A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi.
| Autor: | Timothy T Perkins, Robert A Kingsley, Maria C Fookes, Paul P Gardner, Keith D James, Lu Yu, Samuel A Assefa, Miao He, Nicholas J Croucher, Derek J Pickard, Duncan J Maskell, Julian Parkhill, Jyoti Choudhary, Nicholas R Thomson, Gordon Dougan |
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| Jazyk: | angličtina |
| Rok vydání: | 2009 |
| Předmět: | |
| Zdroj: | PLoS Genetics, Vol 5, Iss 7, p e1000569 (2009) |
| Druh dokumentu: | article |
| ISSN: | 1553-7390 1553-7404 |
| DOI: | 10.1371/journal.pgen.1000569 |
| Popis: | 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. |
| Databáze: | Directory of Open Access Journals |
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