KAPA Library Preparation Kit
The DNA was sheared using Covaris LE220-Plus ultrasonicator, and fragments of 150–300 bp were size-selected using AMPure XP beads (Agencourt Bioscience). The libraries were constructed using the KAPA Library Preparation Kit with no PCR Library Amplification/Illumina series (Roche). After ligation, of the xGen™ Methyl UDI-UMI Adapters (Integrated DNA Technologies), the DNA was treated with sodium bisulfite using the EpiTect Bisulfite kit (Qiagen) following the manufacturer's instructions. Enrichment for adaptor-ligated DNA was carried out through seven PCR cycles using KAPA HiFi HotStart Uracil+ReadyMix PCR 2x Kit (Roche-Kapa Biosystems). Library quality was monitored using the Agilent 2100 Bioanalyzer DNA 7500 assay, and the library concentration was estimated using quantitative PCR using the KAPA Library Quantification Kit for Illumina® Platforms, v1.14 (Roche)