A Strand-Specific RNA-Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi
AuthorPerkins, TT; Kingsley, RA; Fookes, MC; Gardner, PP; James, KD; Yu, L; Assefa, SA; He, M; Croucher, NJ; Pickard, DJ; ...
Source TitlePLoS Genetics
PublisherPUBLIC LIBRARY SCIENCE
University of Melbourne Author/sDougan, Gordon
AffiliationMicrobiology and Immunology
Document TypeJournal Article
CitationsPerkins, T. T., Kingsley, R. A., Fookes, M. C., Gardner, P. P., James, K. D., Yu, L., Assefa, S. A., He, M., Croucher, N. J., Pickard, D. J., Maskell, D. J., Parkhill, J., Choudhary, J., Thomson, N. R. & Dougan, G. (2009). A Strand-Specific RNA-Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi. PLOS GENETICS, 5 (7), https://doi.org/10.1371/journal.pgen.1000569.
Access StatusOpen Access
High-density, strand-specific cDNA sequencing (ssRNA-seq) was used to analyze the transcriptome of Salmonella enterica serovar Typhi (S. Typhi). By mapping sequence data to the entire S. Typhi genome, we analyzed the transcriptome in a strand-specific manner and further defined transcribed regions encoded within prophages, pseudogenes, previously un-annotated, and 3'- or 5'-untranslated regions (UTR). An additional 40 novel candidate non-coding RNAs were identified beyond those previously annotated. Proteomic analysis was combined with transcriptome data to confirm and refine the annotation of a number of hpothetical genes. ssRNA-seq was also combined with microarray and proteome analysis to further define the S. Typhi OmpR regulon and identify novel OmpR regulated transcripts. Thus, ssRNA-seq provides a novel and powerful approach to the characterization of the bacterial transcriptome.
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