GSM9472529: scATAC enriched HSPCs from pooled spleen cells  of untreated controls replicate 1; Mus musculus; ATAC-seq
On day 11, mice were euthanized. Spleens were harvested, and single-cell suspensions were prepared by passing the tissue through a 70 µm cell strainer followed by red blood cell (RBC) lysis. For each group (GM-CSF treated and untreated), cells from C57BL/6 WT and B6.luciferase mice were pooled at a 1:1 ratio. HSPCs were enriched from these pools by cell sorting (FACS Aria III, Becton Dickinson) for the Lin- (Ter119, B220, CD4, CD8, CD11b), and c-Kit+ phenotype. The luciferase sequence flanked by the two primers, Luc 1A: 5' -TCAAAGAGGCGAACTGTGTGTG -3' and Luc 2B: 5' -GGTGTTGGAGCAAGATGGAT -3', was used as a genetic barcode to annotate cells to their respective animals and to bioinformatically analyze individual mice within each group separately. Single-cell ATAC-seq libraries were prepared using the Chromium Next GEM Single Cell ATAC Reagent Kit v1.1(10x Genomics) according to the manufacturer's protocol (CG000209, Rev D). Briefly, nuclei were isolated from freshly collected sorted HSPCs. The 10x Genomics Nuclei Isolation protocol (CG000124, Rev G) was used with minor modifications. Nuclei were counted and assessed for integrity using a Countess II FL Automated Cell Counter (Thermo Fisher Scientific). Approximately 10,000 nuclei per sample were loaded onto a Chromium Next GEM Chip H for gel bead-in-emulsion (GEM) generation and barcoding on the Chromium Controller (10x Genomics).