Fig 2: Quality control metrics for FACS and in vivo ATAC-seq libraries.a, FACS gating scheme used to isolate 5 cell populations from the SVZ of young and old GFAP-GFP mice. Negative controls (fluorescence minus one (FMO) controls) for each stain are indicated. Negative controls (FMO controls) were stained with all antibodies other than the one(s) for which it was the negative control. b-d Changes in FACS markers with age for all sorted live cells (b), sorted live qNSCs (c), and sorted live aNSCs (d). Normalized scaled fluorescence intensity of indicated FACS markers (EGFR, GFAP, and PROM1) of young and old sorted cells used for generating ATAC-seq libraries from freshly isolated cells from the SVZ neurogenic niche. n = 8 young male and female GFAP-GFP mice and n = 11 old male and female GFAP-GFP mice, combined over 2 independent experiments. Data normalized to young mean of each individual experiment. Boxplots display median, and lower and upper quartiles. Minimum and maximum within 1.5× the interquartile range (whiskers) indicated. Dots outside whiskers represent outliers. Dots represent mean fluorescence intensity for an individual animal, normalized to mean of experiment. P-values calculated using a two-tailed Mann-Whitney test. The change in marker expression in all live cells in (b) likely reflects changes in cell type composition that occur with age. e, Insert size distribution histograms of all paired-end reads from a single representative ATAC-seq library for each of the 5 cell types freshly isolated from the SVZ of both young and old animals. f, Heatmap of ATAC-seq enrichment at genome-wide transcription start sites (TSSs) ± 2000 base pairs for all 5 cell types in both young and old conditions. Data from independent experiments are in Source Data. Ages of animals used provided in Source Data. Source data