title: GSM3415716: MShef4_J11_BSseq; Homo sapiens; Bisulfite-Seq
library_construction_protocol: Genomic DNA was isolated (DNeasy kit, Qiagen) from each parental cell line, all clones and subclones Libraries were prepared as previously described (von Meyenn et al. 2016) by sonicating 500ng genomic DNA using a Covaris Sonicator into 300-400bp long fragments, followed by end-repair, A-tailing and methylated adapter (Illumina) ligation using NEB NGS library preparation reagents.  Subsequently, libraries were bisulphite-treated using the EZ DNA Methylation-Direct Kit (Zymo), followed by library amplification with indexed primers using KAPA HiFi Uracil+ HotStart DNA Polymerase (Roche). All amplified libraries were purified using AMPure XP beads (Agencourt), and assessed for quality and quantity using High-Sensitivity DNA chips on the Agilent Bioanalyzer.