A Strand-Specific RNA-Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi

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Perkins, TT; Kingsley, RA; Fookes, MC; Gardner, PP; James, KD; Yu, L; Assefa, SA; He, M; Croucher, NJ; Pickard, DJ; ...Date
2009-07-01Source Title
PLoS GeneticsPublisher
PUBLIC LIBRARY SCIENCEUniversity of Melbourne Author/s
Dougan, GordonAffiliation
Microbiology and ImmunologyMetadata
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Perkins, 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 Status
Open AccessAbstract
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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