GSM8405737: ChIP_P0_Dnmt1cKO_H3K9me3; Mus musculus; ChIP-Seq
Freshly FACS-sorted cells were fixed with 1% formaldehyde for 10 minutes. For IgG and H3K9me3 ChIP, after quenching and cell lysis, chromatin was sonicated using Bioruptor Sonicator; for Setdb1 ChIP, use CST SimpleChIP protocol following manufacture recommendation. For ChIPseq, the DNA extract was incubated overnight at 4°C with primary antibody. 10 μl of Dynal Protein G magnetic beadswas added to each sample the following day, incubated at 4°C for 2-4 h, followed by washes for several times. Bound complexes were treated with 5ul Tn5 transposase at 37°C for 5min, eluted and crosslinking was reversed by 6-10h incubation at 65°C, cleaned up with MinElute PCR Purification Kit and PCR-amplified for 10-12 cycles. Libraries were purified by Beckman Coulter AMPureXP beads and submitted to Novogene for library quality control (QC). For hMeDIP, fragmented DNA was used for end-repair, A-tailing and ligation of adapters using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs).  10% of the ligated material was saved as input reference and the remaining material was immunoprecipitated using Diagenode's hMeDIP kit (Diagenode, Denville, NJ). Final libraries from input and 5hmC-immunoprecipitate were obtained by PCR amplification using barcoded primers, followed by clean-up using magnetic beads.