GSM9557706: Trp53-/-; sgPten gastric organoid, rep2; Mus musculus; ATAC-seq
Gastric TP and TPA organoids (5×10^4 cells/each group) were harvested and resuspended in 1 mL ice-cold PBS, followed by centrifugation at 500 g for 5 min. The supernatant was removed, and the pellet was gently resuspended in 50 μL lysis buffer. Tubes were placed on ice for 5 min, then 950 μL wash buffer was added. The mixture was gently pipetted (blown) 5 times and centrifuged at 500 g for 5 min at 4 °C. The sediment was collected for downstream reactions. ATAC-seq libraries were constructed using a Chromatin Profile Kit (Novoprotein, Cat. N248-01A). The sediment was resuspended in 40 μL fragmented mixture and transferred to PCR tubes for incubation at 37 °C for 30 min. The reaction was stopped by adding 10 μL stop buffer and incubating at 55 °C for 5 min. DNA extraction beads were used to purify the fragments. Transposed DNA fragments were amplified using the PCR system provided in the kit with the following conditions: 72 °C for 3 min, 98 °C for 30 s, followed by 9–18 cycles of 98 °C for 15 s, 60 °C for 15 s, and 72 °C for 10 s, and a final extension at 72 °C for 2 min. Amplified libraries were purified using DNA Clean Beads.The Illumina X plus platform was utilized to sequence the library.