_S_P4_Pcitri_tr1tr2combo
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Short Name: P4_Pcitri_tr1tr2combo Title: Combining tr1 and tr2 P. citri de novo transcriptomes into one transcriptome set Description: Production of one set of transcripts that will be easier for the readers of the planned publication 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/1044
Projects: SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Contr...
Study position: 10
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Created: 16th May 2022 at 10:28
Last updated: 6th Nov 2024 at 15:25
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https://orcid.org/0000-0003-3644-7827PhD in Biotechnology, Research Associate at Department of Biotechnology and Systems Biology, National Institute of Biology
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
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
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
Files connected to study: _S_P4_Pcitri_tr1tr2combo
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_T31_mealybug
Study: _S_P4_Pcitri_tr1tr2combo
Short Name: 01_renameFASTA-Bioinfo Assay Class: DRY Assay Type: Bioinfo Title: Renaming tr1 and tr2 FASTA sequences Description: Renaming is neccessary to avoid duplicate sequence names pISA Assay creation date: 2021-12-16 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_tr1tr2combo
Short Name: 02_CDHIT-Bioinfo Assay Class: DRY Assay Type: Bioinfo Title: Combining tr1 and tr2 using CD-HIT-EST Description: Merging and removing redundant sequences (100% identical or contained) from the merged tr1 and tr2 set pISA Assay creation date: 2021-12-16 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_tr1tr2combo
Assay Class: DRY Assay Type: Bioinfo Title: Combining short read de novo transcriptome with IsoSeq Description: After first round of CDHIT to combine both versions of the denovo Pcitri transcriptome, CDHIT was run again to combine it with IsoSeq isoforms and perpare a consolidates transcriptomic sequence resource for P. citri pISA Assay creation date: 2022-07-01 pISA Assay creator: Mojca Jutersek Phenodata: ../../phenodata_20190523.txt Featuredata: Data: Principal investigator: Diego Orzaez ...
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_T31_mealybug
Study: _S_P4_Pcitri_tr1tr2combo
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_Pcitri_tr1tr2combo/_A_02_CDHIT-Bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_Pcitri_tr1tr2combo/_A_01_renameFASTA-Bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_Pcitri_tr1tr2combo/_A_02_CDHIT-Bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_Pcitri_tr1tr2combo/_A_03_CDHIT2-Bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_Pcitri_tr1tr2combo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_Pcitri_tr1tr2combo/_A_01_renameFASTA-Bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
Transcriptome sequences merged from de novo assembly and IsoSeq sequence data.
Creator: Mojca Juteršek
Submitter: Mojca Juteršek
Table with InterPro annotations, matches to Pcitri.v1 genome and differential expression between mated and virgin P.citri females for the transcripts in the consolidated P. citri transcriptome.
Creator: Mojca Juteršek
Submitter: Mojca Juteršek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_Pcitri_tr1tr2combo/_A_02_CDHIT-Bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_Pcitri_tr1tr2combo/_A_02_CDHIT-Bioinfo/
Creator: Marko Petek
Submitter: Marko Petek
