GSM9724105: hESC_2, MeDIP-seq; Homo sapiens; MeDIP-Seq
Methylated DNA enrichment was carried out with the MethylMiner kit (Invitrogen) following the manufacturer's protocol. Briefly, 500 ng of sheared genomic DNA per sample was incubated with magnetic Dynabeads coated with the human MBD2 methyl-CpG binding domain to selectively capture methylated fragments; bound DNA was eluted with high-salt buffer and purified with a MinElute PCR Purification Kit (Qiagen). The library_strategy is registered as MeDIP-Seq in GEO as an umbrella term for methylated-DNA enrichment sequencing; the actual enrichment used MBD2 affinity pulldown rather than an anti-5mC antibody. Captured methylated DNA was ligated to Illumina sequencing adaptors, size-selected on a 2% agarose gel to retain 200-300 bp inserts, and amplified for 18 PCR cycles. Sequencing was performed by BGI on an Illumina HiSeq 2000 as 49 bp paired-end reads (BGI project F14FTSNCHT0026_Q-HUMiwnI).