Cells were resuspended in 50 μl of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin by pipetting up and down three times. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 (without NP40 or digitonin) was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 10 min at 500 r.c.f. in a pre-chilled (4 °C) fixed-angle centrifuge. Supernatant was removed with two pipetting steps, as described before, and nuclei were resuspended in 50 μl of transposition mix (25 μl 2× TD buffer (recipe in Supplementary Protocol 1) 2.5 μl transposase (100 nM final), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water) by pipetting up and down six times. Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 1,000 r.p.m. Reactions were cleaned up with Zymo DNA Clean and Concentrator 5 columns. All libraries were amplified with a target concentration of 20 μl at 4 nM, which is equivalent to 80 femtomoles of product. Following amplification, libraries were purified with Ampure XP beads using two-sided size selection to remove primer dimers and fragments >1000 bp.