Gm12878 cells

ZymoBIOMICS HMW DNA Standards were purchased from Zymo Research. GM12878 cells were purchased from Coriell Institute and propagated in Dulbecco’s Modified Eagle Media (DMEM) with fetal bovine serum (FBS), penicillin, and streptomycin at 37°C and 5% CO₂. Cells were then snap frozen in pellets of roughly 2 million cells, and DNA was extracted from the cell pellets using the Nanobind Cells, Blood, Bacteria (CBB) Big DNA Kit from Circulomics according to the manufacturer’s specifications. The extracted DNA was then directly sheared without dilution to 30kb using the Diagenode Megaruptor 2. Sheared samples were processed twice in a row on these settings due to the viscosity of the extracted DNA. Before library preparation, short fragments of DNA were depleted from the samples using the Circulomics Short Read Eliminator XS (SRE XS) kit, according to the manufacturer’s specifications.

GM12878 cells (Coriell) were grown in RPMI 1640 (Gibco) with 15% FBS to a concentration of 500,000 to 1 million cells per mL. Mouse ES cells (v6.5 from Novus Biologicals: NBP1-41162) were grown in Knockout DMEM (Gibco) with 15% FBS and LIF (Millipore) to about 80% confluence. Detached adherent or suspension cells were then pelleted and resuspended in freshly made 1% formaldehyde (Thermo Fisher) at a volume of 1 mL of formaldehyde for every one million cells. Cells were incubated at room temperature for 10 minutes with rotation. Glycine was then added to a final concentration of 125 mM to quench the formaldehyde. Cells were incubated at room temperature for 5 minutes with rotation. Cells were pelleted and washed in PBS, then pelleted again and stored at −80° C or immediately taken into the HiChIP protocol.

Human, female GM12878 cells (Coriell Institute for Medical Research, Camden, NJ) were maintained in RPM11640,15% FBS, 2mM L-glutamine (GE Healthcare Life Sciences, Pittsburg, PA) and penicillin (100 U/ml)-streptomycin (100 μg/ml) at 2x10⁵ – 1x10⁶ cells/ml and maintained at 37°C with 5% CO₂.

GM12878 cells (Coriell) were cultured in RPMI-1640 supplemented with L-glutamine (Gibco), 15% heat-inactivated fetal bovine serum (FBS) (Gibco), and 1% penicillin/streptomycin (Thermo Fisher Scientific). HT1080 (American Type Culture Collection, ATCC) were cultured in EMEM (ATCC) supplemented with 10% FBS and 1% penicillin/streptomycin. MDA-MB-231 (ATCC) and HEK293T (ATCC) cells were maintained in DMEM (Gibco) supplemented with 10% FBS, 1% L-glutamine, and 1% penicillin/streptomycin. DU145 (ATCC) and K562 (ATCC) cells were cultured in RPMI-1640 supplemented with 10% FBS and 1% penicillin/streptomycin. NB4 cells (DSMZ) were cultured in RPMI-1640 supplemented with 10% charcoal-stripped FBS (Gibco) and 1% penicillin/streptomycin. All-trans retinoic acid (ATRA, Sigma) was dissolved in DMSO at a concentration of 10 mM. Cells were incubated at 37 °C and 5% CO₂. Genomic DNA was extracted from K562 and NB4 cells using the Quick-DNA MiniPrep kit (Zymo).