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

High-density, strand-specific cDNA sequencing (ssRNA�Cseq) 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�Cseq was also combined with microarray and proteome analysis to further define the S. Typhi OmpR regulon and identify novel OmpR regulated transcripts. Thus, ssRNA�Cseq provides a novel and powerful approach to the characterization of the bacterial transcriptome.