A Comparison Of Methods For Strand-Specific RNA-seq

RNA-seq is a powerful tool for gene expression profiling, novel transcript identification and transcript structure characterization such as alternative splicing.. However conventional RNA-seq does not retain transcript strand information. Strand specific RNA-seq, on the other hand, can provide strand information to enable studies on antisense transcripts as well as to accurately quantify overlapping transcripts. To assess the fidelity of different strand specific methods, we compared several commercially available kits using B73 corn line RNA spiked with ERCC RNA control RNA. We found that the strandedness of the different library kits varied between 97.1-99.8%. Linearity of read counts to transcript abundance, as measured by Pearson’s R, varied between 0.86-0.96. In our experiment, RNA ligation based method outperformed dUTP 2^nd strand based method.