GSM6879749: ImmatureB.2; Mus musculus; Hi-C
In situ Hi-C was performed as previously described (Rao Et. al. Cell 2014). Briefly, WT and Brwd1-/- small pre-B and WT immature B cells (5x10^6 for each stage) were crosslinked with 1% formaldehyde following a wash with ice cold PBS. Membranes were lysed to keep nuclei intact followed by restriction digestion with 100U of MboI (NEB R0147). The DNA ends were marked with biotin, ligated proximally and crosslinks were reversed. DNA shearing and size selection were then performed for fragments 300-500 bp. The amount of DNA was quantified with the Qubit dsDNA High Sensitivity Assay (Life technologies, Q32854), and biotin pull down was done to prepare the final in-situ Hi-C libraries (in duplicate). Libraries were prepered  using Immumina Library preparation kit and sequenced on the Illumina NovaSeq 6000.