(UCLA Data) For each sample 50-100 ng of purified genomic DNA was digested with 20 U of MspI (NEB, cat # R0106L) at 37°C o/n in the presence of RNase Cocktail Mix (Ambion, cat # AM2286). End-repair and dA-tailing was performed by the addition of Klenow Fragment 3'->5' exo- (NEB, cat # M0212L) in the presence of dATP, dGTP and d5mCTP (Fermentas). Adapter Ligation was performed by the addition of 0.3 µl of Illumina TruSeq methylated Adapters (Illumina, TruSeq Nano cat# FC-121-4001) and 2 µl of Illumina Ligation Mix 2 (Illumina, TruSeq Nano cat# FC-121-4001). Samples were pooled and purified using an equal volume of SPRI beads (Beckman Coulter, cat # B23318). Size-selection was performed using SPRI beads to enrich for fragments from 200 to 300 bp. Bisulfite treatment was performed using Epitect Bisulfite kit (QIAGEN, cat # 59104) according to manufacturer's protocol, except that two consecutive rounds of conversion are performed, for a total of 10 hr of incubation. Purified converted DNA was PCR amplified using MyTaq HS Mix (Bioline, cat# BIO-25045) and TruSeq PCR Primer Cocktail (Illumina, TruSeq Nano cat# FC-121-4001) according to the following protocol: initial denaturation at 98°C for 30s; 12 cycles of 98°C for 15s, 60°C for 30s, 72°C for 30s; final extension at 72°C for 5 min. Amplified libraries were purified twice with an equal amount of SPRI beads to remove primer and adapter dimers. Libraries were sequenced 100 bp single-end on an Illumina HiSeq4000.