We performed RNA-sequencing on 19 matched tumor-normal pairs. Total RNA was extracted using the Qiagen RNeasy Mini kit. RNA-seq libraries were constructed according to manufacturer’s instructions using Illumina Stranded Total RNA Sample Prep Kit v2 (Illumina, San Diego, CA), Ribo-Zero Gold option (Epicenter, Madison, WI), and 1 μg total RNA. We validated the completed libraries with Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA), and applied the libraries to an Illumina flow cell via the Illumina Cluster Station. RNA-seq reads (2 × 101 bp) were aligned to the human genome (hg19) using TopHat2-2.0.12 (default parameter and—library-type fr-firststrand). Transcript abundances at the gene level were estimated by Cufflinks70. The normalized counts of RNA sequencing data of 35 tumors from the TCGA cohort were obtained from the Genomic Data Commons Portal.