GSM4989529: CMS2-iTerg-IP; Mus musculus; OTHER
DNA (5 to 10 μg in 130 μl tris-EDTA buffer) was sheared with a Covaris E220 using microTUBE for 4 min. DNA was cleaned up with Ampure XP beads, processed with NEBNext End Repair and A-tail Modules (NEB, Ipswich, MA, USA), and ligated to methylated Illumina adaptors (NEB). DNA was then bisulfite-treated (MethylCode, Thermo Fisher Scientific), denatured, and immunoprecipitated with anti-CMS serum (in-house) and a mixture of protein A and G Dynabeads (Thermo Fisher Scientific). Libraries for immunoprecipitated DNA were generated by PCR with barcoded primers (NEBNext Multiplex Oligos for Illumina; NEB) for 15 cycles using KAPA HiFi HotStart Uracil+ ReadyMix (Roche), followed by a cleanup with Ampure XP beads (Beckman Coulter), and sequenced with a HiSeq 2500 (Illumina, San Diego, CA, USA) with paired-end 50-bp reads.
GEO
GSM4989529