GSM7305479: Large preB_inducible IkE5 deletion, 4OHT induction D12; Mus musculus; Hi-C
Cells were crosslinked with 1% formaldehyde at RT for 10 minutes, and then quenched by the addition of 0.125 M glycine for 10 minutes. Cells were then washed with ice-cold PBS, snap frozen and stored at -80C before use. In situ Hi-C was performed following the established protocol (Rao et al., 2014) with minor modifications. Briefly, nuclei were permeabilized, and DNA was digested overnight with 100 U MboI. The ends of the restriction fragments were labeled using biotin-14-dATP and then ligated in a 1.2 mL final volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of ~400 bp with a Covaris E220 evolution instrument (Covaris, Woburn, MA). Ligation junctions were then pulled down with streptavidin beads, and DNA fragments were end-repaired, dA-tailed and Illumina adapters ligated. Libraries were produced by 8 cycles of PCR amplification with KAPA Hifi DNA polymerase (Roche). The Hi-C libraries were size selected with AMPure XP beads and sequenced in house with an Illumina NEXTseq550 system and a Novaseq 6000 system at the Knapp Center for Biomedical Discovery, University of Chicago.