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

Georgia Giannoukos1*, Dawn M Ciulla1, Katherine Huang1, Brian J Haas1, Jacques Izard23, Joshua Z Levin1, Jonathan Livny1, Ashlee M Earl1, Dirk Gevers1, Doyle V Ward1, Chad Nusbaum1, Bruce W Birren1 and Andreas Gnirke1

Author affiliations

1 Genome Sequencing and Analysis Program, The Broad Institute of MIT and Harvard, 320 Charles Street and 301 Binney Street, Cambridge, MA 02141, USA

2 Department of Molecular Genetics, The Forsyth Institute, 245 First Street, Cambridge, MA 02142, USA

3 Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, 188 Longwood Ave, Boston, MA 02115, USA

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Citation and License

Genome Biology 2012, 13:r23  doi:10.1186/gb-2012-13-3-r23

Published: 28 March 2012


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.