RNA-seq of HCT116 and HCT116-DKO colon cancer cell lines

RNA-seq was performed on parental HCT116 colon cancer cell line and on HCT116 DKO (double knock-out) cell line, which contains genetic knockouts of both DNA methyltransferases DNMT1 (-/-) and DNMT3b (-/-). Total RNA was isolated from HCT116 and HCT116-DKO cell lines using Rneasy Mini Kit (Qiagen) from HCT116 and HCT116-DKO cell lines. Duplicate strand-specific RNA libraries were generated from 1 μg of RNA using TruSeq stranded total RNA with Ribo-Zero Gold (Illumina). Sequencing was performed at Fox Chase Cancer Center Genomic Facility using paired end reads on the HiSeq2500 platform (Illumina). Sequenced reads were aligned to the hg19 genome assembly using TopHat2. RPKM were calculated using RSeQC package. In particular, RPKM_count.py script was used. For comparing RPKM values between cell lines count values were first normalized using quantile normalization.