GSM9452933: SNL_TO_KLF4; Mus musculus; OTHER
CUT&RUN was performed using the Cutana CUT&RUN protocol version 2.1 (EpiCypher). In brief, 500,000 organoid cells per CUT&RUN reaction were washed in Wash Buffer with 0.05% digitonin, incubated with activated ConA beads (EpiCypher Cat # 21-1401), and subject to antibody binding overnight (anti-KLF4, R&D Systems AF3158, 0.5 µg; anti-H3K27Ac, CST 8173S, 0.5 µg; IgG, CST 2729S, 0.5 µg). pAG-MNase was used to digest the chromatin, the released DNA fragments were purified using an NEB Monarch Spin PCR & DNA Cleanup Kit (NEB # T1135). 5 ng of DNA per reaction was used as input for library preparation using the NEBNext Ultra II DNA Library Prep Kit (NEB # E7645S). Libraries were sequenced on a NovaSeq instrument with 150 bp paired end reads targeting 5 to 10M reads per sample.