GSM8387259: day4_noLif, Nsd1, HA Cut&Run; Mus musculus; OTHER
Cut&Run was performed following the EpiCypher CUTANA CUT&RUN Protocol. Briefly, one million live cells were washed and immobilized onto activated ConA magnetic beads (Bangs Laboratories: BP531) by incubation at RT for 10min, followed by permeabilization and incubation with HA antibody (1:100 dilution) on nutator overnight at 4 °C. On the next day, the cell-bead slurry was washed twice and incubated with pAG-MNase (1:20 dilution, EpiCypher: 15-1116) for 10min at RT, followed by addition of CaCl2 and 2h incubation at 4 °C for targeted chromatin cleavage by activated MNase. After chromatin digestion, stop buffer was added and chromatin fragments released into supernatant were purified using the Monarch DNA Cleanup Kit (NEB: T1030) per manufacturer's instruction. Cut&Run library was prepared using the NEB Ultra II DNA Library Prep Kit (NEB: E7645).