GSM5127043: Young-CMS-seq-IP-rep1; Homo sapiens; OTHER
Genomic DNA was extracted from approximately 1 million hMSCs using the DNeasy Blood and Tissue kit (Qiagen #69504) and was sonicated to ~300bp with a Covaris focused ultrasonicator. Sonicated genomic DNA was ligated to methylated NEBNext Illumina adaptors using the NEBNext Ultra II DNA Library Prep (NEB, #E7645). Following bisulfite conversion with the EZ DNA methylation-lightning kit (Zymo Research, #D5030), samples were incubated with an anti-CMS antibody (from PMID:  PMC3124347) bound to protein A/G Dynabeads (Thermo Fisher #10003D and #10001D). ChIP'ed DNA underwent phenol/chloroform/isoamyl acid cleanup and precipitation. Libraries were amplified for 10 PCR cycles with KAPA HiFi Uracil+ polymerase (KAPA Biosystems, #KK2801).