GSM7720243: 3T3_HiC_C4_rep1; Mus musculus; Hi-C
sisHiC experiments were performed as previously described (Z. Du et al., 2017.). Briefly, 50,000-100,000 1% formaldehyde (Sigma) fixed cells were treated with 50 uL lysis buffer (10 mM Tris•HCl pH 7.4, 10 mM NaCl, 0.1 mM EDTA, 0.5 % NP-40 and freshly added ROCHE cOmplete protease inhibitor cocktail at 0.01 tablet/mL) in PCR tubes on ice for 50 min. Cell nucleus were pelleted through a centrifuge at 3000 rpm for 5 min. 10 uL 0.5% SDS was added and cells were incubated at 62°C for 10 min. 25 uL water and 5 uL 10% Triton X-100 were then added and cells were incubated at 37°C for 15 min. 5 uL NEBuffer 2 and 2 uL MboI were then added and digestion was performed overnight at 37°C with rotation. After chromatin digestion, biotin end repair, proximity ligation, and reverse crosslink were performed. The ligated DNA was then sheared and fragments with biotin were pulled down with straptavidin beads. DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA was purified by AMPure beads or DNA purification kit according to the DNA amount. Library DNA was amplified by KAPA DNA polymerase. The amplified DNA was size selected using SPRI beads.