MethylC-Seq sequencing data was processed using the Illumina analysis pipeline and FastQ format reads were aligned to the human reference genome (hg18) using the Bowtie algorithm30 as described previously18 with minor modifications (see Supplementary Materials). mRNA-Seq reads were uniquely aligned to the human reference (hg18) and quantified using the TopHat31 and Cufflinks32 algorithms. Base calling and mapping of Chip-Seq reads was performed using the Illumina analysis pipeline.
