GSM4978094: D6_shCTCF_SSEA1+ [BL-Hi-C]; Mus musculus; Hi-C
The BL-Hi-C libraries were performed as previous described. Briefly, the cells were treated with 1% formaldehyde for 10 min at RT and the crosslink was quenched by adding 2.5 M glycine. Then, the cells were treated with 0.1% SDS FA lysis buffer and 1% SDS FA lysis buffer. After that, the genome was digested with enzyme HaeIII into fragments with blunt-ends, which were treated with adenine and ligated with bridge linker containing biotin for 4 hr at 16°C. The unligated DNA fragments were digested with DNA exonuclease. Next, the cells were treated with SDS and proteinase K to digest proteins, and the DNA was purified using phenol-chloroform extraction with ethanol precipitation. Then, the DNA was fragmented into 300 bp on average by sonication and the biotin-labeled DNA fragments were pulled down with streptavidin coated M280 beads. The BL-Hi-C libraries were constructed into standard Illumina libraries.