The in situ Hi-C protocol from the 4DN Nucleosome Consortium was followed. Briefly, five million cells were crosslinked for each experiment and DpnII was used for DNA digestion followed ligation. To shear the DNA after ligation, ultra-sonication (Sonic Dismembrator model 500, Fisher Scientific) was used with ten timed on-pulses of 5 s each. Subsequently, to generate the library, each end of the isolated DNA fragments (isolation performed using Dynabeads MyOne Streptavidin T1 beads) was trimmed and ligated with the following adaptor oligonucleotide duplexes: Hi-C1_for and Hi-C1_rev, Hi-C2_for and Hi-C2_rev, Hi-C3_for and Hi-C3_rev, Hi-C4_for and Hi-C4_rev, and then amplified using the oligonucleotides HiC_for and HiC_rev (Supplementary Table 1). Alternatively, the NEBNext Ultra II Kit (NEB E7645) and Multiplex Oligos (NEB E7600S) were used for making the library. Four independent experiments from three biological replicates were combined for analyses. As controls, we used in vitro stimulated wild-type B cells and control KO B cells as previously published8 (link).