GSM5024976: ZT-WT2-GC3-E1-R2-T1; Homo sapiens; Hi-C
10M formaldehyde cross-linked cells were lysed and digested overnight at 37°C with 400 units of DpnII (NEB). Next, the DNA ends were marked with biotin-14-dATP (Thermo Fisher Scientific #19524016) for 4 hours at 23°C and ligated for 4 hours at 16°C. To remove proteins and reverse crosslink, DNA was treated with proteinase K overnight at 65°C. DNA was then purified using phenol:chloroform and biotin was removed from unligated ends. Ligation products were fragmented by sonication to an average size of 200bp and size selected with Ampure XP beads (Beckman Coulter, # A63880) to fragments ranging from 100 to 350 bp. End repair was performed on the DNA fragments to obtain blunt ends and biotinylated ligation products were purified using streptavidin beads (Thermo Fisher Scientific #65001). dA-tailing was then performed and the TrueSeq DNA LT kits Set A (Illumina, #15041757) was used for adapter ligation and PCR amplification. PCR primers were removed using Ampure XP beads. The Hi-C libraries were sequenced using 50 bp paired end reads on Illumina HiSeq4000.