GSM6692757: SCH9_scATAC; Homo sapiens; ATAC-seq
Tumor tissue was collected at the time of surgical resection and immediately processed. Tumor samples were minced and dissociated using the Human Tumor Dissociation Kit (Miltenyi Biotech, Bergisch Gladbach, Germany) per manufacturer guidelines. The dissociated cell suspensions were then passed through 40µm filter, pelleted through centrifugation, and resuspended in AutoMACS Rinsing Solution with 0.5% bovine serum albumin. Red blood cell lysis was performed on all samples with Gibco ACK Lysing Buffer and was followed by debris removal via density gradient when necessary (Debris Removal Solution, Miltenyi Biotech). Cell viability was confirmed to be >80% using 0.4% Trypan Blue staining and manual counting with a hemocytometer. Nuclei isolation was then performed according to the 10X Demonstrated Protocol “Nuclei Isolation for Single Cell ATAC Sequencing” (Rev D). scATAC-seq libraries were prepared using the 10X Chromium Next GEM Single Cell ATAC Reagent Kits v1.1 (10X Genomics) according to the manufacturer's protocols (SingleCell_ATAC_ReagentKits_v1.1_UserGuide_RevD). In brief, nuclei were incubated in a transposition mixture including a transposase to fragment open chromatin regions. Transposed nuclei were then loaded onto the 10X Next GEM Chip H to generate GEMs, followed by sample indexed library amplification.