Computational protocol: Transcriptome analysis of Vibrio parahaemolyticus in type III secretion system 1 inducing conditions

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Protocol publication

[…] Purified mRNA was used to prepare individually barcoded (indexed) RNA-Seq libraries with a TruSeq RNA Sample Prep kit (Illumina, Catalog #RS-122-2001). RNA-Seq libraries were sequenced on a MiSeq Benchtop Sequencer (Illumina Inc.) using version 2 chemistry and reads were base called with CASAVA1.8 pipeline (Illumina Inc.) to generate paired-ended 150-bp reads. The data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus (Edgar et al., ; Barrett et al., , ) and are accessible through GEO Series accession number GSE51423 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE51423). RNA sequence analysis was performed using CLC Genomics Workbench (version 6.0.5). Sequence data was mapped to reference genomes for V. parahaemolyticus strain RIMD 2210633 chromosomes 1 and 2 (NCBI Reference Sequence NC_004603.1 and NC_004605.1, respectively) (Makino et al., ). Mapping for RNA-Seq was allowed 20 additional upstream and downstream bases for each gene and a paired distance range of 0–300 bases. Up to two mismatches were allowed, with 90% alignment to the reference sequence and 80% similarity required for inclusion as a mapped read. […]

Pipeline specifications

Software tools BaseSpace, CLC Genomics Workbench
Databases GEO
Application RNA-seq analysis
Organisms Vibrio parahaemolyticus, Mus musculus
Diseases Foodborne Diseases, Gastroenteritis, Infection, Drug-Related Side Effects and Adverse Reactions