GSM5351463: TSC_HiC_rep1; Mus musculus; Hi-C
Libraries for Hi-C were generated as previously described (Kadota et al., 2020). Detailed protocol for Hi-C library preparation is available at Protocols.io (https://www.protocols.io/view/iconhi-c-protocol-ver-1-0-4mjgu4n). Briefly, collected cells were washed by 5% FBS/PBS, then fixed by 1% formaldehyde (Polyscience #18814-10) in 5% FBS/PBS for 10 min. To stop fixation, 2.5 M Glycine was added then incubated for 5 min. Fixed cells were washed and stored at -80 °C. Totally 2x106 fixed cells were lysed, permeabilized, and then digested with DpnII enzyme (4-bps cutter). Digested fragment ends were next filled with biotinylated nucleotides and the resulting blunt-end fragments were ligated. After reverse cross-linking, ligation products were purified to obtain Hi-C DNA. 1 µg of Hi-C DNA was fragmented by sonication and the biotinylated ligation junctions were pulled down with streptavidin beads. Then, library preparation was performed on beads.