotiana project. Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_01_toNewGenome-CLC-mapping, _A_02_limmavoomDE-R, _A_02a_limmavoomDEbylines-R, _A_03_NewGenome-MapMan, _A_04_GSEA-Stat, _A_05_Phenotype_analysis-Stat, _A_06_SxPv1-0_Illumina-Centrifuge, _A_07_NbAUSv1-0-InterPro, _S_P4_SxP10-newG-DE-files
Short Name: P4_SxP10-oldG-DE Title: SxPv1.0 RNA-seq analysis using old Nb genome Description: Analysis of RNA-seq data (Illumina short reads) of two lines of SexyPlants (SxP v1.0) utilising the published (old) genome of Nicotiana benthamiana. Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: No
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_00_SxP_photos-phenotyping, _A_01_RNA1-RNAisol, _A_02_FastQC-bioinfo, _A_03_mapping-CLC, _A_03a_mapping2-STAR, _A_04_Mercator-bioinfo, _A_05_DEstat-R, _A_05a_DEstat2-R, _A_05b_DElow-wt-R, _A_06_MapMan-bioinfo, _A_07_transgenes-CLC, _S_P4_SxP10-oldG-DE-files
Short Name: P4_SxP1012-finalG Title: Reanalysis of SxP Illumina reads with Nb genome V3.5 Description: * Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Short Name: P4_SxP12-newG-DE Title: Gene expression analysis of Sxp 1.2 Description: exp4 in phenodata Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_01_SxPv12_fastq-QC, _A_02_SxPv12_mapping-CLC, _A_03_SxPv12_limmavoom_DE-R, _A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA, _S_P4_SxP12-newG-DE-files
Short Name: P1_SPv10T2andT3 Title: Characterization of SPv1.0 plants of the T2 and T3 generations Description: Plants of the SxP v1 second and third generation were grown in the greenhouse and leaf samples were collected for analysing their metabolome (via GC-MS) and transcriptome (via RNA-seq). Phenotypic data such as plant height was also recorded. Raw Data: pISA Study creation date: 2018-11-09 pISA Study creator: ElenaMG Principal investigator: Diego Orzaez License: Creative Commons Attribution ...
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_SPv10T2Analysis-GCMS, _A_SPv10T3Analysis-GCMS, _A_SPv10_phenotyping-Images, _S_P1_SPv10T2andT3-files
Short Name: P1_SPv1TransientExp Title: Transient expression in Nicotiana benthamiana leaves of constructs for SPv1 Description: The constructs for stable transformation of SPv1.X versions were tested transiently via agroinfiltration of Nicotiana benthamiana leaves. Pheromone content was analysed via GC-MS Raw Data: pISA Study creation date: 2019-12-08 pISA Study creator: ElenaMG Principal investigator: Diego Orzaez License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to ...
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_SPv10EaDActAnalysis-GCMS, _A_TransientSPv11andSPv12-GCMS, _S_P1_SPv1TransientExp-files
Short Name: P1_SxPAltAcTransferases Title: Study of alternative acetyltransferases for future SxP versions Description: Study of transient expression of different acetyltransferase genes responsible of the catalysis of the conversion of Z11-16OH into Z11-16OAc, assayed in Nicotiana benthamiana WT plants. Raw Data: pISA Study creation date: 2021-11-25 pISA Study creator: RMF Principal investigator: Diego Orzaez License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: ...
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_SxPAlternativeAcetyltransferases-GCMS, _S_P1_SxPAltAcTransferases-files
Short Name: P1_SxPv10vsSxP12 Title: Comparison between SxPv1.0 and SxPv1.2 Description: Volatilome characterization of SxPv1.0 T3 plants, SxPv1.2 T1 plants and WT plants. Raw Data: pISA Study creation date: 2020-11-01 pISA Study creator: RMF Principal investigator: Diego Orzaez License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_LeavesSxPv10vsv12-GCMS, _A_RootsSxPv10vsv12-GCMS, _A_SxPv10vsv12-phenotyping, _S_P1_SxPv10vsSxP12-files
Short Name: SxPv12T2Analysis Title: Analysis of second generation of SxPv1.2 plants Description: Characterization of SxPv1.2 T2 plants. Raw Data: pISA Study creation date: 2021-12-09 pISA Study creator: RMF Principal investigator: Diego Orzaez License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes Institutions involved: Instituto de Biología Molecular y Celular de Plantas (IBMCP), Spain; Institute of Agrochemistry and Food Technology (IATA), Spain; The ...
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Short Name: CoExpNetViz Title: CoExpNetViz Description: Coexpression analyses with CoExpNetViz tool. Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_01_SxP_Data_Only-CoExp, _A_02_Nb_datasets-CoExp, _S_P4_CoExpNetViz-files
Investigation files _I_T21_SXPsysbio
Short Name: P1_SPv10T0andT1 Title: Characterization of SPv1.0 plants of the T0 and T1 generations Description: SP v1.0 plants were generated and studied (T0), as well as the first generation (T1). Plants were grown in the greenhouse and leaf samples were collected for analysing their metabolome (via GC-MS). Phenotypic data such as plant height was also recorded. Raw Data: pISA Study creation date: 2021-11-01 pISA Study creator: AlfredoQR Principal investigator: Diego Orzaez License: Creative ...
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_SP10T0Analysis-GCMS, _A_SP10T1Analysis-GCMS, _S_P1_SPv10T0andT1-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: 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
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
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
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
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
Supplementary Information linked together
Submitter: Maja Zagorscak
Biological problem addressed: Model Analysis Type
Investigation: _I_STRT
Study: SupplementaryInformation
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
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
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
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
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
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
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA/
Creator: Marko Petek
Submitter: Marko Petek
Download
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_03_SxPv12_limmavoom_DE-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_03_SxPv12_limmavoom_DE-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_03_SxPv12_limmavoom_DE-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_03_SxPv12_limmavoom_DE-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_03_SxPv12_limmavoom_DE-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_02_SxPv12_mapping-CLC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_03_SxPv12_limmavoom_DE-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_03_SxPv12_limmavoom_DE-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_03_SxPv12_limmavoom_DE-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_02_SxPv12_mapping-CLC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/
Creator: Marko Petek
Submitter: Marko Petek
Abstract (Expand)
Authors: Marko Petek, Maja Zagorščak, Andrej Blejec, Živa Ramšak, Anna Coll, Špela Baebler, Kristina Gruden
Date Published: 21st Nov 2021
Publication Type: Journal
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
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_03_SxPv12_limmavoom_DE-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_03_SxPv12_limmavoom_DE-R/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_02_SxPv12_mapping-CLC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_01_SxPv12_fastq-QC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_01_SxPv12_fastq-QC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_01_SxPv12_fastq-QC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_01_SxPv12_fastq-QC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_01_SxPv12_fastq-QC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_01_SxPv12_fastq-QC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_01_SxPv12_fastq-QC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_01_SxPv12_fastq-QC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_02_SxPv12_mapping-CLC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_01_SxPv12_fastq-QC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_01_SxPv12_fastq-QC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_01_SxPv12_fastq-QC/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_SxP12-newG-DE/_A_01_SxPv12_fastq-QC/
Creator: Marko Petek
Submitter: Marko Petek
