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

Authors

Georgia Giannoukos, The Broad Institute of MIT and HarvardFollow
Dawn M. Ciulla, The Broad Institute of MIT and Harvard
Katherine Huang, The Broad Institute of MIT and Harvard
Brian J. Haas, The Broad Institute of MIT and Harvard
Jacques Izard, The Forsyth Institute & Infection and Immunity, Harvard School of Dental MedicineFollow
Joshua Z. Levin, The Broad Institute of MIT and Harvard
Jonathan Livny, The Broad Institute of MIT and Harvard
Ashlee M. Earl, The Broad Institute of MIT and Harvard
Dirk Gevers, The Broad Institute of MIT and Harvard
Doyle V. Ward, The Broad Institute of MIT and Harvard
Chad Nusbaum, The Broad Institute of MIT and Harvard
Bruce W. Birren, The Broad Institute of MIT and Harvard
Andreas Gnirke, The Broad Institute of MIT and Harvard

Date of this Version

3-28-2012

Citation

2012 Giannoukos et al.

Comments

Giannoukos et al. Genome Biology 2012, 13:r23 http://genomebiology.com/2012/13/3/r23

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.