Hi-C of homo sapiens: BJ
1-3 x 106 freshly harvested cells were crosslinked using 1% methanol-free formaldehyde (Pierce, Cat. No. 28906) in 1x PBS pH 7.4 for 10 min with gentle agitation on a platform rocker. Crosslinking reactions were quenched with 200 mM Glycine at RT 5 min with rotation at 10 RPM followed by 15 min incubation on ice. Crosslinked cells were washed in 1x PBS pH 7.4, frozen as dry pellets, and stored at -80 . Hi-C assays were performed on frozen crosslinked cell pellets using the ARIMA High Coverage HiC Kit (ARIMA Genomics, Cat. No. A101030) and libraries were prepared using Arima Library Prep Kit v2 (ARIMA Genomics, Cat. No. A303011) per manufacturers instructions. 1.5 g of proximally-ligated DNA suspended in 130 L of the elution buffer was added to a microTUBE (Covaris, Cat. No. 520045) and sonicated using a Covaris E220 with the following parameters: Temperature (4-7 C), Peak Incident Power (105), Duty Factor (5%), Cycles per Burst (200), Treatment time (75 s). Post-sonication QC was performed on a TapeStation HSD5000 (Agilent Technologies, Cat. No. 5067-5592) to verify that fragment sizes were between 550-600 bp prior to size selection. Size selection was performed with AMPure XP beads (Beckman Coulter, Cat. No. A63881) to collect fragments >400 bp. 200 ng of size-selected DNA was put into biotin enrichment. The enriched products were end-repaired, adapter-ligated, and tagged with manufacturer supplied P7 and P5 8 bp index pairs using 5 cycles of PCR. The final bead-purified libraries were quantified by Qubit dsDNA HS (Thermo Fisher, Cat. No. Q33231) and TapeStation HSD5000 screentape, pooled, and re-quantified. The pool was sequenced on a NovaSeqX 10B flow cell (Illumina, Cat. No. 20085594) for 151 x 151 cycles with a 1% PhiX spike-in to 25x coverage.