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A Strand-Specific RNA–Seq Analysis of the Transcriptome of the Typhoid Bacillus Salmonella Typhi
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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Next-generation transcriptome assembly
Martin, J. A., & Wang, Z. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3068 · Cited by 1,253
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Carstens, B. C., Pelletier, T. A., Reid, N. M., & Satler, J. D. (2013) · Molecular Ecology · doi:10.1111/mec.12413 · Cited by 1,248
Hydrogen peroxide sensing, signaling and regulation of transcription factors
Marinho, H. S., Real, C., Cyrne, L., Soares, H., & Antunes, F. (2014) · Redox Biology · doi:10.1016/j.redox.2014.02.006 · Cited by 850
Computational analysis of bacterial RNA-Seq data
McClure, R., Balasubramanian, D., Sun, Y., Bobrovskyy, M., Sumby, P., Genco, C. A., Vanderpool, C. K., & Tjaden, B. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt444 · Cited by 591
Metadata
- Authors
- 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.
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2009-07-17
- Volume
- 5
- Issue
- 7
- Pages
- e1000569
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- OpenAlex
- W1979622547
- Cited by
- 243
- References
- 4
- FWCI
- 17.47
- Type
- journal article
- Language
- en
- Open access
- gold
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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. https://doi.org/10.1371/journal.pgen.1000569
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