title: GSM8650799: Mouse_Brain_H3K27me3_2; Mus musculus; OTHER
library_construction_protocol: The CUT&RUN procedure was performed following the standard protocol described by Meers et al. (1). Fresh brain tissue was homogenized, and nuclei were isolated using a lysis buffer optimized for brain tissue, followed by incubation with Concanavalin A-coated magnetic beads. The isolated nuclei were then incubated overnight at 4°C with the respective antibodies targeting the histone marks H3K4me3, H3K27ac, H3K27me3 and IgG. Antibody concentrations were optimized according to the manufacturer's recommendations. Following antibody binding, the nuclei were treated with Protein A/GMNase fusion protein to cleave the chromatin at the antibody-bound sites. After MNase activation, the DNA fragments were released and collected for downstream sequencing. CUT&RUN libraries were prepared from the released DNA fragments using the NEBNext Ultra II DNA Library Prep Kit (New England BioLabs). The libraries were sequenced using Illumina NovaSeq 6000 with paired-end 50 base pair (50-PE) reads at a sequencing depth of approximately 40 million reads per sample.