GSM8113480: 2, Control, snATAC; Homo sapiens; ATAC-seq
Frozen brain tissue pieces were placed in 500 μL chilled 0.1× Lysis Buffer (1X lysis buffer diluted with lysis dilution buffer) and immediately homogenized 15 times using a pellet pestle (Fisherbrand™ Pellet Pestle™ Cordless Motor with RNase-Free Disposable Pellet Pestles, Catalog No.12-141-364). The homogenized tissues were then incubated for 15 mins followed by addition of 500 μL of chilled Wash Buffer and filtration through a 70 μm Cell Strainer (Miltenyi Biotech). In the next step, a sucrose gradient (Nuclei PURE Prep Nuclei Isolation Kit, Cat\#NUC201-1KT, Sigma) was prepared and nuclei were spun at 13,000 g for 45 minutes at 4°C. After centrifugation, the debris and myelin from the top of the sucrose gradient were removed. Nuclei were resuspended, washed, filtered (through a 40 μm cell strainer), counted (using a cell counter), and then incubated in a Transposition Mix. Transposed nuclei were loaded on 10X Genomics Next GEM Chip H (10x Genomics) to generate single-cell GEMS. GEMs were then transferred, incubated, and cleaned for further processing.  Single nuclei ATAC-seq libraries were prepared using the Chromium Single Cell ATAC v2 (10x Genomics) reagents kit as per the manufacturer's instructions. Library size distribution and average fragment length, of each library, were assessed with Agilent TapeStation High Sensitivity D5000 ScreenTapes and the concentrations were quantitated using Qubit Fluorometer.  Libraries were sequenced on a NovaSeq 6000 (Illumina) in paired-end mode (read1N: 50 cycles, index i7: 8, index i5:16 cycles, read 2N:50 cycles) to generate approximately 500 M reads per sample. snATAC-seq, snRNA-seq, RNA-seq