A comprehensive analysis and comparison of seven methods for strand-specific RNA sequencing (RNA-seq), together with recommendation of which techniques perform best, is published online this week in Nature Methods.
It is becoming easier to analyze the entirety of an organism's RNA, with massively parallel sequencing techniques, but the large number of sample preparation methods leaves many users confused as to which approach is more appropriate for their particular experiment.
Joshua Levin and colleagues provide guidance with the analysis of the most commonly used protocols for strand-specific RNA analysis. These protocols allow one to annotate the structure of transcribed genes, quantify the expression level of each transcript and measure the extent to which genes are transcribed into several isoforms. They also preserving strand information ― that is, they identify transcripts that are derived from the sense or the antisense strand of DNA, which yields important information about the function of the RNA because antisense transcripts are likely to play a regulatory role.