Extended Data Fig. 4: The neurogenic niche responds to interferon-γ.

a, t-SNE plot showing levels of expression of Ifngr1 and Ifngr2 (summed)—which encode the interferon-γ receptor—in 14,685 cells clustered as in Fig. 1a. A darker colour indicates a higher summed expression of Ifngr1 and Ifngr2. Note that there is a lack of correlation between the age-dependent changes in Ifngr1 and Ifngr2 levels and changes in the interferon-γ response (Fig. 3a), possibly because of post-transcriptional changes of the interferon-γ receptor. b, Violin plots showing expression of Ifngr1 and Ifngr2 (summed) by age and cell type. Decrease in microglia is significant at P < 10⁻¹⁵ and others are not significant, two-sided Wilcoxon rank-sum test. Horizontal lines in violin plots denote median summed Ifngr1 and Ifngr2 expression. See Supplementary Table 3 for exact cell counts. c, MSigDB Hallmarks (v.6.1) GSEA results for old compared with young astrocytes/qNSCs, aNSCs/NPCs, neuroblasts, oligodendrocyte progenitor cells, oligodendrocytes, endothelial cells, microglia, macrophages and T cells in the neurogenic niche. The normalized enrichment score is presented for each pathway with FDR < 0.05. Other cell types did not show pathways that met this FDR cutoff. d, Combined log-normalized expression values of genes in interferon-γ response hallmark in various cell types of the SVZ. Single cells were grouped by cell type and age (Supplementary Table 3). e, FACS analysis of STAT1 levels in the young and old NSCs lineage (PROM1⁺CD45⁻CD31⁻CD24⁻O4⁻), freshly isolated from the brains of five young (5 months old) and four old (26 months old) male mice. Data are mean ± s.e.m. of the mean STAT1 fluorescence of the approximately 500 cells analysed for each mouse. Each dot represents around 500 cells from 1 mouse. *P = 0.016, two-sided Wilcoxon rank-sum test. Data shown are from one experiment (all experiments are plotted in Extended Data Fig. 5d). f, FACS analysis of STAT1 levels in endothelial cells freshly isolated from the brains of five young (5 months old) and four old (26 months old) male mice. Data are mean ± s.e.m. of the mean STAT1 fluorescence of the approximately 500 cells analysed for each mouse. Each dot represents around 500 cells from 1 mouse. *P = 0.016, two-sided Wilcoxon rank-sum test. g, Immunofluorescence staining of SVZ brain sections from young (4 months old) and old (29 months old) male mice showing BST2 levels in microglia. Green, BST2; red, IBA1 (microglia maker); blue, DAPI. Scale bar, 20 µm. h, t-SNE plot of 14,685 single-cell transcriptomes with points coloured by putative cell-cycle phase (G0/G1, G2/M or S) as predicted using the CellCycleScoring function in Seurat. i, t-SNE plot of 14,685 single-cell transcriptomes clustered as in Fig. 1a showing levels of expression of Bst2 in cells of the SVZ neurogenic niche. Darker colour indicates higher expression of Bst2. j, Violin plots showing Bst2 expression by age and cell type. Horizontal lines in violin plots denote median Bst2 expression. Increase in astrocytes/qNSCs is significant at P = 6.4 × 10⁻¹⁴, increase in oligodendrocytes at P = 0.025, increase in microglia at P < 2.2 × 10⁻¹⁶, and others are not significant, two-sided Wilcoxon rank-sum test. See Supplementary Table 3 for exact cell counts.