a, PCA of 562 old cells in the neural stem cell lineage (astrocytes/qNSCs and aNSCs/NPCs) performed only using genes in the interferon-γ response hallmark from MSigDB (Supplementary Table 8). ‘interferon-γ-high’ cells (dark red with black ring) are defined as old cells exhibiting an average expression of genes in the interferon-γ response hallmark pathway in the top 5% of old cells. b, PCA as in a, but with a separate PCA performed for each of three 10x Genomics replicates (n = 162, n = 315 and n = 85 cells) and for the dataset generated with Fluidigm C1 technology (n = 137 cells). c, Average of normalized expression values of genes in interferon-γ response hallmark for young and old cells in cells of the NSC lineage (astrocytes/qNSCs and aNSCs/NPCs). Cells are grouped by age. Interferon-high cells (in black) are defined as cells that exhibit an average expression of genes in the interferon-γ response hallmark pathway in the top 5% of the cells analysed within each 10x Genomics replicate. Note that replicate three contains approximately twofold more young cells than old cells. Horizontal lines in violin plots denote median interferon-γ response pathway expression. See Supplementary Table 3 for exact cell counts. d, FACS analysis of STAT1-positive cells in the young and old NSC lineage (PROM1+CD45−CD31−CD24−O4−). Left, FACS histograms of STAT1 fluorescence in PROM1+ cells isolated from the SVZ from two representative young (3 months old) and old (20 months old) male mice. Right, quantification of the percentage of STAT1-high cells in 15 young (3–5 months old) and 14 old (19–26 months old) mice. Data are mean ± s.e.m. of the percentage of cells that are STAT1-high of the approximately 500 cells analysed for each mouse. Each dot represents approximately 500 cells from 1 mouse. The combined results from five independent experiments are shown (for independent experiments, see Supplementary Table 12). ***P = 5.08 × 10−6, two-sided Wilcoxon rank-sum test. e, The gene encoding the surface marker BST2 is expressed in the old NSC lineage and is correlated with genes that belong to interferon-γ signalling. Data are shown as a heat map with log-normalized expression of Bst2 and other select genes in the interferon-γ response hallmark pathway. Cells are clustered on the basis of expression of this gene set. The ages of the mice from which the cells are isolated is indicated in a bar above the heat map. f, Live FACS analysis for BST2 in cultured NSCs after interferon-γ treatment for 48 h. g, Abundance of total STAT1 protein in BST2-positive compared with BST2-negative aNSCs/NPCs isolated from nine old (25 months old) mice, as measured by intracellular FACS. Data are mean ± s.e.m. of total STAT1 fluorescence. Each dot represents cells from one mouse. The combined results from two independent experiments are shown (for independent experiments, see Supplementary Table 12). *P = 0.04, two-sided Wilcoxon rank-sum test. h, FACS quantification for Ki-67, a marker of cycling cells, in BST2-positive and BST2-negative aNSCs/NPCs from 15 old (23–25 months old) mice. Data are mean ± s.e.m. of percentage of cells that are Ki-67 positive of the approximately 100 cells analysed for each mouse. Each dot represents around 100 cells from 1 mouse. The combined results from three independent experiments are shown (for independent experiments, see Supplementary Table 12). ***P = 7.80 × 10−4, two-sided Wilcoxon rank-sum test.