GSM6597701: E14  mESC, CAPS+, rep2; Mus musculus; OTHER
For isolation of genomic DNA, cells were harvested by centrifugation for 5 min at 1,000× g and room temperature. DNA was extracted with Quick-DNA Plus kit (Zymo Research) according to the manufacturer's protocol. Genomic DNA was spiked with 0.5% of CpG-methylated lambda DNA and 0.25% of unmodified 2 kb spike-in control. DNA samples were fragmented by Covaris M220 and size-selected to 300–500 bp with 0.55–0.85× Ampure XP beads according to the manufacturer's protocol. The sonicated DNA was additionally spiked with 0.05% of 144 mer spike-in after size-selection with Ampure XP beads. End-repair and A-tailing reaction and ligation of NEBNext Adaptor for Illumina were prepared with KAPA HyperPrep Kit according to the manufacturer's protocol. The uracil in the loop of NEBNext Adaptor was removed by adding 6  ml of USER Enzyme (New England Biolabs) to the ligation reaction and incubating at 37 °C for 45 min. The reaction was purified with 0.8× Ampure XP beads by washing twice with 80% acetonitrile/water (v/v).