_S_P4_AdPathGenes

Actions

Order Assays

Overview
Related items

Short Name: P4_AdPathGenes Title: Additional search for genes involved in P citri sex pheromone production pathway Description: Search for additional pathway genes using coexpression etc Raw Data: Principal investigator: Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

SEEK ID: https://fairdomhub.org/studies/1037

Investigation: _I_T31_mealybug

Projects: SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Contr...

Study position: 3

Help

Tree Split Graph

Export PNG

Click below to download a copy of the image

Download

Creators and Submitter

Creator

Marko Petek

Submitter

Marko Petek

Activity

Views: 808

Created: 16th May 2022 at 10:26

Last updated: 6th Nov 2024 at 15:25

Related items

People (1)
Programmes (1)
Projects (1)
Investigations (1)
Assays (3)
Data files (29)
Documents (21)

Advanced People list for this Study with search and filtering

Marko Petek

Projects: pISA-tree, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, _p_RNAinVAL

Institutions: National Institute of Biology

https://orcid.org/0000-0003-3644-7827

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

PhD in Biotechnology, Research Associate at Department of Biotechnology and Systems Biology, National Institute of Biology

Advanced Programmes list for this Study with search and filtering

NIBSys

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

Advanced Projects list for this Study with search and filtering

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

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

Organisms: Planococcus citri, Nicotiana benthamiana, Penicillium chrysogenum

Advanced Investigations list for this Study with search and filtering

_I_T31_mealybug

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

All creators

Marko Petek

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

Snapshots: No snapshots

Created: 16th May 2022 at 10:26, Last updated: 6th Nov 2024 at 15:25

Advanced Assays list for this Study with search and filtering

_S_P4_AdPathGenes-files

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

All creators

Marko Petek

Files connected to study: _S_P4_AdPathGenes

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T31_mealybug

Study: _S_P4_AdPathGenes

Organisms: No organisms

SOPs: No SOPs

Data files: _STUDY_METADATA.TXT

Snapshots: No snapshots

Created: 16th May 2022 at 10:27, Last updated: 6th Nov 2024 at 15:25

_A_01-CoEXpNetViz_tr2-coexpr

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

All creators

Marko Petek

Short Name: 01-CoEXpNetViz_tr2-coexpr Assay Class: DRY Assay Type: coexpr Title: Using CoEXpNetViz to search P citri de novo tr2 Description: We used bait genes of mevalonate pathway to try to find other pathway members pISA Assay creation date: 2019-11-21 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20190523.txt Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T31_mealybug

Study: _S_P4_AdPathGenes

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT, input/Mevalonate_blasting.txt, input/bait_genes.txt, input/gene_expression_matrix_link.txt, output/network/P_citri_alldata_RNAseq_TMMcpms.t..., output/network/P_citri_alldata_RNAseq_TMMcpms.t..., output/network/P_citri_alldata_RNAseq_TMMcpms.t..., output/network/README.txt, output/network/correlations_per_family.txt

Snapshots: No snapshots

Created: 16th May 2022 at 10:31, Last updated: 6th Nov 2024 at 15:25

_A_02-CoEXpNetViz_gen-coexpr

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

All creators

Marko Petek

Short Name: 02-CoEXpNetViz_gen-coexpr Assay Class: DRY Assay Type: coexpr Title: Using CoEXpNetViz to search P citri genome Description: We used bait genes of mevalonate pathway encoded in the genome to try to find other pathway members pISA Assay creation date: 2019-11-21 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20190523.txt Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T31_mealybug

Study: _S_P4_AdPathGenes

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT, input/IPS_extract.P_citri.v0.braker.txt, input/Mevalonate_blasting.txt, input/Mevalonate_pathway_candidates.xlsx, input/Mevalonate_pathway_candidates_updated.xlsx, input/bait_genes.txt, input/gene_expression_matrix_link.txt, output/network_up5down5percent/interesting_gene..., output/network_up5down5percent/network/P_citri_..., output/network_up5down5percent/network/P_citri_..., output/network_up5down5percent/network/P_citri_..., output/network_up5down5percent/network/README.txt, output/network_up5down5percent/network/correlat..., output/network_upper1percent/P_citri_RNAseq_log..., output/network_upper1percent/network/P_citri_RN..., output/network_upper1percent/network/P_citri_RN..., output/network_upper1percent/network/P_citri_RN..., output/network_upper1percent/network/README.txt, output/network_upper1percent/network/correlatio...