_S_P4_Pcitri_tr1

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Investigation: _I_T3.1_mealybug project: _p_SUSPHIRE Short Name: P4_Pcitri_tr Title: P. citri transcriptome study Description: We are interested in certain mealybugs both because they are important pests and very difficult to control but because their sex pheromones are irregular terpenoids, which are (a) very cool molecules and (b) extremely difficult and expensive to make using chemistry.In our project, we will be doing comparative transcriptomics of virgin and mated females to attempt to identify the genes involved in the sex pheromone biosynthesis pathway. We are only interested in the genes for specific classes of enzymes; and we hope the data will be useful to others. Raw Data: GSE179660 Principal investigator: Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

SEEK ID: https://fairdomhub.org/studies/1043

Investigation: _I_T31_mealybug

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

Study position: 7

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Creators and Submitter

Creator

Marko Petek

Submitter

Marko Petek

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Views: 682

Created: 16th May 2022 at 10:27

Last updated: 6th Nov 2024 at 15:25

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People (1)
Programmes (1)
Projects (1)
Investigations (1)
Assays (6)
Data files (17)
Documents (45)

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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

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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

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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

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_I_T31_mealybug

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

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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

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

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_S_P4_Pcitri_tr1-files

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

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Marko Petek

Files connected to study: _S_P4_Pcitri_tr1

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T31_mealybug

Study: _S_P4_Pcitri_tr1

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_05_assembly1-rnaSPAdes

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

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Marko Petek

Short Name: 05_assembly1-rnaSPAdes Assay Class: DRY Assay Type: rnaSPAdes Title: P citri de-novo transcriptome assembly Description: P citri VF RNA-seq samples were assembled using rnaSPAdes assembler Phenodata: ../../phenodata_20181003.txt Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T31_mealybug

Study: _S_P4_Pcitri_tr1

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT, output/params.txt, scripts/Pcitri_assembly1_spades_commands.txt

Snapshots: No snapshots

Created: 16th May 2022 at 10:34, Last updated: 6th Nov 2024 at 15:25

_A_06_assembly1-IPS

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

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Marko Petek

Short Name: 06_assembly1-IPS Assay Class: DRY Assay Type: IPS Title: Assembly1 InterProScan Description: InterProScan run for assembly1 transcripts. AA sequences were obtained by runing transeq and filtering to 3 longest ORFs per transcript. Phenodata: ../../phenodata_20181003.txt Featuredata: Data: ../_A_assembly1-rnaSPAdes/output/soft_filtered_transcripts.fasta

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T31_mealybug

Study: _S_P4_Pcitri_tr1

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT, output/IPS_softfiltered_all/soft_filtered_trans..., scripts/Pcitri_assembly1_IPS_commands.txt

Snapshots: No snapshots

Created: 16th May 2022 at 10:34, Last updated: 6th Nov 2024 at 15:25

_A_07_mapAs1ToGenome-STAR

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

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Marko Petek

Short Name: 07_mapAs1ToGenome-STAR Assay Class: DRY Assay Type: STAR Title: Map Assembly1 transcripts to P citri reference genome Description: STARlong mapper was used to map de-novo assembled transcripts to P. citri reference genome. Phenodata: ../../phenodata_20181003.txt Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T31_mealybug

Study: _S_P4_Pcitri_tr1

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT, scripts/Pcitri_assembly1_STARlong_commands.txt

Snapshots: No snapshots

Created: 16th May 2022 at 10:34, Last updated: 6th Nov 2024 at 15:25

_A_08_mapReadsToAs1-STAR

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

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Marko Petek

Short Name: 08_mapReadsToAs1-STAR Assay Class: DRY Assay Type: STAR Title: Map RNAseq reads to de-novo assembly1 Description: STAR mapper was used to map back P citri RNA-Seq reads used for generation of the de-novo assembly1. Phenodata: ../../phenodata_20181003.txt Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T31_mealybug

Study: _S_P4_Pcitri_tr1

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT, scripts/Pcitri_assembly1_STAR_commands.txt

Snapshots: No snapshots

Created: 16th May 2022 at 10:34, Last updated: 6th Nov 2024 at 15:25

_A_09_As1_tr_limmaDE-R

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

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Marko Petek

Short Name: 09_As1_tr_limmaDE-R Assay Class: DRY Assay Type: R Title: Assembly1 transcripts differential expression analysis using limma voom package Description: Using output files of mapReadsToAs1 generated by STAR, the counts were analyzed for differential expression in R using limma voom approach. Analyst: MPE Phenodata: ../../phenodata_20190523.txt Featuredata: Data: ../_A_08_mapReadsToAs1-STAR/output

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T31_mealybug

Study: _S_P4_Pcitri_tr1

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT, output/PCA_PC1_top10genes.txt, output/PCA_PC2_top10genes.txt, output/P_citri_alldata_RNAseq_logFC_padj_TMMcpm..., output/P_citri_alldata_RNAseq_logFC_padj_TMMcpm..., output/Pcitri_tr1_counts_STAR_bothStr.txt

Snapshots: No snapshots

Created: 16th May 2022 at 10:35, Last updated: 6th Nov 2024 at 15:25

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