GSM8711795: organoid, PA-treated, rep2; Mus musculus; ATAC-seq
Organoids were dissociated by TrypLE Express for 10 min at 37 °C, passed through a 40 μm filter, and a total of 50,000 cells were centrifuged and washed twice with PBS. Cells were resuspended in 50 μl of buffer with TDE1 enzyme (10 mM Tris-HCl (pH 7.5), 5 mM MgCl2, 30% PBS, 0.1% NP-40 (Sigma-Aldrich, 11332473001), 5% dimethylformamide, and Nextera Tn5 Transposase (Illumina, FC-121-1030) in H2O) and incubated at 37 °C for 30 min with gentle agitation. DNA was isolated using the Qiagen MinElute PCR Purification Kit (QIAGEN, 28004). ATAC-seq libraries were PCR amplified using NEBNext High-Fidelity 2× PCR Master Mix (New England Biolabs, M0541S) for the appropriate numbers of cycles determined by RT–qPCR as previously described. The 2×75 paired-end sequencing was performed on an Illumina NextSeq 500.