title: A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi.
abstract: 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.
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Timothy T
authors.initials: TT
authors.lastname: Perkins
authors.forename: Robert A
authors.initials: RA
authors.lastname: Kingsley
authors.forename: Maria C
authors.initials: MC
authors.lastname: Fookes
authors.forename: Paul P
authors.initials: PP
authors.lastname: Gardner
authors.forename: Keith D
authors.initials: KD
authors.lastname: James
authors.forename: Lu
authors.initials: L
authors.lastname: Yu
authors.forename: Samuel A
authors.initials: SA
authors.lastname: Assefa
authors.forename: Miao
authors.initials: M
authors.lastname: He
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Croucher
authors.forename: Derek J
authors.initials: DJ
authors.lastname: Pickard
authors.forename: Duncan J
authors.initials: DJ
authors.lastname: Maskell
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.forename: Jyoti
authors.initials: J
authors.lastname: Choudhary
authors.forename: Nicholas R
authors.initials: NR
authors.lastname: Thomson
authors.forename: Gordon
authors.initials: G
authors.lastname: Dougan
mesh_terms: D001426:Bacterial Proteins / Q000032:analysis; D018076:DNA, Complementary; D020869:Gene Expression Profiling; D040901:Proteomics; D012329:RNA, Bacterial / Q000032:analysis / Q000235:genetics; D012485:Salmonella typhi / Q000235:genetics*; D017423:Sequence Analysis, RNA
chemical_list: D001426:Bacterial Proteins; D018076:DNA, Complementary; D012329:RNA, Bacterial