F2_H_Elution
2ug of genomic DNA was digested overnight with 64 units of MspI (NEB). Digested DNA was purified using QIAquick Nucleotide Removal Kit (Qiagen). End-repair, A-tailing at the 3 end, methylated indexed adapter ligation at the terminal ends were performed using the KAPA Hyper Prep Kit (KAPABiosystems) and SeqCap Adapter Kits (Roche). After library purification with AMPure beads (Beckman), library size ranging from 150bp to 350bp (30bp  230bp of MspI digested DNA plus 120bp of adapters) was excised by BluePippin with 3% agarose gel cassette (Marker Q3). Size-selected library was treated with EZ DNA Methylation-Lightning Kit (Zymo Research) for Bisulfite Conversion. To amplify bisulfite converted library, PfuTurbo Cx Hotstart DNA Polymerase (Agilent) and Library Amplification Primer Mix (KAPABiosystems) were used for 12 cycles of amplification. Amplified library was assessed the library quality and quantity using 2100 Bioanalyzer high sensitivity DNA assay (Agilent) and Qubit dsDNA high sensitivity assay (Life Technologies), respectively. The libraries were denatured and diluted to optimal concentration and applied in the cluster generation steps. HiSeq PE Cluster Kit v4 with cbot was used for cluster generation on the flow cell.