GSM8290342: KO_rep2; Mus musculus; Hi-C
The Hi-C experiment was performed following the in situ Hi-C protocol a total of 1 x 106 cells were isolated and crosslinked with 1% formaldehyde for 10 min at room temperature, and next, 2.5 M glycine solution was added at a final concentration of 0.2 M. Then, the cells were collected, flash-frozen in liquid nitrogen and stored at -80°C. The fixed cells were then lysed on ice-cold Hi-C lysis buffer for 30 minutes on ice, followed by Mbo I (NEB, R0147) digestion overnight. The next day, treat sample at 62 ° C for 10 min to inactivate Mbo I, and then biotin-14-dATP (Life Technologies, 19524-016) was added to label the digested ends. Then, add ligation master mix (NEB, B0202 & M0202) and connect overnight. On the third day, use Covaris LE220 (Covaris) to break the end-ligated DNA fragments to a suitable length, followed by size selection with AMPure XP beads (Beckman Coulter, A63881). Dynabeads MyOne Streptavidin T1 beads (Life Technologies, 65602) pull down the biotin-labeled fragments, and these fragments are the fragments that truly represent chromatin interactions.