_S_P4_Pcitri_IsoSeq

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Short Name: P4_Pcitri_IsoSeq Title: P citri Iso-Seq transcriptome generation and search for new sex pheromone biosynthesis genes Description: PacBio IsoSeq transcriptome sequencing and data analysis Raw Data: SRR15093694 Principal investigator: Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

SEEK ID: https://fairdomhub.org/studies/1042

Investigation: _I_T31_mealybug

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

Study position: 9

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Creators and Submitter

Creator

Marko Petek

Submitter

Marko Petek

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Views: 765

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 (30)
Documents (63)

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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_IsoSeq-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_IsoSeq

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T31_mealybug

Study: _S_P4_Pcitri_IsoSeq

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_NGI-IsoSeq

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

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Marko Petek

Short Name: 01_NGI-IsoSeq Assay Class: WET Assay Type: IsoSeq Title: Raw data and SMRTLink analysis performed by NGI Sweden Description: Data downloaded from NGI Sweden with analysis leading to polished high-quality full-length Iso-Seq isoforms pISA Assay creation date: 2020-09-18 pISA Assay creator: MPE Phenodata: ../../phenodata_20190523.txt Featuredata: Data: SRR15093694

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T31_mealybug

Study: _S_P4_Pcitri_IsoSeq

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, output/pt_025_001.flnc.report.csv.zip, output/pt_025_001.unpolished.cluster_report.csv...

Snapshots: No snapshots

Created: 16th May 2022 at 10:33, Last updated: 6th Nov 2024 at 15:25

_A_02_cDNAcupcake-dry

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

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Marko Petek

Short Name: 02_cDNAcupcake-dry Assay Class: DRY Assay Type: dry Title: cDNA cupcake pipeline analysis of P. citri IsoSeq data Description: Pipeline with scripts for Iso-Seq after clustering step pISA Assay creation date: 2021-09-18 pISA Assay creator: MPE 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_Pcitri_IsoSeq

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, input/pt_025_001.flnc.report.csv.zip, input/pt_025_001.summary.csv, input/pt_025_001.unpolished.cluster_report.csv.zip, output/Pcitri.collapsed.abundance.txt, output/Pcitri.collapsed.filtered.abundance.txt, output/Pcitri.collapsed.filtered.rep.fa.seqleng..., output/Pcitri.collapsed.filtered.rep.fa.stats.txt, output/Pcitri.collapsed.group.txt, output/Pcitri.collapsed.group.txt.unfuzzy, output/Pcitri.collapsed.read_stat.txt.zip, output/Pcitri.ignored_ids.txt, reports/NGI_ProjectInfo.txt, scripts/Pcitri_IsoSeq_cDNAcupcake_commands.txt, scripts/download_from_NGI.txt

Snapshots: No snapshots

Created: 16th May 2022 at 10:33, Last updated: 6th Nov 2024 at 15:25

_A_03-IPS

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

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Marko Petek

Short Name: 03-IPS Assay Class: DRY Assay Type: IPS Title: InterProScan for P citri unmapped transcripts Description: Prediction of ORF usning ANGEL (https://github.com/PacificBiosciences/ANGEL) and InterProScan Pfam domain search for all Iso-Seq isoforms that did not map to the P citri genome pISA Assay creation date: 2020-09-21 pISA Assay creator: MPE Phenodata: None Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T31_mealybug

Study: _S_P4_Pcitri_IsoSeq

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, output/Pcitri.IsoSeq_nonred.dumb.pep.rmstar.tsv, output/Pcitri.ignored_ids.dumb.final.pep.rmstar..., reports/Pcitri.ignored_ids.dumb.final.pep.rmsta..., scripts/IsoSeq_ANGEL_IPS_commands.txt

Snapshots: No snapshots

Created: 16th May 2022 at 10:33, Last updated: 6th Nov 2024 at 15:25

_A_04_mapIllumina-STAR

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

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Marko Petek

Short Name: 04_mapIllumina-STAR Assay Class: DRY Assay Type: STAR Title: Mapping Illumina reads to P citri Iso-Seq transcriptome Description: Mapping and counting Illumina reads to P citri Iso-Seq transcriptome using STAR pISA Assay creation date: 2020-10-01 pISA Assay creator: MPE 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_Pcitri_IsoSeq

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, scripts/Pcitri_map_Illumina_to_IsoSeq_commands.txt

Snapshots: No snapshots

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

_A_05_DE_limma-R

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

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Marko Petek

Short Name: 05_DE_limma-R Assay Class: DRY Assay Type: R Title: DE analysis for Illumina reads mapped to P citri IsoSeq transcriptome Description: Differential expression analysis for Illumina RNA-Seq reads mapped to P citri IsoSeq transcriptome pISA Assay creation date: 2020-10-01 pISA Assay creator: MPE Analyst: MPE 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_Pcitri_IsoSeq

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, output/P_citri_IlluminaToIsoSeq_logFC_padj_TMMc..., output/Pcitri_IlluminaMapToIsoSeq_counts_STAR_b..., reports/P_citri_IlluminaToIsoSeq_logFC_padj_TMM...

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

Showing 20 out of a possible 30 Data files Advanced Data files list for this Study with search and filtering