input/Input_links.txt Version 1
_p_SUSPHIRE/_I_T31_mealybug/_S_P4_cand_all/_A_candidatemining-bioinfo/
SEEK ID: https://fairdomhub.org/data_files/5847?version=1
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input/Input_links.txt
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Candidates from the P. citri genome: O:\DEJAVNOSTI\OMIKE\pISA-Projects\_p_SUSPHIRE\_I_T3.1_mealybug\_S_P4_genomes\_A_IPS-bioinfo\input\Planococcus_citri_Pcitri.v0.braker.proteins.fa.interproscan.tsv O:\DEJAVNOSTI\OMIKE\pISA-Projects\_p_SUSPHIRE\_I_T3.1_mealybug\_S_P4_Pcitri_tr\_A_limma_min10counts-R\output\min10counts.xlsx O:\DEJAVNOSTI\OMIKE\pISA-Projects\_p_SUSPHIRE\_I_T3.1_mealybug\_S_P4_Pcitri_tr\_A_limma_min50counts-R\output\O:\DEJAVNOSTI\OMIKE\pISA-Projects\_p_SUSPHIRE\_I_T3.1_mealybug\_S_P4_Pcitri_tr\_A_limma_min50counts-R\output Candidates from the P. citri de novo transcriptome v1: O:\DEJAVNOSTI\OMIKE\pISA-Projects\_p_SUSPHIRE\_I_T3.1_mealybug\_S_P4_Pcitri_tr\_A_assembly1-IPS\output\IPS_softfiltered_all\soft_filtered_transcripts.pep.filtered.tsv O:\DEJAVNOSTI\OMIKE\pISA-Projects\_p_SUSPHIRE\_I_T3.1_mealybug\_S_P4_Pcitri_tr\_A_assembly1-IPS\output\transeq\soft_filtered_transcripts.pep.filtered O:\DEJAVNOSTI\OMIKE\pISA-Projects\_p_SUSPHIRE\_I_T3.1_mealybug\_S_P4_Pcitri_tr\_A_assembly1-rnaSPAdes\output\hard_filtered_transcripts.fasta O:\DEJAVNOSTI\OMIKE\pISA-Projects\_p_SUSPHIRE\_I_T3.1_mealybug\_S_P4_Pcitri_tr\_A_assembly1-rnaSPAdes\output\soft_filtered_transcripts.fasta O:\DEJAVNOSTI\OMIKE\pISA-Projects\_p_SUSPHIRE\_I_T3.1_mealybug\_S_P4_Pcitri_tr\_A_assembly1-rnaSPAdes\output\transcripts.fasta Candidates from the P. citri de novo transcriptome v2: O:\DEJAVNOSTI\OMIKE\pISA-Projects\_p_SUSPHIRE\_I_T3.1_mealybug\_S_P4_Pcitri_tr2\_A_01_assembly2-rnaSPAdes\output\soft_filtered_transcripts.fasta
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Created: 16th May 2022 at 10:41
Last updated: 6th Nov 2024 at 15:25
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Version 1 (earliest) Created 16th May 2022 at 10:41 by Marko Petek
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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
Short Name: P4_IDScandidates Title: Generation of the candidate list for cis and trans IDS enzymes from P. citri Description: From the P. citri genome and both de novo transcriptome assembly versions we mined homologues of trans(PF00348, IPR000092) and cis (PF01255, IPR001441) IDS enzymes Raw Data: Principal investigator: Špela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_T31_mealybug
Assays: _A_IDIsearch-Bioinfo, _A_MSA-bioinfo, _A_OtherMealybugCandidates-Alignment, _A_Strep_CLDS-bioinfo, _A_candidatemining-bioinfo, _A_smallIDSsubunit-motifs, _S_P4_cand_all-files
Short Name: candidatemining-bioinfo Assay Class: DRY Assay Type: bioinfo Title: Mining of IDS homologues from genome and de novo transcriptomes of P. citri Description: We selected homologues of cis and trans IDS enzymes in P. citri genome and both versions of the de novo transcriptome. Selection was done based on IPRscan results. pISA Assay creation date: 2019-06-05 pISA Assay creator: Mojca Jutersek 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_cand_all
