title: GSM3331344: HiC_Snf2hko_2; Mus musculus; OTHER
library_construction_protocol: Hi-C was performed as previously described (Rao et al., 2014) with modifications. In brief, 5 million mouse ES cells were fixed using formaldehyde and lysed in 500μl of Lysis Buffer (10 mM Tris-HCl pH8.0; 10 mM NaCl; 0.2% NP40; 1X Protease inhibitors). Nuclei were permeabilised and digested with 400U of MboI restriction enzyme (NEB #R0147M). 5'overhangs were filled with incorporation of biotin-14-dATPs (ThermoFisher #19524016) using DNA Polymerase I Large (Klenow) fragment (NEB #M0210L) and resulting blunt-ends were ligated with T4 DNA Ligase (NEB #M0202T). After reverse-crosslinking, RNAseA and Proteinase K treatment, DNA was purified using AMPure XP beads and 2μg of purified DNA was sheared using Covaris S220 Focused-ultrasonicator to an average size of 300-500bp. The biotin ligation junctions were then captured using Dynabeads MyOne Streptavidin T1 beads (ThermoFisher #65601). End-repairing, A-tailing, Illumina adapter ligation and indexing PCR amplification (8-10 cycles) were performed on beads before final purification with AMPure XP beads. Resulting libraries were analysed and quantified using Agilent Bioanalyzer and sequenced.