Assays

Files connected to study: _S_P4_Pcitri_tr1

Short Name: 05_DE_limma-R Assay Class: DRY Assay Type: R Title: DE analysis for Illumina reads mapped to P citri IsoSeq transcriptome Description: Differential expression analysis for Illumina RNA-Seq reads mapped to P citri IsoSeq transcriptome pISA Assay creation date: 2020-10-01 pISA Assay creator: MPE Analyst: MPE Phenodata: ../../phenodata_20190523.txt Featuredata: Data:

Short Name: 05_assembly1-rnaSPAdes Assay Class: DRY Assay Type: rnaSPAdes Title: P citri de-novo transcriptome assembly Description: P citri VF RNA-seq samples were assembled using rnaSPAdes assembler Phenodata: ../../phenodata_20181003.txt Featuredata: Data:

Short Name: 06_assembly1-IPS Assay Class: DRY Assay Type: IPS Title: Assembly1 InterProScan Description: InterProScan run for assembly1 transcripts. AA sequences were obtained by runing transeq and filtering to 3 longest ORFs per transcript. Phenodata: ../../phenodata_20181003.txt Featuredata: Data: ../_A_assembly1-rnaSPAdes/output/soft_filtered_transcripts.fasta

Short Name: 07_mapAs1ToGenome-STAR Assay Class: DRY Assay Type: STAR Title: Map Assembly1 transcripts to P citri reference genome Description: STARlong mapper was used to map de-novo assembled transcripts to P. citri reference genome. Phenodata: ../../phenodata_20181003.txt Featuredata: Data:

Files connected to study: _S_P4_Pcitri_IsoSeq

Short Name: 01_NGI-IsoSeq Assay Class: WET Assay Type: IsoSeq Title: Raw data and SMRTLink analysis performed by NGI Sweden Description: Data downloaded from NGI Sweden with analysis leading to polished high-quality full-length Iso-Seq isoforms pISA Assay creation date: 2020-09-18 pISA Assay creator: MPE Phenodata: ../../phenodata_20190523.txt Featuredata: Data: SRR15093694

Short Name: 02_cDNAcupcake-dry Assay Class: DRY Assay Type: dry Title: cDNA cupcake pipeline analysis of P. citri IsoSeq data Description: Pipeline with scripts for Iso-Seq after clustering step pISA Assay creation date: 2021-09-18 pISA Assay creator: MPE Phenodata: ../../phenodata_20190523.txt Featuredata: Data:

Short Name: 03-IPS Assay Class: DRY Assay Type: IPS Title: InterProScan for P citri unmapped transcripts Description: Prediction of ORF usning ANGEL (https://github.com/PacificBiosciences/ANGEL) and InterProScan Pfam domain search for all Iso-Seq isoforms that did not map to the P citri genome pISA Assay creation date: 2020-09-21 pISA Assay creator: MPE Phenodata: None Featuredata: Data:

Short Name: 04_mapIllumina-STAR Assay Class: DRY Assay Type: STAR Title: Mapping Illumina reads to P citri Iso-Seq transcriptome Description: Mapping and counting Illumina reads to P citri Iso-Seq transcriptome using STAR pISA Assay creation date: 2020-10-01 pISA Assay creator: MPE Phenodata: ../../phenodata_20190523.txt Featuredata: Data:

Files connected to study: _S_P4_Pcitri_genome_extSamples

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/

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:

Short Name: 01_mapToGenomeAll-STAR Assay Class: DRY Assay Type: STAR Title: Mapping all available Illumina RNA-Seq reads to the genome Description: Mapping and counting all available Illumina RNA-Seq reads to the genome using STAR pISA Assay creation date: 2019-12-04 pISA Assay creator: MPE Phenodata: ../../phenodata_20190523.txt Featuredata: Data:

Short Name: 02_mapToGenomeAll_limma-R Assay Class: DRY Assay Type: R Title: Differential gene expression analysis Description: Differential gene expression analysis in R using limma package pISA Assay creation date: 2019-12-16 pISA Assay creator: MPE Analyst: MPE Phenodata: ../../phenodata_20190523.txt Featuredata: Data:

Files connected to study: _S_P4_Pcitri_genome

Short Name: Terzyme-bioinfo Assay Class: DRY Assay Type: bioinfo Title: Terzyme analysis Description: Terzyme is a predictive algorithm for identification, classification and assignment of broad substrate unit to terpene synthase (TPS) and prenyl transferase (PT) enzymes. Data: pISA Assay creation date: 2018-11-23 pISA Assay creator: MPE Phenodata: None Featuredata: Data:

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: