For both Drosophila S2 and human A375 cells, Hi-C was performed using the Arima Hi-C (Arima Genomics) kit, following the manufacturer's protocol A160134 v01.  The only exception is for A375 replicate 1 conditions, the Hi-C protocol from Golloshi et al., 2018 was used instead of Arima. Library amplification was performed using the NEBNext Ultra II kit (NEB;E7645S).