GSM9682478: JFS2426_WSUAML_GLIS2_rep1; Homo sapiens; OTHER
Cells were harvested, washed in cold PBS, and nuclei were isolated according to the AutoCUT&RUN protocol (Janssens et al., 2018; Epigenetics Chromatin 11:74). Nuclei were incubated overnight at 4°C with primary antibodies targeting mSWI/SNF complex subunits (SMARCC1, SMARCB1, SMARCA4), the CBFA2T3::GLIS2 fusion protein components (CBFA2T3, GLIS2), or histone modifications (H3K27me3, H3K4me1, H3K4me3, H3K27ac), or IgG isotype control. Following primary antibody incubation, nuclei were incubated with protein A-MNase fusion (pA-MNase). Chromatin cleavage was initiated by addition of CaCl₂ at 0°C. Released DNA fragments were purified for library preparation. CUT&RUN libraries were prepared at the Fred Hutchinson Cancer Center Genomics Core using the AutoCUT&RUN protocol. Paired-end 150 bp sequencing was performed on an Illumina instrument.