title: GSM2123564: Population Hi-C (haploid); Mus musculus; OTHER
library_construction_protocol: 5-10 million Haploid mouse ES 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 as follows. Briefly, sonicated DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. Biotinylated junctions were captured on streptavidin M-280 dynabeads and the blunt, phosphorylated ends were treated with Klenow fragment  exo minus) and dATP to yield a protruding 3- 'A' base for ligation of custom adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 10 cycles and library fragments of ~300-700 bp (insert plus adaptor and PCR primer sequences) were isolated using AMPure beads (Beckman). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2500 following the manufacturer's protocols.
attributes.tag: GEO Accession
attributes.value: GSM2123564