2.6. Whole transcriptome sequencing (RNA-Seq)

For each samples, we used the illumine TruSeq RNA Sample preparation kit to prepare RNA-Seq libraries. For analysis of mRNA level, we obtained the trimmed reads, which include 30 nucleotides from the 5′ end of each read. The trimmed reads were aligned to the human reference genome (hg19) using GSNAP^[13] (version 2012-12-20). We used R package DEGseq^[14] to calculate gene expression as reads per kilobase per million mapped reads with RefSeq gene annotation (“refFlat” table downloaded from UCSC genome browser, last accessed on 2012/08/06).