Methylome capture of HG001 using TrueMethyl oxidative bisulite sequencing, oxidative replicate
200 ng of genomic DNA was spiked with 1% unmethylated Lambda gDNA and fragmented to 400 bp (Covaris). Fragmented DNA was processed for end-repair, A-tailing, and ligation using NEBs methylated hairpin adapter. Ligation was performed at 16C overnight in a thermocycler. The USER enzyme reaction was performed the next morning, according to the manufacturer's protocol, before Ampure XP bead cleanup of the ligated DNA. Each sample was then split into 2 aliquots to perform oxidation + bisulfite conversion or mock (water) + bisulfite conversion according to the NuGen OxBS module instructions (Tecan/NuGen). PCR amplification was performed using NEBs dual-indexing primers and KAPA Uracil+ HiFi enzyme for a total of 10 cycles.