_S_P4_Pcitri_genome

Actions

Order Assays

Overview
Related items

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

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: 168

Created: 16th May 2022 at 10:27

Last updated: 6th Nov 2024 at 15:25

Related items

People (1)
Programmes (1)
Projects (1)
Investigations (1)
Assays (5)
Data files (25)
Documents (53)

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.

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_Pcitri_genome-files

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

All creators

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

All creators

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

All creators

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

Snapshots: No snapshots

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

All creators

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

Snapshots: No snapshots

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

All creators

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