ChEC-seq was performed as previously described (Grünberg et al., 2016; PMID: 27797823; Zentner et al., 2015; PMID: 26490019) with following modifications. The final calcium concentration in the reaction mixture was 0.2 mM (2 mM in the original protocol) and MNase digestion was done for 5 min for all collected samples. Stop buffer was supplemented with D. melanogaster MNase-digested DNA (1 ng/ml stock concentration) in the amount calculated based on S. cerevisiae culture A600 measurement (volume = A600 x 8 ul). Sequencing libraries were prepared similarly as described (Warfield et al., 2017; PMID: 28918900) with several modifications. 1/6 vol of the final ChEC DNA sample was used as an input. Final adapter concentration during ligation was 6.5 nM. Following ligation, two-step cleanup was performed using 0.25X vol AMPure XP reagent in the first step and 1.1X vol in the second step. 18 cycles were used for library amplification.