title: GSM9557715: anti-ARID1A, Trp53-/-; sgPten gastric organoid, rep1; Mus musculus; OTHER
library_construction_protocol: We analyzed gastric organoids with two engineered genotypes: Trp53−/−; Pten−/− (TP) and Trp53−/−; Pten−/−; Arid1a−/− (TPA). sgRNAs targeting Pten and Arid1a were introduced into Trp53−/−; Cas9-EGFP gastric organoids to generate the corresponding genotypes. TP organoids served as the control group, and an IgG control was included to account for nonspecific background binding. Organoids from each group were collected for downstream CUT&Tag-seq library preparation and comparative differential binding analyses. TP and TPA organoids were used for ARID1A CUT&Tag. The chromatin was combined with ChiTag™ 2.0 Transposome, then fragmented using Tagmentation Buffer for 1 h at 37 °C. ChIP DNA was purified using DNA Clean Beads and amplified using the PCR system from this kit. PCR conditions were as follows: 72 °C for 3 min, 98 °C for 30 s, followed by 10–25 cycles of 98 °C for 15 s, 60 °C for 15 s, and 72 °C for 10 s, then 72 °C for 2 min. Amplified libraries were purified using DNA Clean Beads. The purified ChIP DNA was used for library preparation.