GSM8403655: E13.5, Soma, female, replicate 1, Hi-C; Mus musculus; Hi-C
GFP-positive cells (PGC) and GFP-negative cells (Somatic) were isolated by fluorescence-activated cell sorting (FACS) using Aria IIu (BD Bioscience) or Aria III (BD Bioscience) flow cytometer. Hi-C library generation was performed as described previously (Nagano et al., 2017), with some modifications. Per replicate, 10,000 cells were fixed in 2% PFA for 10 minutes, lysed in lysis buffer (30 minutes on ice), and digested with DpnII (NEB) overnight at 37C rotating (950rpm). Restriction overhangs were filled-in with Klenow (NEB) using biotin-14-dATP (Jena Bioscience), and ligation was performed in ligation buffer for 4 hours at 16C (T4 DNA ligase; Life Technologies). After overnight decrosslinking at 65C, the ligated DNA was tagmented to produce fragments of 300-700 bp range. Ligation products were isolated using MyOne C1 streptavidin beads (Life Technologies), followed by washing with Wash&Binding buffer and nuclease-free water. Isolated Hi-C ligation products on the beads were then used directly for PCR amplification (total of 5 PCR cycles), and the final Hi-C library was purified with AMPure XP beads (Beckman Coulter). The libraries were paired-end sequenced on HiSeq 2500 with ~500mln paired reads per replicate.