WES of Caki-2 cell line: ctrl_1month_rep3
Cells were grown as monolayers in Dulbeccos modified Eagle medium (DMEM, Invitrogen, CA, USA), supplemented with 10% (v/v) FBS, 1% (v/v) nonessential amino acids, 1% (v/v) L-glutamine and 100U/ml penicillin-streptomycin and maintained at 37C in a humidified atmosphere with 5% CO2. The genomic DNA from cells was prepared using the QIAamp DNA Mini Kit (Qiagen) following the manufacturers instructions and the quality and quantity of purified DNA was assessed by NanoDrop 2000 (Thermo Fisher Scientific) and gel electrophoresis. Genomic DNA was extracted from control, DNMT3A and SETD2 knockout carcinoma cell lines following 1, 3 and 6 months in culture. Whole-exome capture libraries were constructed using 100 ng of DNA from Caki-2 cells (controls and KOs) and the Agilent SureSelect Human All Exon V6 Kit. Whole-exome sequencing libraries were sequenced as paired-end 150-bp sequence tags with a coverage of 50 using Illumina Illumina HiSeq platform.