Total RNA was extracted from the matched tissue samples used for DNA methylation analysis using the RNeasy Mini Kit (Qiagen, catalog no. 75144) according to the manufacturer's instructions. Extracted RNA was treated with DNase I (Thermo Fisher Scientific, catalog no. AM2222) to remove genomic DNA contamination. RNA integrity and concentration were assessed using agarose gel electrophoresis and spectrophotometry prior to library preparation. RNA-seq libraries were prepared by Genesky Biotechnologies using the TruSeq Stranded mRNA Library Preparation Kit (Illumina). Polyadenylated RNA (polyA+) was enriched with oligo(dT) magnetic beads and fragmented, followed by first- and second-strand cDNA synthesis. The resulting cDNA was end repaired, A-tailed, and ligated to indexed sequencing adapters according to the Illumina protocol. Adapter-ligated fragments were PCR amplified and purified to generate the final libraries, which were quantified and quality-checked prior to sequencing on the Illumina HiSeq 2000 platform (paired-end 100 bp reads).