Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

Georgia Giannoukos, Dawn M. Ciulla, Katherine Huang, Brian J. Haas, Jacques Izard, Joshua Z. Levin, Jonathan Livny, Ashlee M. Earl, Dirk Gevers, Doyle V. Ward, Chad Nusbaum, Bruce W. Birren, Andreas Gnirke

Research output: Contribution to journalArticle

113 Citations (Scopus)

Abstract

We have developed a process for transcriptome analysis of bacterial communities that accommodates both intact and fragmented starting RNA and combines efficient rRNA removal with strand-specific RNA-seq. We applied this approach to an RNA mixture derived from three diverse cultured bacterial species and to RNA isolated from clinical stool samples. The resulting expression profiles were highly reproducible, enriched up to 40-fold for non-rRNA transcripts, and correlated well with profiles representing undepleted total RNA.

Original languageEnglish (US)
Article numberr23
JournalGenome biology
Volume13
Issue number3
DOIs
StatePublished - Mar 28 2012

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Transcriptome
transcriptome
RNA
Bacteria
bacterium
bacteria
Gene Expression Profiling
transcriptomics
bacterial communities
ribosomal RNA
fold
sampling

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

Cite this

Giannoukos, G., Ciulla, D. M., Huang, K., Haas, B. J., Izard, J., Levin, J. Z., ... Gnirke, A. (2012). Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Genome biology, 13(3), [r23]. https://doi.org/10.1186/gb-2012-13-3-r23

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. / Giannoukos, Georgia; Ciulla, Dawn M.; Huang, Katherine; Haas, Brian J.; Izard, Jacques; Levin, Joshua Z.; Livny, Jonathan; Earl, Ashlee M.; Gevers, Dirk; Ward, Doyle V.; Nusbaum, Chad; Birren, Bruce W.; Gnirke, Andreas.

In: Genome biology, Vol. 13, No. 3, r23, 28.03.2012.

Research output: Contribution to journalArticle

Giannoukos, G, Ciulla, DM, Huang, K, Haas, BJ, Izard, J, Levin, JZ, Livny, J, Earl, AM, Gevers, D, Ward, DV, Nusbaum, C, Birren, BW & Gnirke, A 2012, 'Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes', Genome biology, vol. 13, no. 3, r23. https://doi.org/10.1186/gb-2012-13-3-r23
Giannoukos, Georgia ; Ciulla, Dawn M. ; Huang, Katherine ; Haas, Brian J. ; Izard, Jacques ; Levin, Joshua Z. ; Livny, Jonathan ; Earl, Ashlee M. ; Gevers, Dirk ; Ward, Doyle V. ; Nusbaum, Chad ; Birren, Bruce W. ; Gnirke, Andreas. / Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. In: Genome biology. 2012 ; Vol. 13, No. 3.
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