GSM6123253: MM_432_S3; Homo sapiens; ATAC-seq
Approximately 25 mg of frozen, ground pancreas from each donor was resuspended in 1 ml nuclei permeabilization buffer (10mM Tris-HCL (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20 (Sigma), 0.1% IGEPAL-CA630 (Sigma) and 0.01% Digitonin (Promega) in water) and incubated for 10 min at 4°C. Nuclei were filtered with a 30 µm filter (CellTrics) and pelleted with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf). Nuclei were washed  with 1ml Wash buffer (10mM Tris-HCL (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20, and 1% BSA (Proliant 7500804) in molecular biology-grade water). Nuclei were pelleted and resuspended in 30 µL of 1X Nuclei Buffer (10x Genomics). Nuclei were counted using a hemocytometer, and 15,360 nuclei were used for tagmentation. Single nucleus ATAC-seq libraries were generated using the Chromium Chip E Single Cell ATAC kit (10x Genomics, 1000086) and indexes (Chromium i7 Multiplex Kit N, Set A, 10x Genomics, 1000084) following manufacturer instructions. Final libraries were quantified using a Qubit fluorimeter (Life technologies) and the nucleosomal pattern was verified using a Tapestation (High Sensitivity D1000, Agilent). Libraries were sequenced on NextSeq 500, HiSeq 4000 or NovaSeq 6000 sequencers (Illumina) and reads were trimmed afterwards to fit into corresponding analysis pipeline. Single nucleus ATAC-seq with 10X Chromium Chip E Single Cell ATAC kit