Paired-end RNA-seq was carried out on an Illumina HiSeq 2000. We obtained 101-bp mate-paired reads from cDNA fragments with an average size of 250-bp (standard deviation for the distribution of inner distances between mate pairs is approximately 100 bp). RNA-seq reads were aligned to the human genome (GRCh37/hg19) using the software TopHat (version 2.0.8) [40]. We counted the number of fragments mapped to each gene annotated in the GENCODE database (version 18), which included multiple categories of annotated transcripts [41], and quantified transcript abundance as FPKM (fragments per kilobase of exon per million fragments mapped).
