A Team of researchers at the Broad Institute set out to establish a robust and scalable RNA-seq process applicable to cultured bacteria as well as to complex community transcriptomes.
They determined that an effective process should:
a) reduce rRNA sequences to very low levels
b) accurately maintain relative representation of transcript sequences
c) be equally successful for any species
d) work well with RNA of varying quality
e) be highly reproducible
Their resulting process does accommodate both intact and fragmented starting RNA and combines efficient rRNA removal with strand-specific RNA-seq. Application of this approach to an RNA mixture derived from three diverse cultured bacterial species and to RNA isolated from clinical samples resulted in highly reproducible expression profiles that correlated well with profiles representing undepleted total RNA.
- 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 Biol 13(3), R23. [article]