single nucleus ATAC-seq of human PBMCs
For single nucleus ATAC sequencing (snATAC-seq) experiments, viable single cell suspensions from each sample were used to generate snATAC-seq data using the 10x Chromium platform according to the manufacturer's protocols (10x Genomics, protocols CG000169; CG000168). Briefly, >100,000 cells from each sample were centrifuged and the supernatant was removed without disrupting the cell pellet. Lysis Buffer was added for 5 minutes on ice to generate isolated and permeabilized nuclei, and the lysis reaction was quenched by dilution with Wash Buffer. After centrifugation to collect the washed nuclei, diluted Nuclei Buffer was used to re-suspend nuclei at the desired nuclei concentration as determined using a Countess II FL Automated Cell Counter and combined with ATAC Buffer and ATAC Enzyme to form a Transposition Mix. Transposed nuclei were immediately combined with Barcoding Reagent, Reducing Agent B and Barcoding Enzyme and loaded onto a 10x Chromium Chip H for droplet generation followed by library construction. The barcoded sequencing libraries were subjected to bead clean-up and checked for quality on an Agilent 4200 TapeStation, quantified by KAPA qPCR, and pooled for sequencing on an Illumina NovaSeq 6000 (2x50bp libraries).