New RNA-seq technologies are now being developed that compare with microarrays for profiling gene expression.
A new study describes a robust RNA-seq strategy for multiplex analysis of RNA samples based on deep sequencing:
- An oligo-dT linked to an adaptor sequence is used to prime cDNA synthesis.
- Solid phase selection is performed.
- Second strand synthesis is initiated using a random primer linked to another adaptor sequence.
- The library is released from the beads and amplified using a bar-coded primer together with a common primer.
This method preserves strand information, permits rapid identification of potentially new polyadenylation sites, and profiles gene expression in a highly cost effective manner.
The authors have applied this technology to determine the transcriptome response to knockdown of the RNA binding protein TLS, and compared the result to current microarray technology, demonstrating the ability of MAPS to robustly detect regulated gene expression.
- Fox-Walsh K, Davis-Turak J, Zhou Y, Li H, Fu XD. (2011) A multiplex RNA-seq strategy to profile poly(A(+)) RNA: Application to analysis of transcription response and 3′ end formation. Genomics [Epub ahead of print]. [abstract]