Assays

Short Name: TPS_phy-bioinfo Assay Class: DRY Assay Type: bioinfo Title: Terpene synthases phylogeny Description: Philogenetica analysis with ClustalOmega and Phylogeny.fr web service pipeline pISA Assay creation date: 2018-11-23 pISA Assay creator: MPE Phenodata: None Featuredata: Data:

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/

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/

Files connected to study: _S_P4_cand_genomic

Short Name: g14825_recon-bioinfo Assay Class: DRY Assay Type: bioinfo Title: TPS gene g14825 reconstruction Description: Reconstruction of g14825 exon structure by checking RNA-seq mapped reads vs the genome-predicted gene model pISA Assay creation date: 2018-11-23 pISA Assay creator: MPE Phenodata: ../../phenodata_20181003.txt Data: /FITO_ws/markop/pcitri_bam Genome reference files: ../../_S_P4_Pcitri_tr/_A_RNAseq-CLC/input/

Short Name: IPS-bioinfo Assay Class: DRY Assay Type: bioinfo Title: InterProScan results analysis Description: Anaylsis of IPS results pISA Assay creation date: 2018-11-23 pISA Assay creator: MPE Phenodata: None Featuredata: Data:

Short Name: MAST-bioinfo Assay Class: DRY Assay Type: bioinfo Title: Search for MEME motif in proteome of P. citri Description: Using MEME software to look for motifs in proteins that resemble those found in plants producing similar compounds to mealybug sex pheromones pISA Assay creation date: 2018-11-23 pISA Assay creator: MPE Phenodata: None Featuredata: Data:

Short Name: MEME-bioinfo Assay Class: DRY Assay Type: bioinfo Title: Finding motifs in candidate protein sequences using MEME Description: Using MEME software to look for motifs in proteins that resemble those found in plants producing similar compounds to mealybug sex pheromones pISA Assay creation date: 2018-11-23 pISA Assay creator: MPE Phenodata: None Featuredata: Data:

Short Name: IDIsearch-Bioinfo Assay Class: DRY Assay Type: Bioinfo Title: Search of IDI candidates from Pcitri sequences Description: Identifying isopentenyl isomerase candidate genes from genomic and transcriptomic sequences of Pcitri. pISA Assay creation date: 2021-12-31 pISA Assay creator: Mojca Jutersek Phenodata: None Featuredata: Data:

Short Name: MSA-bioinfo Assay Class: DRY Assay Type: bioinfo Title: Multiple sequence alignment of cis and trans candidate IDS Description: MSA and phylogenetic analysis of candidates in MEGA pISA Assay creation date: 2019-06-05 pISA Assay creator: Mojca Jutersek Phenodata: ../../phenodata_20190523.txt Featuredata: Data:

Short Name: OtherMealybugCandidates-Alignment Assay Class: DRY Assay Type: Alignment Title: Alignment of other mealybug candidate enzymes Description: We created alignments and phylogenetic trees of P. citri IDS candidates with IDS homologs mined from the genomes of two other species: Planococcus ficus and Planococcus longispinus, to determine which of the candidates are evolutionarily conserved and their phylogenetic relationships among the three species. pISA Assay creation date: 2021-03-02 ...

Short Name: smallIDSsubunit-motifs Assay Class: DRY Assay Type: motifs Title: Search for P. citri homologs of small IDS subunits Description: Since in plants, some IDS enzymes require a small non-catalytical subunit for their functioning, we decided to determine, whether we could find homologs of such proteins in P. citri sequences and test them in combination with IDS candidates. We performed a motif search in the P.citri proteome. pISA Assay creation date: 2021-04-13 pISA Assay creator: MJU ...

Short Name: Strep_CLDS-bioinfo Assay Class: DRY Assay Type: bioinfo Title: Search for Streptomyces CLDS homologue in the generated transcriptomes of P. citri Description: Using BLAST to seqrch for homologues of Streptomyces Cyclolavandulyl diphosphate synthase in P. citri transsctiptome tr1 and tr2 pISA Assay creation date: 2019-12-30 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20181003.txt Featuredata: Data:

Files connected to study: _S_P4_AdPathGenes

Files connected to study: _S_P4_cand_all

Short Name: 01-CoEXpNetViz_tr2-coexpr Assay Class: DRY Assay Type: coexpr Title: Using CoEXpNetViz to search P citri de novo tr2 Description: We used bait genes of mevalonate pathway to try to find other pathway members pISA Assay creation date: 2019-11-21 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20190523.txt Featuredata: Data:

Short Name: 02-CoEXpNetViz_gen-coexpr Assay Class: DRY Assay Type: coexpr Title: Using CoEXpNetViz to search P citri genome Description: We used bait genes of mevalonate pathway encoded in the genome to try to find other pathway members pISA Assay creation date: 2019-11-21 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20190523.txt Featuredata: Data:

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:

Short Name: Trans2-EcoliExpr Assay Class: WET Assay Type: EcoliExpr Title: Candidate sequence from P. citri Trans2 Description: Expression in E. coli and activity testing of Trans2 pISA Assay creation date: 2020-11-04 pISA Assay creator: IG Candidate sequence gbk file (file path or link): _S_P4_expressionEcoli/reports/sequences/pCR-BluntTrans02_2.gb Expression plasmid: pMAL-c5X Host E coli strain: BL21(DE3)pLysS Expression temperature: 30C Date of sample collection: 2020-11-05 Sample purification ...

Short Name: Trans39-EcoliExpr Assay Class: WET Assay Type: EcoliExpr Title: Candidate sequence from P. citri Trans39 Description: Expression in E. coli and activity testing of Trans39 pISA Assay creation date: 2020-11-08 pISA Assay creator: IG Candidate sequence gbk file (file path or link): _S_P4_expressionEcoli/reports/sequences/pCR-BluntTrans39_3.gb Expression plasmid: pMAL-c5X Host E coli strain: BL21(DE3)pLysS Expression temperature: 30C Date of sample collection: 2020-11-09 Sample purification ...

Short Name: Trans57-EcoliExpr Assay Class: WET Assay Type: EcoliExpr Title: Candidate sequence from P. citri Trans57 Description: Expression in E. coli and activity testing of PcTrans57 pISA Assay creation date: 2020-11-25 pISA Assay creator: IG Candidate sequence gbk file (file path or link): _S_P4_expressionEcoli/reports/sequences/pMAL-c5Xtrans57.gb Expression plasmid: pMAL-c5X Host E coli strain: BL21(DE3)pLysS Expression temperature: 30C Date of sample collection: 2020-11-26 Sample purification ...

Short Name: Trans64-EcoliExpr Assay Class: WET Assay Type: EcoliExpr Title: Candidate sequence from P. citri Trans64 Description: Expression in E. coli and activity testing of Trans64 pISA Assay creation date: 2020-11-04 pISA Assay creator: IG Candidate sequence gbk file (file path or link): _S_P4_expressionEcoli/reports/sequences/pCR-Blunttrans64.gb Expression plasmid: pMAL-c5X Host E coli strain: BL21(DE3)pLysS Expression temperature: 30C Date of sample collection: 2020-11-05 Sample purification ...

Short Name: Trans94-EcoliExpr Assay Class: WET Assay Type: EcoliExpr Title: Candidate sequence from P. citri Trans94 Description: Expression in E. coli and activity testing of Trans94 pISA Assay creation date: 2020-08-04 pISA Assay creator: IG Candidate sequence gbk file (file path or link): _S_P4_expressionEcoli/reports/sequences/pMAL-c5Xtrans94.gb Expression plasmid: pMAL-c5X Host E coli strain: BL21(DE3)pLysS Expression temperature: 30C Date of sample collection: 2020-08-05 Sample purification ...

Short Name: Pc2704-EcoliExpr Assay Class: WET Assay Type: EcoliExpr Title: Candidate sequence from P. citri Pc2704 Description: Expression in E. coli and activity testing of Pc2704 pISA Assay creation date: 2019-06-05 pISA Assay creator: IG Candidate sequence gbk file (file path or link): _S_P4_expressionEcoli/reports/sequences/pMAL-c5XPc2704.gb Expression plasmid: pMAL-c5X Host E coli strain: BL21(DE3)pLysS Expression temperature: 30C Date of sample collection: 2019-06-06 Sample purification ...

Short Name: Pc32607-EcoliExpr Assay Class: WET Assay Type: EcoliExpr Title: Candidate sequence from P. citri Pc32607 Description: Expression in E. coli and activity testing of Pc32607 pISA Assay creation date: 2019-05-30 pISA Assay creator: IG Candidate sequence gbk file (file path or link): _S_P4_expressionEcoli/reports/sequences/pMAL-c5XPc32607.gb Expression plasmid: pMAL-c5X Host E coli strain: BL21(DE3)pLysS Expression temperature: 30C Date of sample collection: 2019-05-31 Sample purification ...

Short Name: Pc7366II-EcoliExpr Assay Class: WET Assay Type: EcoliExpr Title: Candidate sequence from P. citri Pc7366II Description: Expression in E. coli and activity testing of Pc7366II pISA Assay creation date: 2020-01-29 pISA Assay creator: IG Candidate sequence gbk file (file path or link): _S_P4_expressionEcoli/reports/sequences/pMAL-c5x_Pc7366II_sequenced..gb Expression plasmid: pMAL-c5X Host E coli strain: BL21(DE3)pLysS Expression temperature: 30C Date of sample collection: 2020-01-30 ...

Short Name: PcCis24-EcoliExpr Assay Class: WET Assay Type: EcoliExpr Title: Candidate sequence from P. citri Description: Expression in E. coli and activity testing of PcCis24 pISA Assay creation date: 2020-07-08 pISA Assay creator: IG Candidate sequence gbk file (file path or link): _S_P4_expressionEcoli/reports/sequences/pMAL-c5Xcis24.gb Expression plasmid: pMAL-c5X Host E coli strain: BL21(DE3)pLysS Expression temperature: 18 Date of sample collection: 2020-07-09 Sample purification protocol ...

Short Name: Trans1153-EcoliExpr Assay Class: WET Assay Type: EcoliExpr Title: Candidate sequence from P. citri Trans1153 Description: Expression in E. coli and activity testing of Trans1153 pISA Assay creation date: 2019-08-13 pISA Assay creator: IG Candidate sequence gbk file (file path or link): _S_P4_expressionEcoli/reports/sequences/pMAL-c5Xtrans1153.gb Expression plasmid: pMAL-c5X Host E coli strain: BL21(DE3)pLysS Expression temperature: 30C Date of sample collection: 2019-08-14 Sample ...

Short Name: MeUppS-EcoliExpr Assay Class: WET Assay Type: EcoliExpr Title: Candidate sequence from Moranella endobia Description: Expression in E. coli and activity testing pISA Assay creation date: 2020-07-01 pISA Assay creator: IG Candidate sequence gbk file (file path or link): _S_P4_expressionEcoli/reports/sequences/pMAL-c5XMeUppS.gb Expression plasmid: pMAL-c5X Host E coli strain: BL21(DE3)pLysS Expression temperature: 30 Date of sample collection: 2020-07-02 Sample purification protocol ...

Short Name: Node14610-EcoliExpr Assay Class: WET Assay Type: EcoliExpr Title: A candidate sequence from P. citri Node14610 Description: Expression in E. coli and activity testing of Node14610 pISA Assay creation date: 2019-05-14 pISA Assay creator: IG Candidate sequence gbk file (file path or link): _S_P4_expressionEcoli/reports/sequences/pMAL-c5XNode14610.gb Expression plasmid: pMAL-c5X Host E coli strain: BL21(DE3)pLysS Expression temperature: 30C Date of sample collection: 2019-05-15 Sample ...