title: GSM8121013: HFSCs 1, CNR Rarg; Mus musculus; OTHER
library_construction_protocol: To resuspend HFSCs, 3D cultures were washed with sterile PBS, dissociated into single cell suspensions using TrpLE-Express (Gibco) for 15min at 37°C. After filtering, cells were pelleted and CNR was performed as previously described in Skene et al., 2018 with minor modifications. Briefly, cells were crosslinked with 1% formaldehyde and quenched with glycine. After washes, nuclei were incubated with concanavalin-A beads, followed by antibody incubation overnight. ConA-bead-bound nuclei were incubated with MNase to cut DNA and the fragments were relaesed by CaCl2 addition. Sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina. PCR-amplified libraries were purified using 1× ratio of SPRI beads (Beckman) and eluted in 15 μl EB buffer (Qiagen).