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.
Synthetic biology data management spreadsheet: https://fairdomhub.org/data_files/6036
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: T33_MonoterpenoidsFungi Title: Detection of Coccoidea pheromones or precursors in engineered fungi Description: Detection of lavandulol or lavandulyl acetate in different engineered fungi (SxF) lines by GC-MS-MS Phenodata: ./phenodata_20211223.txt pISA Investigation creation date: 2021-12-23 pISA Investigation creator: Sandra Vacas Principal investigator: Ismael Navarro License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Short Name: T32_CandidateGeneExpressionTesting Title: Candidate gene expression and testing Description: The purpose of this investigation is to express transiently candidate genes for Pcitri sex pheromone biosynthesis. This genes could act either as genes catalyzing steps related to the biosynthesis of precursors of the pheromone itself, either for the final steps of the biosynthesis. After expression, the monoterpenoid production function of those genes is checked by GCMS. Phenodata: ...
Short Name: T24_phero Title: Pheromone Content and EAG response Description: Investigate pheromone content and electrophysiological response of target insects to extracts of plants and fungi expressing Lepidoptera pheromones Phenodata: ./phenodata_21Sep21.txt pISA Investigation creation date: 21-Sep-21 pISA Investigation creator: Sandra Vacas Principal investigator: Ismael Navarro License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Studies: Investigation files, _S_P5_EAGresponse, _S_P5_PhContentPlants, _S_P5_PhEmissionPlants
Assays: _A_EAG_manual-EAG, _A_GC-MS-EAD-EAG, _A_PhCont_fr20-GC-MS, _A_PhCont_fr80-GC-MS, _A_PhCont_fresh-GC-MS, _A_emission_nontruncated-GC-MS, _A_emission_truncated-GC-MS, _I_T24_phero-files, _S_P5_EAGresponse-files, _S_P5_PhContentPlants-files, _S_P5_PhEmissionPlants-files
Short Name: T23_SxF Title: Moth pheromone production in filamentous fungi SxF Description: Demonstration of moth pheromone production in filamentous fungi by solvent extractions of liquid cultures and mycelial biomass and GC-MS/MS analysis. Constitutive and inducible expression of moth pheromones in filamentous fungi Penicillium species will be developed using a dCas9-based copper inducible system. An initial proof of concept will also be performed in P. digitatum using constitutive promoters. ...
Submitter: Marko Petek
Studies: Investigation files, _S_P1_ConstExp_Pdigitatum, _S_P5_SxFliquids, _S_P5_SxFmycelia
Assays: _A_FS-GC-MS, _A_FSM-GC-MS, _A_SRM-GC-MS, _A_SRMM-GC-MS, _A_qRTPCRMothPheromonesEnzymes-Q-RT-PCR, _I_T23_SxF-files, _S_P1_ConstExp_Pdigitatum-files, _S_P5_SxFliquids-files, _S_P5_SxFmycelia-files
Short Name: T22_SxPv2 Title: Sexy Plant version 2: inducible and regulable SxP versions Description: The purpose of this investigation is to optimize the SxP version 1, with a switchable expression and increased compound release. Phenodata: ./phenodata_20210920.txt 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 ...
Short Name: T12_CuInducible Title: Production and testing of copper inducible dCas9EV system for moth pheromone production Description: dCas9EV system used to activate the synthetic promoters made in T11 was coupled to a copper-inducible promoter made of CBS repeats and a minimal DFR promoter. Such system will be induced via CUP2 protein, which binds to CBS motif in presence of copper. This cascade-like system was tested for production of the moth pheromone pathway. Phenodata: ./phenodata_20210107.txt ...
Submitter: Marko Petek
Studies: Investigation files, _S_P1_TransientExp_Nb
Assays: _A_AgroinfFinalConstructsdCas9EV-GCMS, _A_AgroinfGuidedPathwaywithConstitutivedCas9EV-GCMS, _A_AgroinfNonGuidedPathwaywithCopperInducibledCas9EV-GCMS, _A_AgroinfNonGuidedPathwayywithConstitutivedCas9EV-GCMS, _I_T12_CuInducible-files, _S_P1_TransientExp_Nb-files
Short Name: T11_dCas9SynProm Title: Development of synthetic promoters inducible by dCasEV2.1 system Description: The aim of this work is to design a range of synthetic promoters with negligible basal expression that are activated by using the "dead" Cas9 activation system developed in our lab (dCasEV2.1, Selma et al., 2019). Such tool will then be used for creating synthetic regulatory cascades where the expression of the genes for the pheromone biosynthesis can be controlled by a single dCas9 ...
Short Name: T31_mealybug Title: Mealybug genome and transcriptome analyses Description: Searching for enzymes involved in the mealybug pheromone biosynthesis pathways. These pheromones are known to be released by virgin females. Phenodata: ./phenodata_20190523.txt Featuredata: Principal investigator: Heribert Warzecha, Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Studies: Investigation files, _S_P3_expressionEcoli, _S_P4_AdPathGenes, _S_P4_Pcitri_IsoSeq, _S_P4_Pcitri_genome, _S_P4_Pcitri_genome_extSamples, _S_P4_Pcitri_tr1, _S_P4_Pcitri_tr1tr2combo, _S_P4_Pcitri_tr2, _S_P4_cand_all, _S_P4_cand_genomic
Assays: _A_01-CoEXpNetViz_tr2-coexpr, _A_01_NGI-IsoSeq, _A_01_RNAseq-CLC, _A_01_assembly2-rnaSPAdes, _A_01_mapToGenomeAll-STAR, _A_01_renameFASTA-Bioinfo, _A_02-CoEXpNetViz_gen-coexpr, _A_02_CDHIT-Bioinfo, _A_02_assembly2-IPS, _A_02_cDNAcupcake-dry, _A_02_limma-R, _A_02_mapToGenomeAll_limma-R, _A_03-IPS, _A_03_CDHIT2-Bioinfo, _A_03_limma_min50counts-R, _A_03_mapAs2ToGenome-STAR, _A_04_limma_min10counts-R, _A_04_mapIllumina-STAR, _A_04_mapReadsToAs2-STAR, _A_05_As2_tr_limmaDE-R, _A_05_DE_limma-R, _A_05_assembly1-rnaSPAdes, _A_06_assembly1-IPS, _A_07_mapAs1ToGenome-STAR, _A_08_mapReadsToAs1-STAR, _A_09_As1_tr_limmaDE-R, _A_C98F-EcoliExpr, _A_IDIsearch-Bioinfo, _A_IPS-bioinfo, _A_MAST-bioinfo, _A_MEME-bioinfo, _A_MSA-bioinfo, _A_MeUppS-EcoliExpr, _A_Node14610-EcoliExpr, _A_Node14610DmTP-EcoliExpr, _A_OtherMealybugCandidates-Alignment, _A_Pc1599-EcoliExpr, _A_Pc23180-EcoliExpr, _A_Pc2704-EcoliExpr, _A_Pc32607-EcoliExpr, _A_Pc7366II-EcoliExpr, _A_PcCis24-EcoliExpr, _A_Strep_CLDS-bioinfo, _A_TPS_phy-bioinfo, _A_Terzyme-bioinfo, _A_Trans1153-EcoliExpr, _A_Trans2-EcoliExpr, _A_Trans39-EcoliExpr, _A_Trans57-EcoliExpr, _A_Trans64-EcoliExpr, _A_Trans94-EcoliExpr, _A_candidatemining-bioinfo, _A_g14825_recon-bioinfo, _A_smallIDSsubunit-motifs, _I_T31_mealybug-files, _S_P3_expressionEcoli-files, _S_P4_AdPathGenes-files, _S_P4_Pcitri_IsoSeq-files, _S_P4_Pcitri_genome-files, _S_P4_Pcitri_genome_extSamples-files, _S_P4_Pcitri_tr1-files, _S_P4_Pcitri_tr1tr2combo-files, _S_P4_Pcitri_tr2-files, _S_P4_cand_all-files, _S_P4_cand_genomic-files
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: P5_SxF_lav_ac Title: Detection of lavandulyl acetate in extracts of engineered fungi Description: Detection of lavandulyl acetate in extracts of engineered fungi (SxF) by GC-MS-MS Raw Data: pISA Study creation date: 2021-12-23 pISA Study creator: Sandra Vacas Principal investigator: Ismael Navarro License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_T33_MonoterpenoidsFungi
Assays: _A_LA_liq-GC-MS, _A_LA_myc-GC-MS, _S_P5_SxF_lav_ac-files
Short Name: P5_SxF_lavandulol Title: Detection of lavandulol in SxF extracts Description: Detection of lavandulol in extracts of engineered fungi by GC-MS-MS Raw Data: pISA Study creation date: 2021-12-23 pISA Study creator: Sandra Vacas Principal investigator: Ismael Navarro License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_T33_MonoterpenoidsFungi
Assays: _A_L_liq-GC-MS, _A_L_myc-GC-MS, _S_P5_SxF_lavandulol-files
Investigation files _I_T33_MonoterpenoidsFungi
Submitter: Marko Petek
Investigation: _I_T33_MonoterpenoidsFungi
Assays: _I_T33_MonoterpenoidsFungi-files
Investigation files _I_T32_CandidateGeneExpressionTesting
Submitter: Marko Petek
Investigation: _I_T32_CandidateGeneExpressionTesting
Short Name: TransientLPPSCPPS Title: Transient expression of lavandulyl pirophosphate synthase (LPPS) and chrysanthemyl pirophhosphate synthase (CPPS) Description: The purpose of this study is to perform the transient expression of LPPS and CPPS gene for the production of lavandulol and chrysanthemol, respectively. Production is measured by GCMS of samples. Raw Data: pISA Study creation date: 2021-12-03 pISA Study creator: RMF Principal investigator: Diego Orzaez License: Creative Commons Attribution ...
Submitter: Marko Petek
Investigation: _I_T32_CandidateGeneExpressionTesting
Assays: _A_TransientCompLPPSCPPS-GCMS, _S_TransientLPPSCPPS-files
Short Name: P5_PhContentPlants Title: Quantification of total moth pheromone contents in SxP Description: Quantification of the total pheromone content in SxPv1.2 plants Raw Data: pISA Study creation date: 21-Sep-21 pISA Study creator: Sandra Vacas Principal investigator: Ismael Navarro License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_T24_phero
Assays: _A_PhCont_fr20-GC-MS, _A_PhCont_fr80-GC-MS, _A_PhCont_fresh-GC-MS, _S_P5_PhContentPlants-files
Short Name: P5_PhEmissionPlants Title: Quantification of the pheromone emitted by SxP plants Description: Quantification of the quantity of pheromone emitted by SxPv1.2 plants by volatile collection and GC-MS/MS analysis Raw Data: pISA Study creation date: 21-Sep-21 pISA Study creator: Sandra Vacas Principal investigator: Ismael Navarro License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_T24_phero
Assays: _A_emission_nontruncated-GC-MS, _A_emission_truncated-GC-MS, _S_P5_PhEmissionPlants-files
Investigation files _I_T24_phero
Short Name: P5_EAGresponse Title: Electrophysiological response of moths to SxP extracts Description: Electrophysiological response of Sesamia nonagrioides males to selected fractions of the SxPv1.2 extracts Raw Data: pISA Study creation date: 21-Sep-21 pISA Study creator: Sandra Vacas Principal investigator: Ismael Navarro License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_T24_phero
Assays: _A_EAG_manual-EAG, _A_GC-MS-EAD-EAG, _S_P5_EAGresponse-files
Short Name: P1_ConstExp_Pdigitatum Title: Constitutive expression of moth pheromone pathway in Penicillium digitatum. Description: For this Proof of Concept, the three enzymes of the moth pheromones route were assembled in TUs using fungal promoters and terminators, and transformed into Penicillium digitatum. Pheromone production of the selected transformants will be assessed via GC-MS. Raw Data: pISA Study creation date: 2020-18-04 pISA Study creator: ElenaMG Principal investigator: Diego Orzaez ...
Submitter: Marko Petek
Investigation: _I_T23_SxF
Assays: _A_qRTPCRMothPheromonesEnzymes-Q-RT-PCR, _S_P1_ConstExp_Pdigitatum-files
Short Name: P5_SxFliquids Title: Pheromone detection in liquid extracts of SxF Description: Pheromone detection in liquid extracts of modified filamentous fungi (SxF) by liquid-liquid solvent extraction and GC-MS/MS analysis Raw Data: pISA Study creation date: 21-Sep-22 pISA Study creator: Sandra Vacas Principal investigator: * License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_T23_SxF
Assays: _A_FS-GC-MS, _A_SRM-GC-MS, _S_P5_SxFliquids-files
Short Name: P5_SxFmycelia Title: Pheromone detection in SxF mycelial biomass Description: Pheromone detection in the mycelial biomass of modified filamentous fungi by solid-liquid solvent extraction and GC-MS/MS analysis Raw Data: pISA Study creation date: 21-Sep-22 pISA Study creator: Sandra Vacas Principal investigator: * License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_T23_SxF
Assays: _A_FSM-GC-MS, _A_SRMM-GC-MS, _S_P5_SxFmycelia-files
Investigation files _I_T23_SxF
Investigation files _I_T22_SxPv2
Short Name: P1_TransgenicStableSxPv2 Title: Generation of Sexy Plant version 2: transgenic plants with the moth sex pheromones biosynthetic pathway genes regulated by synthetic promotors. Description: The purpose of this study is to generate transgenic stable lines of Nicotiana benthamiana plants ready to express the moth sex pheromone biosynthetic pathway in a regulable way. The moth sex pheromones biosynthetic pathway genes are regulated by synthetic promotors, so in a basal state, the plants ...
Submitter: Marko Petek
Investigation: _I_T22_SxPv2
Assays: _A_SxPGuidedPathway-GCMS, _A_SxPNonGuidedPathway-GCMS, _A_SxPdCasEVNonGuidedPathway-GCMS, _S_P1_TransgenicStableSxPv2-files
Investigation files _I_T12_CuInducible
Short Name: P1_TransientExp_Nb Title: Agroinfiltration of copper inducible system in Nicotiana benthamiana Description: The copper inducible dCasEV was tested transiently in Nicotiana benthamiana leaves together with the moth pheromone pathway under the regulation of the synthetic promoters created in T11 Raw Data: https://zenodo.org/communities/susphire/search?page=1&size=20 pISA Study creation date: 2020-10-28 pISA Study creator: ElenaMG Principal investigator: Diego Orzaez License: Creative ...
Submitter: Marko Petek
Investigation: _I_T12_CuInducible
Assays: _A_AgroinfFinalConstructsdCas9EV-GCMS, _A_AgroinfGuidedPathwaywithConstitutivedCas9EV-GCMS, _A_AgroinfNonGuidedPathwaywithCopperInducibledCas9EV-GCMS, _A_AgroinfNonGuidedPathwayywithConstitutivedCas9EV-GCMS, _S_P1_TransientExp_Nb-files
Investigation files _I_T11_dCas9SynProm
Short Name: P1_SynProm_Nbenthamiana Title: Transient expression in Nicotiana benthamiana of the synthetic promoters developed Description: Different A1 and A2 Different A1 and A2 promoter pieces were designed containing as much random sequence as possible, and the target sequence for the guideRNA 1 of SlDFR promoter. In the same way, some minimal promoters containing only the TATA-Box signal and the 5'UTR region were designed as "core promoter" pieces. Different synthetic promoters were then ...
Submitter: Marko Petek
Investigation: _I_T11_dCas9SynProm
Assays: _A_20190208-LUM, _A_20190717-LUM, _A_20191209-LUM, _A_20200219-LUM, _A_20200302-LUM, _A_20200818-LUM, _A_20201112-LUM, _A_20211221-LUM, _S_P1_SynProm_Nbenthamiana-files
Short Name: P4_Pcitri_tr1tr2combo Title: Combining tr1 and tr2 P. citri de novo transcriptomes into one transcriptome set Description: Production of one set of transcripts that will be easier for the readers of the planned publication Raw Data: Principal investigator: Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_T31_mealybug
Assays: _A_01_renameFASTA-Bioinfo, _A_02_CDHIT-Bioinfo, _A_03_CDHIT2-Bioinfo, _S_P4_Pcitri_tr1tr2combo-files
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
Spreadsheet with metadata on synthetic biology parts, transcriptional units, modules, and genotypes used in the SUSPHIRE project
Creators: None
Submitter: Marko Petek
Download_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lavandulol/_A_L_myc-GC-MS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lavandulol/_A_L_myc-GC-MS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lavandulol/_A_L_liq-GC-MS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lavandulol/_A_L_myc-GC-MS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lavandulol/_A_L_myc-GC-MS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lavandulol/_A_L_liq-GC-MS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lavandulol/_A_L_liq-GC-MS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lavandulol/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lavandulol/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lavandulol/_A_L_liq-GC-MS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lav_ac/_A_LA_myc-GC-MS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lav_ac/_A_LA_myc-GC-MS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lav_ac/_A_LA_myc-GC-MS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lav_ac/_A_LA_liq-GC-MS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lav_ac/_A_LA_liq-GC-MS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lav_ac/_A_LA_myc-GC-MS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lav_ac/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lav_ac/
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_T33_MonoterpenoidsFungi/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lav_ac/_A_LA_liq-GC-MS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lav_ac/_A_LA_myc-GC-MS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lavandulol/_A_L_liq-GC-MS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T33_MonoterpenoidsFungi/_S_P5_SxF_lavandulol/_A_L_myc-GC-MS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T32_CandidateGeneExpressionTesting/_S_TransientLPPSCPPS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T32_CandidateGeneExpressionTesting/_S_TransientLPPSCPPS/_A_TransientCompLPPSCPPS-GCMS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T32_CandidateGeneExpressionTesting/_S_TransientLPPSCPPS/_A_TransientCompLPPSCPPS-GCMS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T24_phero/_S_P5_EAGresponse/_A_GC-MS-EAD-EAG/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T24_phero/_S_P5_EAGresponse/_A_GC-MS-EAD-EAG/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T24_phero/_S_P5_PhContentPlants/_A_PhCont_fr20-GC-MS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T24_phero/_S_P5_PhContentPlants/_A_PhCont_fr80-GC-MS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T24_phero/_S_P5_PhContentPlants/_A_PhCont_fr80-GC-MS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T24_phero/_S_P5_PhContentPlants/_A_PhCont_fresh-GC-MS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T24_phero/_S_P5_PhEmissionPlants/_A_emission_nontruncated-GC-MS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T24_phero/_S_P5_PhEmissionPlants/_A_emission_truncated-GC-MS/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T24_phero/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T24_phero/_S_P5_EAGresponse/_A_EAG_manual-EAG/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T24_phero/_S_P5_EAGresponse/_A_EAG_manual-EAG/
Creator: Marko Petek
Submitter: Marko Petek
