Extended Data Fig. 2: Chromatin accessibility clustering and correlation with gene expression.

a, Hierarchical clustering using Pearson’s correlation of raw chromatin accessibility libraries (un-normalized) of all 5 cell types freshly isolated from the SVZ of young and old animals. Biological replicates are noted as numbers following age and cell type. b, mRNA expression of Ascl1 in all 5 SVZ cell types in young and old conditions from published bulk RNA-seq dataset (see Methods). Each dot represents the VST-normalized mRNA expression value from a single RNA-seq library. For endothelial cells, astrocytes, and NPCs 4 libraries were made per condition using n = 8 young male and n = 8 young female GFAP-GFP mice (pairs of male and female mice were pooled), and n = 8 old male and n = 8 old female GFAP-GFP (pairs of male and female mice were pooled). For qNSCs and aNSCs, 3 libraries were made per condition using n = 6 young male and n = 6 young female GFAP-GFP mice (pairs of male and female mice were pooled), and n = 6 old male and n = 6 old female GFAP-GFP (pairs of male and female mice were pooled), mice except for the young qNSC condition which consisted of 2 libraries. Data are mean ± SEM. c, Decile plot of correlation between promoter accessibility levels (from ATAC-seq data) and mean gene expression values (from single cell RNA-seq data, see Methods). Promoters were binned into deciles based on accessibility level and boxplots were generated to correlate promoter bins with average gene expression for young and old endothelial cells, astrocytes, qNSCs, aNSCs, and NPCs. Each dot represents the gene expression level of an individual promoter binned based on chromatin accessibility signal. Y-axis constrained between 0 and 1 to facilitate boxplot visualization. Boxplot indicates median, and lower and upper quartiles. Minimum and maximum within 1.5× the interquartile range (whiskers) indicated. Dots outside whiskers represent outliers. n = 6 young male and n = 6 female GFAP-GFP mice (pairs of male and female mice were pooled), and n = 9 old male and n = 9 old female GFAP-GFP mice (pairs of male and female mice were pooled), combined over 3 independent experiments.