GSM5218920: GTAC_KO_CD8_TruSeq_3_TTAGGCATCT; Mus musculus; Hi-C
Freshly sorted cells were kept on ice and typically diluted to 100K-1M cells/ml in media (min volume of 1ml). The cells were immediately crosslinked with 2% formaldehyde for 10 min, quenching with 0.2M glycine for 5 min at room temperature and 5 min on ice, followed by permeabilizing them with nuclei intact, digesting the DNA with MboI (4-cutter restriction enzyme), filling the 5′-overhangs while incorporating biotin-14-dATP (a biotinylated nucleotide), followed by ligating the resulting blunt-end fragments, shearing the DNA to a 400–700-bp fragment size using a Covaris ME220 focused ultra-sonicator, capturing the biotinylated ligation junctions with streptavidin beads. Libraries were prepared according to Illumina's instructions with 10–12 rounds of PCR amplification, and finally analyzed the resulting fragments with paired-end sequencing.