Thursday, June 21, 2012

rRNA removal from insect RNA

Genomic analysis has greatly increased our understanding of bacterial-insect interactions. Yet there remains a need for effective methods to remove insect rRNA to enable comprehensive, transcriptome-based studies. In a recent publication, Kumar et al. investigated the performance of the Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) with insect samples. Eggs derived from a horizontal gene transfer of the Wolbachia bacterial genome into Drosophila ananassae were chosen as a model system. The authors performed paired-end RNA-Seq of untreated and Ribo-Zero-treated D. ananassae egg RNA using the Illumina® GAIIx system.

The authors conclude that the Ribo-Zero Kit (designed for human samples) efficiently removed >98% of D. ananassae rRNA from total RNA samples and that the Ribo-Zero-treated sample yielded a 6.2-fold increase in detection of mRNA transcripts. They further conclude that, based on their data, three times as many transcripts can be analyzed in a differential gene expression study that requires at least 100 reads per transcript. Finally, in D. ananassae, as in many insects, the 23S rRNA is naturally cleaved into two fragments. The Ribo-Zero treatment was found to efficiently remove both halves of the cleaved rRNA.

ResearchBlogging.orgKumar, N. et al. (2012). Efficient subtraction of insect rRNA prior to transcriptome analysis of
Wolbachia-Drosophila lateral gene transfer BMC Res Notes, 5 DOI: 10.1186/1756-0500-5-230

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