The University of Massachusetts Medical School Animal Care and Use Committees approved all animal work.
mESCs (v.6.5, Novus Biologicals: NBP1-41162) were cultured in knockout DMEM (Gibco) + 15% fetal bovine serum and leukemia inhibitory factor (Millipore) to 80% confluence. GM12878 (Coriell) cells were grown in RPMI 1640 (Gibco) with 15% fetal bovine serum to a concentration of 500,000 to 1 million cells per ml. lincRNA-EPS-knockout mice were obtained from a previous study22 (link). BMDMs were differentiated from bone marrow cells with 20% L929 supernatant for 7 d.
Detached cell lines were pelleted and resuspended in fresh 1% formaldehyde (Thermo Fisher) or 1% glutaraldehyde (Sigma) at a volume of 1 ml cross-linker for million cells. Cells were incubated at room temperature for 10 min with rotation. Glycine was added at a final concentration of 125 mM to quench the cross-linker, and cells were incubated at room temperature for 5 min with rotation. Finally, cells were pelleted and washed with PBS, pelleted again and stored at −80 °C or immediately taken into the HiChIP or HiChIRP protocols9 (link).
mESCs (v.6.5, Novus Biologicals: NBP1-41162) were cultured in knockout DMEM (Gibco) + 15% fetal bovine serum and leukemia inhibitory factor (Millipore) to 80% confluence. GM12878 (Coriell) cells were grown in RPMI 1640 (Gibco) with 15% fetal bovine serum to a concentration of 500,000 to 1 million cells per ml. lincRNA-EPS-knockout mice were obtained from a previous study22 (link). BMDMs were differentiated from bone marrow cells with 20% L929 supernatant for 7 d.
Detached cell lines were pelleted and resuspended in fresh 1% formaldehyde (Thermo Fisher) or 1% glutaraldehyde (Sigma) at a volume of 1 ml cross-linker for million cells. Cells were incubated at room temperature for 10 min with rotation. Glycine was added at a final concentration of 125 mM to quench the cross-linker, and cells were incubated at room temperature for 5 min with rotation. Finally, cells were pelleted and washed with PBS, pelleted again and stored at −80 °C or immediately taken into the HiChIP or HiChIRP protocols9 (link).
