GSM8669076: mSIorg_48h; Mus musculus; ATAC-seq
The sorted and cryopreserved cells from each organoid time point were thawed in a 37°C water bath and washed three times with 0.8% BSA-PBS. After the third wash, cells were transferred into BSA-coated 0.2 mL PCR tubes. Nuclei were then isolated using a low-input nuclei isolation protocol (Demonstrated protocol CG000169 • Rev D, 10x Genomics), with an 8-minute lysis time. Propidium iodide was used to identify the nuclei, and counting was performed using the MoxiGo II counter (Orflo Technologies). Nuclei were loaded to achieve a target recovery of 10,000 nuclei; if recovery was insufficient, all available nuclei were loaded instead. scATAC-seq libraries were generated using the Chromium Single Cell ATAC Library & Gel Bead Kit (PN-1000110) following the user guide (CG000168 • Rev A, 10x Genomics). Libraries were sequenced on the Illumina NovaSeq platform.