GSM8553446: H3K9me3_mGFP_Control_2C_rep2; Mus musculus; OTHER
Low-input CUT&RUN was performed as described in detail in the methods section of the accompanying paper. Late 2-cell stage embryos (48 hours post-hCG) with intact zona pellucida were washed in a buffer containing 0.5 mM spermidine, 0.1% BSA, and 1× protease inhibitor cocktail. They were then transferred to an antibody buffer (anti-H3K9me3 antibody diluted 1:100 in wash buffer containing Triton-X and EDTA) and incubated overnight at 4 °C. After washing, the embryos were incubated with pAG-MNase (diluted 1:20 or 1:200) for 1 hour at room temperature. The embryos were washed again and transferred to a calcium buffer for 30 minutes or 2 hours at 4 °C for targeted chromatin digestion. The reaction was stopped with an EGTA-STOP buffer, followed by a 30-minute incubation at 37 °C to release chromatin fragments. The supernatant was collected, and DNA was extracted using the QIAquick kit. Illumina library preparation was carried out with 15 or 18 PCR cycles. See methods of the accompanying paper for more information.