GSM7507184: Population Hi-C EED KO ES replicate 1; Mus musculus; Hi-C
Four to five million cells were fixed for 5 min with 2 % formaldehyde in PBS and then the reaction was quenched for another 5 min in 0.125 M glycine. Nuclei were then extracted by incubating cells on ice for 30 min (inverting every 10 min) in 10 mM Tris pH 8.0, 10 mM NaCl, 0.2 % NP-40 (IGEPAL CA-630) and protease inhibitor cocktail (Roche). Population Hi-C libraries were prepared using an adaptor ligation method. Briefly, sonicated blunt-ended biotinylated junctions of ~300 bp in size were captured on streptavidin M-280 dynabeads. The blunt ends were A-tailed with Klenow (3'→5' exo-) before ligation with adaptor sequences containing unique barcode.  After adaptor ligation DNA was PCR amplified with Illumina primers for 8-10 cycles and library fragments of ~500 bp (insert plus adaptor and PCR primer sequences) were purified using AMPure beads (Beckman). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Hiseq 4000 following the manufacturer's protocols. Population Hi-C