title: GSM7868937: atac_A32B32 male; Homo sapiens; ATAC-seq
library_construction_protocol: Frozen brain tissue sections were dounced for 5mins in the lysis buffer. The lysis suspension was homogeneously mixed by pipetting up and down 10-15 times following which only 80% of the lysis solution was mixed with 5ml of wash buffer to make diluted nuclei suspensions. The samples were mixed and passed through a 30-um cell strainer to remove cellular debris and washed twice in 10ml wash buffer. Next, Optiprep cushion was created followed by gradient centrifugation for 30mins at 10,000g and resuspended in 1ml wash buffer. Nuclei were counted with Hoescht 33342 (1:2000) three times (average was used) with Cell countess (Olumpys). Nuclei were then spun down at 500g for 5mins and diluted in 1xNB (10x Genomics)_x005F_x000D_ to obtain a final concentration of 3080 nuclei/ul. Equal volume of nuclei suspensions from a male and female subject (either from case or control) were pooled together to obtain a final concentration of 3080 nuclei/ul. The combined nuclei were loaded in one of the lanes of 10x microfluidic chip. Each microfluidic chip was loaded with at least four multiplexed libraries representing both cases and controls. Single-cell capture and library preparations were done using 10x Genomics Chromium Single Cell v1.1 reagents following the protocol outlined by the user guide [https://www.10xgenomics.com/support/single-cell-atac/documentation/steps/library-prep/chromium-single-cell-atac-reagent-kits-user-guide-v-1-1-chemistry]. Cell Ranger atac v2.0 was used for alignment against the GRCh38 reference available on the 10x Genomics website (refdata-cellranger-arc-GRCh38-2020-A-2.0.0). 10x snATAC-seq