HiC of mus musculus: HPC5 cell line
Hi-C was performed using 5 million HPC5 according to the manufacturers instructions (Arima Hi-C kit(#A410030). Cells were crosslinked with 2% formaldehyde for 10 min at room temperature, followed by quenching using Arima Stop solution. After washing with PBS, the cell pellet was collected and stored at -80C until use. Nuclei were permeabilized using Arima lysis buffer and crosslinked chromatin was digested using the Arima restriction enzyme (RE) cocktail. The ends of restriction fragments were labeled with biotinylated nucleotides and ligated using a Arima enzymes A1, A2, B, C, and D. After reversal of crosslinks using Arima conditioning solution, the ligated DNA was purified with AMPure XP Beads (#A63880) and sheared to a size of 400 bp with a Covaris M220 ultrasonicator (500295).  After enrichment using Arima enrichment beads, DNA fragments were used for constructing a sequencing library using NEBNext Ultra II DNA library prep kit (#E7103) which was then subjected to Illumina sequencing.