Comparison of mRNA-seq quantification from libraries obtained using either HD or standard Illumina adapters in A thaliana, in wildtype and DCL1 mutants

One method of directional cloning of fragmented mRNA is based on single strand RNA ligation, for which ligation bias occurrs if the adapters have single sequences. The sequencing bias affects the mRNA quantification and subsequently the differential expression analysis. High definition (HD) adapters [Sorefan et al 2012, Xu et al 2015] can be used to diminish the cloning bias during library construction. HD adapters and standard illumina adapters were used to construct mRNA-seq libraries for a side by side comparison. Overall design: same RNA samples (wild type and dcl1 mutants) were used to generate mRNA-seq libraries created using HD and standard illumina adapters.