GSM5578328: ESC_1; Mus musculus; Hi-C
in situ Hi-C library preparation was performed as described previously (Belaghzal et al., 2017, Rao et al., 2014) with minor modifications. We used the whole harvested cells for mESCs and EpiLCs, and FACs-sorted BV-positive cells for d2 mPGCLCs and d4c7 mPGCLCs, and FACS-sorted AAG-positive cells for GSCs and GSCLCs. 2.5 x 106 cells were used for one replicate. The cells were fixed by 1% formaldehyde (Sigma) /HBSS and lysed in lysis buffer (10 mM Tris-HCl pH8.0, 10 mM NaCl, 0.2% NP-40) for 30 min on ice with frequent inversion. The cells were digested by 500 U of DpnII (NEB) overnight at 37°C. Following biotin filling (Thermo Fisher Scientific, 19524-016; NEB, M0210S), proximity ligation (Thermo Fisher Scientific, 15224090) and reverse crosslinking, DNA was purified by ethanol precipitation and sheared to 200-400bp fragments using Covaris E220 sonicator (Covaris) at 4°C (10% Duty Factor, 200 cycles/burst, 175 W Peak Incident Power, 110 s). Ligation fragments containing biotin were immobilized on MyOne Streptavidin T1 beads (Thermo Fisher Scientific) Library preparation was performed using NEB library preparation kit (NEB, E7645S; NEB, E7335S) according to manufacturer's guidance. The libraries were amplified 8 cycles and DNA fragments between 300-800bp were selected using AMPure XP beads (Corning).