GSM7061611: D28_scATAC; Mus musculus; ATAC-seq
For ScATAC-seq of tumor tissues or normal colon epithelium, fresh tissue, collected from 6-10 mice for a pooled sample, was dissociated into single cell by using tumor Dissociation Kit (Miltenyi, 130-096-730). Further nuclei isolation was performed by Chromium Nuclei Isolation Kit(10XGenomics). Briefly, the supernatant was discarded and the cells resuspended in 1 ml of 0.04% BSA (#A7906, Millipore Sigma) in PBS. About 600,000 cells were transferred to a new tube for further lysis. To remove the supernatant, cells were centrifuged again for 10 minutes at 700 rcf and 4 °C and resuspended in 1 ml of chilled lysis buffer. Cells were lysed for 10 minutes on ice and 1 ml of wash buffer was added to stop the reaction. Then, the suspension was filtered through a 40 mm Cell Strainer (#352235, BD Biosciences), and cells were centrifuged and resuspended in 500 ul of chilled Diluted Nuclei Buffer aiming to target 9000 nuclei. The final nuclei concentration was determined, and we proceeded with the transposition, GEM generation and barcoding, and library construction according to the Chromium Next GEM Single Cell ATAC v1.1 user guide (#1000175, 10XGenomics).