Efficient and Robust RNA-seq Process for Cultured Bacteria and Complex Community Transcriptomes

Authors

Georgia Giannoukos, Broad Institute of the Massachusetts Institute of Technology and Harvard UniversityFollow
Dawn M. Ciulla, Broad Institute of the Massachusetts Institute of Technology and Harvard University
Katherine Huang, Broad Institute of the Massachusetts Institute of Technology and Harvard University
Brian J. Haas, Broad Institute of the Massachusetts Institute of Technology and Harvard University
Jacques Izard, Forsyth Institute and Harvard UniversityFollow
Joshua Z. Levin, Broad Institute of the Massachusetts Institute of Technology and Harvard University
Jonathan Livny, Broad Institute of the Massachusetts Institute of Technology and Harvard University
Ashlee M. Earl, Broad Institute of the Massachusetts Institute of Technology and Harvard University
Dirk Gevers, Broad Institute of the Massachusetts Institute of Technology and Harvard University
Doyle V. Ward, Broad Institute of the Massachusetts Institute of Technology and Harvard University
Chad Nusbaum, Broad Institute of the Massachusetts Institute of Technology and Harvard University
Bruce W. Birren, Broad Institute of the Massachusetts Institute of Technology and Harvard University
Andreas Gnirke, Broad Institute of the Massachusetts Institute of Technology and Harvard University

ORCID IDs

Izard https://orcid.org/0000-0002-5904-5436

Document Type

Article

Date of this Version

2012

Citation

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.