Thursday, January 6, 2011

Enhanced mapping of the C. elegans transcriptome through multiple RNA-Seq techniques

In a recent publication, Lamm et al. demonstrated the use of Epicentre’s CircLigase ssDNA Ligase for template generation in high-throughput RNA-Seq applications. The authors used a combination of three high-throughput RNA capture and sequencing methods to refine and augment the transcriptome map of Caenorhabditis elegans. The CircLigase method relies on RNA fragmentation, poly(A) tailing, and oligo(dT)-based hybrid capture to generate a cDNA that can be recircularized and PCR-amplified for high-throughput sequencing. The other two methods involved single-strand RNA ligation, and double-stranded cDNA linker ligation.

The authors found that each RNA-Seq approach shows specific limitations and biases, and the use of multiple methods provided a more complete map than was obtained from any single method. They also note the advantages of CircLigase-based and ssRNA-based capture for locating and sequencing the exact 5’ ends of the RNAs, which were extremely difficult to capture using the double-stranded cDNA capture method.

ResearchBlogging.orgLamm, A. et al. (2010). Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome Genome Research DOI: 10.1101/gr.108845.110

No comments: