Extended Data Fig. 7: Region-specific gene expression changes in aging.

(a). Barplot displays the distribution of down-regulated (top) and up-regulated (bottom) DE genes across regions, highlighting genes consistently altered in more than ten brain regions, grouped by pathway. (b) Volcano Plot showing differentially expressed genes in the ventricles of Section 3 when comparing aged versus adult samples, with significant changes highlighted in red. (c) Scatter plots comparing the alterations in differentially expressed genes between ventricle regions from Sections 2 and 3, including a linear regression line. Only DE genes that are identified in both sections are shown. (d) Cell type-specific expression of interferon-related genes during aging. Aggregated, normalized counts per replicate reveal enrichment of interferon pathway genes in ependymal cells. (e) Representative heatmaps of neuronal-related downregulated genes (left) and downregulated genes involved in smooth muscles (right). (f) Representative heatmaps of interferon related (left) and general inflammatory marker genes (Right). (g) Dot plot showing significantly upregulated or downregulated lymphocyte-associated transcripts across annotated brain regions. Only genes meeting significance thresholds (false discovery rate [FDR] ≤ 0.05 and raw fold change ≥ 3) are displayed. Dot size reflects the statistical significance (−log₁₀[FDR]), and color indicates the direction and magnitude of expression change (log₂ fold change), with red indicating upregulation and blue indicating downregulation. Regions are organized by anatomical grouping, and only significant associations are plotted. (h) Representative aging-associated genes displaying similar upregulation or downregulation patterns in the 10X Visium adult and aging dataset. Center line, median; box, interquartile range; whiskers, minimum to maximum. In panel D, n = 4 biologically independent samples per group for all plots unless otherwise indicated. Center line, median; box, interquartile range; whiskers, minimum to maximum.