Hi-C library generated from fresh A549 cells
For Hi-C, 10 e6 cells per aliquot were processed on the day of cell harvest. Cells were resuspended in 1X PBS and cross-linked for exactly 10 min using 37% (w/v) formaldehyde containing 10-15% (v/v) methanol (Sigma, Cat # 252549) at a final concentration of 2% (v/v). Formaldehyde was quenched for 5 min using glycine at a final concentration of 0.2 M. Cross-linked cells were incubated on ice for an additional 15 min, then pelleted by centrifugation and washed in 1X PBS. Washed cells were pelleted by centrifugation, and the dry pellets were snap-frozen on dry ice for long-term storage. These cross-linked cells were subsequently processed for Hi-C analysis per the Arima Hi-C Kit manual (Cat # A160134) using the reagents provided in the kit. In summary, cross-linked cells were lysed and enzymatically treated to create proximally-ligated DNA, which was then purified via AMPure XP Reagent (Beckman, Cat # A63880). This proximally-ligated DNA was used to create DNA libraries for sequencing per the Arima Hi-C Library Preparation user guide (Cat # A160141). DNA libraries were then sequenced via the Illumina NextSeq 2000 sequencer platform at the Los Alamos National Laboratory Genome Center. This data has been approved for public release and assigned the LA-UR number LA-UR-25-23575.