Nuclei were isolated from frozen tissue in accordance with protocol dx.doi.org/10.17504/protocols.io.6t8herw. After isolation, nuclei were cryopreserved in BAM Banker (Wako Chemicals) and stored at -80°C for use in other assays such as scATAC-seq and HiChIP. scATAC-seq library construction: Cryopreserved nuclei were thawed on ice and 65,000 nuclei were transferred to a tube containing 1 ml of RSB-T [10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween]. Nuclei were author/funder. All rights reserved. No reuse allowed without permission. bioRxiv preprint doi: https://doi.org/10.1101/2020.01.06.896159. The copyright holder for this preprint (which was not peer-reviewed) is the pelleted at 500 RCF for 5 minutes at 4°C in a fixed angle rotor. The supernatant was fully removed using two pipetting steps (p1000 to remove down to the last 100 ul, then p200 to remove all remaining supernatant). This pellet was then gently resuspended in 12 ul of 1x Nuclei Buffer (10x 1424 Genomics). To transpose, 5 ul of this nuclei suspension (containing 27,000 nuclei) was transferred to a tube containing 10 ul of transposition mix (10x Genomics). This reaction mixture was 1426 incubated at 37°C for 1 hour to transpose. The remainder of library generation was completed as described in the 10x Genomics Single Cell ATAC Regent Kits User Guide (v1 Chemistry). Nuclei were isolated from frozen tissue in accordance with protocol dx.doi.org/10.17504/protocols.io.6t8herw. After isolation, nuclei were cryopreserved in BAM Banker (Wako Chemicals) and stored at -80°C for use in other assays such as scATAC-seq and HiChIP.