title: GSM9582962: ATAC-seq Apc flox;Lef1 del biol rep 3; Mus musculus; ATAC-seq
library_construction_protocol: Small intestines of Apcfl/fl mice were cut open, washed with PBS, and incubated in 10 mM EDTA in a shaker at 37°C for 10 min. Tissues were washed twice with PBS, and the cells were scraped off with a coverslip. The cells were then centrifuged at 1500 RPM for 5 min, followed by incubation with a digestion mix composed of HBSS with Mg2+ and Ca2+ (Gibco, #14025-050) and supplemented with 1 mg/ml of collagenase type I (Gibco,#17100-017), collagenase type IV (1 mg/ml) (Gibco #17104-019), 4 mg/ml of Dispase II (Sigma Aldrich, #04942078001), and 1 µl/ml of DNase1 (Thermo Fisher Scientific, #EN0521) for 30-40 min at 37°C. After this, DMEM was added, and the cell suspension was filtered through 70 µm and twice through a 40 µm filter and centrifuged for 10 min at 150 RCF. TdTomato+ cells from the mice were sorted using BD Influx (BD Biosciences). To induce the library complexity transposition was performed for 50000 nuclei per sample in triplicates totaling 150000 nuclei. After transposition DNA fragments for each sample were pooled and purified by using Zymo DNA Clean and Concentrator-5 kit. Libraries were amplified by PCR and quantified, and the quality was measured by qPCR and TapeStation 2200.