Assays

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 ...

Short Name: Node14610DmTP-EcoliExpr Assay Class: WET Assay Type: EcoliExpr Title: Candidate sequence from P. citri Node14610 without a predicted mitochondria targeting peptide Description: Expression in E. coli and activity testing pISA Assay creation date: 2019-05-20 pISA Assay creator: IG Candidate sequence gbk file (file path or link): _S_P4_expressionEcoli/reports/sequences/pMAL-c5XNode14610DmTP.gb Expression plasmid: pMAL-c5X Host E coli strain: BL21(DE3)pLysS Expression temperature: 30C ...

Short Name: Pc1599-EcoliExpr Assay Class: WET Assay Type: EcoliExpr Title: Candidate sequence from P. citri Pc1599 Description: Expression in E. coli and activity testing of Pc1599 pISA Assay creation date: 2019-07-01 pISA Assay creator: IG Candidate sequence gbk file (file path or link): _S_P4_expressionEcoli/reports/sequences/pMAL-c5XPc1599.gb Expression plasmid: pMAL-c5X Host E coli strain: BL21(DE3)pLysS Expression temperature: 30C Date of sample collection: 2019-07-02 Sample purification ...

Short Name: Pc23180-EcoliExpr Assay Class: WET Assay Type: EcoliExpr Title: Candidate sequence from P. citri Pc23180 Description: Expression in E. coli and activity testing of Pc23180 pISA Assay creation date: 2019-09-03 pISA Assay creator: IG Candidate sequence gbk file (file path or link): _S_P4_expressionEcoli/reports/sequences/pMAL-c5XPc23180.gb Expression plasmid: pMAL-c5X Host E coli strain: BL21(DE3)pLysS Expression temperature: 30C Date of sample collection: 2019-09-04 Sample purification ...

Files connected to investigation: _I_T31_mealybug

Files connected to study: _S_P3_expressionEcoli

Short Name: C98F-EcoliExpr Assay Class: WET Assay Type: EcoliExpr Title: C98F chimeric protein Description: Expression in E. coli and activity testing of C98F chimeric protein pISA Assay creation date: 2019-05-07 pISA Assay creator: IG Candidate sequence gbk file (file path or link): _S_P4_expressionEcoli/reports/sequences/C98F.gb Expression plasmid: pMAL-c5X Host E coli strain: BL21(DE3)pLysS Expression temperature: 30C Date of sample collection: 2019-05-08 Sample purification protocol (file ...

Assay: ASxPv12limmavoomDE-R Short Name: SxPv12limmavoomDE-R Assay Class: DRY Assay Type: R Title: Differential expression analysis of SxPv1.2 data in R Description: Difefrential expression analysis with limma-voom sript in R of total counts from mapping of SxPv1.2 reads to the NbV1 genome. pISA Assay creation date: 2021-11-10 pISA Assay creator: Mojca Juteršek Analyst: Mojca Juteršek Phenodata: ../../phenodata20191104.txt Featuredata: Data:

Short Name: 04_SxPv12_GeneSetEnrichment-RNAseg-GSEA Assay Class: DRY Assay Type: RNAseq-GSEA Title: GSEA of SxPv1.2 expression data Description: GSEA anaylysis with MapMan3 BINs as gene sets and SxPv1.2 logFC data. pISA Assay creation date: 2021-11-24 pISA Assay creator: Mojca Juteršek Phenodata: ../../phenodata_20191104.txt Featuredata: Data:

Files connected to study: _S_P4_SxP12-newG-DE

Short Name: 03_MapMan-visualisation Assay Class: DRY Assay Type: visualisation Title: Visualisation of DE SxP genes in MapMan. MapMan3 mapping as input. pISA Assay creation date: 2021-12-31 pISA Assay creator: Mojca Jutersek Phenodata: None Featuredata: Data: