title: NY11
design: Five micrograms of genomic DNA from tissue samples was run on a 1% agarose gel and the 10-20kb region excised and isolated with a Qiaex II gel extraction kit (Qiagen) to enrich for mtDNA. 5ng of lambda DNA (Promega) was spiked into each sample prior to conversion with an EpiTect bisufite kit (Qiagen). Libraries for next-generation sequencing were generated with a TruSeq DNA Methylation kit (Illumina) and sequenced on an Illumina HiSeq 2500 with 125bp paired-end reads. Low quality scoring reads and adaptor sequences were removed using Trimmomatic (version 0.36). Remaining reads were aligned to the human genome (hg19) and methylation levels analysed using Bismark (version 0.16.1).