GSM8265297: GM12878 capture EM-seq; Homo sapiens; OTHER
Genomic DNA from the GM12878, K562, and HCT116 cell lines were extracted according to the QIAGEN QIAmp Mini Kit Protocol. The three samples were then mechanically sheared to 300 base pairs using the M220 Focused-ultrasonicator (Covaris, 500295), along with methylated lambda control DNA. 200ng of each sample was enzymatically converted using the NEBNext® Enzymatic Methyl-seq Kit (NEB, E7120) with the manufacturer's protocol. The samples were then indexed during PCR amplification during PCR amplification using EM-Seq™ index primers (NEB 7140). The indexed libraries (200 ng each) were pooled and used as input for the Twist NGS Methylation Detection System for target enrichment. A pre-hybridization solution of blockers and enhancers was created to prepare the pool for hybridization (Twist Bioscience, 104180). The DNA was hybridized with the Twist Human Methylome Panel (Twist Bioscience, 105520), and the targets were bound with streptavidin beads (Twist Bioscience, 100983), followed by a post-capture amplification. The enriched libraries were sequenced to 20X on the Illumina Novaseq PE150 platform.