Assays

Short Name: 04_mapReadsToAs2-STAR Assay Class: DRY Assay Type: STAR Title: Map RNAseq reads to de-novo assembly2 Description: STAR mapper was used to map back P citri RNAseq reads used for generation the de-novo assembly2. pISA Assay creation date: 2019-05-24 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20190523.txt Featuredata: Data:

Short Name: 05_As2_tr_limmaDE-R Assay Class: DRY Assay Type: R Title: Assembly2 transcripts differential expression analysis using limma voom package Description: Using output files of mapReadsToAss2 by STAR the counts were analyzed for differential expression in R using limma voom approach. pISA Assay creation date: 2019-06-19 pISA Assay creator: MPE Analyst: MPE Phenodata: ../../phenodata_20190523.txt Featuredata: Data: ../_A_04_mapReadsToAs2-STAR/output/*.counts

Files connected to study: _S_P4_Pcitri_tr2

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:

Short Name: 01_assembly2-rnaSPAdes Assay Class: DRY Assay Type: rnaSPAdes Title: P citri de-novo transcriptome assembly 2 Description: P citri de-novo transcriptome assembly using SUSPHIRE and mealybug.org RNA-seq datasets pISA Assay creation date: 2019-05-24 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20190523.txt Featuredata: Data:

Short Name: 02_assembly2-IPS Assay Class: DRY Assay Type: IPS Title: Assembly2 InterProScan Description: InterProScan run for de-novo assembly2 transcripts. AA sequences were obtained by runing transeq and filtering to 3 longest ORFs per transcript. pISA Assay creation date: 2019-05-24 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20190523.txt Featuredata: Data: ../_A_01_assembly2-rnaSPAdes/output/soft_filtered_transcripts.fasta

Short Name: 03_mapAs2ToGenome-STAR Assay Class: DRY Assay Type: STAR Title: Mapping assembly2 transcripts to P citri genome Description: Mapping de novo assembled transcripts from SUSPHIRE and Ediburgh RNA-Seq datasets (assembly2) to P citri genome using STARlong. MatchAnnot also run. pISA Assay creation date: 2019-06-19 pISA Assay creator: MPE Phenodata: ../../phenodata_20190523.txt Featuredata: Data:

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 ...

Files connected to study: _S_P4_Pcitri_tr1tr2combo

Short Name: 08_mapReadsToAs1-STAR Assay Class: DRY Assay Type: STAR Title: Map RNAseq reads to de-novo assembly1 Description: STAR mapper was used to map back P citri RNA-Seq reads used for generation of the de-novo assembly1. Phenodata: ../../phenodata_20181003.txt Featuredata: Data:

Short Name: 09_As1_tr_limmaDE-R Assay Class: DRY Assay Type: R Title: Assembly1 transcripts differential expression analysis using limma voom package Description: Using output files of mapReadsToAs1 generated by STAR, the counts were analyzed for differential expression in R using limma voom approach. Analyst: MPE Phenodata: ../../phenodata_20190523.txt Featuredata: Data: ../_A_08_mapReadsToAs1-STAR/output

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:

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: