RNA was prepared into RNA-Seq libraries using an Illumina TruSeq Stranded Total RNA Sample Prep Kit with Ribo-zero Gold (Human/Mouse/Rat) (Illumina). Cytoplasmic and mitochondrial ribosomal RNA was depleted using a Ribo-zero Gold component. Depleted RNA was reverse transcribed into cDNA using SuperScript II reverse transcriptase (Invitrogen). Stranded cDNA sequencing libraries were generated according to Illumina’s procedures. Total RNA-Seq libraries were sequenced paired-end 2 × 100 base pairs (bp) using the Illumina HiSeq 2500 platform according to the manufacturer’s specifications. Low-quality ends and read-through adaptor sequences were trimmed using Cutadapt, version 1.3. The trimmed reads were mapped to the human genome (hg19/GRCh37) using STAR, version 2.3.0. The assignment of reads to gene regions was performed by htseq-count, version 0.5.4p5. These raw counts are taken as input for edgeR package for differential gene expression analysis using the exact and paired Student’s t-test described in the edgeR manual. DAVID (http://david.abcc.ncifcrf.gov/) was used to perform the gene functional annotation analysis. The categories of GO and KEGG pathways were chosen as background databases. All genes of Homo sapiens were used as background gene list. The
