_S_P4_Pcitri_genome

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Short Name: P4_Pcitri_genome Title: P. citri SUSPHIRE samples mapping to genome and differential gene expression analysis Description: Illumina reads from virgin and mated female Pcitri samples were mapped to P. citri genome available at mealybug.org (ensembl) Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes

SEEK ID: https://fairdomhub.org/studies/1040

Investigation: _I_T31_mealybug

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

Study position: 2

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Creators and Submitter

Creator

Marko Petek

Submitter

Marko Petek

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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 (5)
Data files (25)
Documents (53)

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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_genome-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_genome

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T31_mealybug

Study: _S_P4_Pcitri_genome

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_RNAseq-CLC

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

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Marko Petek

Short Name: 01_RNAseq-CLC Assay Class: DRY Assay Type: CLC Title: RNA-Seq analysis of mealybug samples from virgin and mated females Description: Mapping reads to P. citri draft genome using CLC Genomics Workbench Phenodata: ../../phenodata_20181003.txt Creation date: 2018-11-15 Data: http://stork/dirindex/fitostorage/datarepo/ngs_omics/NGS_pci_rna-seq_2018_mpe_Pcitri/data/ Genome reference files: ./input/

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T31_mealybug

Study: _S_P4_Pcitri_genome

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, output/Expression Browser.txt, output/bam_link.txt, output/trimmed_reads_link.txt

Snapshots: No snapshots

Created: 16th May 2022 at 10:32, Last updated: 6th Nov 2024 at 15:25

_A_02_limma-R

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

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Marko Petek

Short Name: 02_limma_min50counts-R Assay Class: DRY Assay Type: R Title: Statistical RNA-Seq analysis in R Description: Statistical analysis using only unique counts using limma-voom in R Phenodata: ../../phenodata_20181003.txt Creation date: 2018-11-15 Data: ./input/

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T31_mealybug

Study: _S_P4_Pcitri_genome

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, input/Expression Browser.txt, output/PCA_PC1_top10genes.txt, output/PCA_PC2_top10genes.txt, output/P_citri_RNAseq_logFC_padj_counts.txt, output/P_citri_RNAseq_logFC_padj_counts.xlsx

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

_A_03_limma_min50counts-R

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

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Marko Petek

Short Name: 03_limma_min50counts-R Assay Class: DRY Assay Type: R Title: Second run of limma-voom pipeline Description: Second run of limma-voom pipeline where 50 counts in at least 3 samples were required for the gene to be included in the analysis Phenodata: ../../phenodata_20181003.txt Creation date: 2018-11-15 Data: ../_A_limma-R/input/

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T31_mealybug

Study: _S_P4_Pcitri_genome

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, output/PCA_PC1_top10genes.txt, output/PCA_PC2_top10genes.txt, output/P_citri_RNAseq_logFC_padj_counts.txt, output/P_citri_RNAseq_logFC_padj_counts_min50.xlsx, output/P_citri_RNAseq_logFC_padj_counts_min50_c..., output/Pcitri_RNAseq_lcpms.txt

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

_A_04_limma_min10counts-R

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

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Marko Petek

Short Name: 04_limma_min10counts-R Assay Class: DRY Assay Type: R Title: limma-voom pipeline in R with min 10 counts in at least 3 rows Description: We tried this to see if we were missing something with min 50 counts, but nothing of much interest was discovered. Analyst: MojcaJ 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_genome

Organisms: No organisms

SOPs: No SOPs

Data files: _Assay_METADATA.TXT, input/Expression Browser.txt, output/PCA_PC1_top10genes.txt, output/PCA_PC2_top10genes.txt, output/P_citri_RNAseq_logFC_padj_min10_counts.txt, output/min10counts.xlsx, scripts/limmavoom_min10.txt

Snapshots: No snapshots

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

Showing 20 out of a possible 25 Data files Advanced Data files list for this Study with search and filtering