GSM3273542: Hi-C_PD14_rep2; Mus musculus; OTHER
2×10^6 cells fixed in 1% formaldehyde were suspended in Hi-C lysis buffer and 100U of MboI restriction enzyme (NEB, R0147) was applied to digest chromatin overnight. Biotin-14-dATP (Life Technologies, 19524016) filled DNA restriction ends distinctly before DNA proximity ligation and crosslink reversal. To make the biotin-marked DNA suitable for high-throughput sequencing using Illumina sequencers, we shear DNA into a size of 300-500 bp using Covaris LE220 (Covaris, Woburn, MA) within 135 s. Sonicated DNA was end-repaired and size selected using AMPure XP beads (Beckman Coulter, A63882), before dATP-tailing step. Biotin-marked DNA was pulled down by Dynabeads Streptavidin T1 beads (Life technologies, 65602). Bead-bound Hi-C DNA was amplified with 13 cycles PCR amplification. Hi-C libraries were performed following NEBnext library preparation manufacturer's protocol (NEB, E7335)