Extended Data Fig. 6: Spatial transcriptomic validation of snRNA-seq data.

(a) Representative MERFISH sections, showing the assigned cell type from Seurat clustering. (b) UMAP clustering of MERFISH cells showing all identified cell types. Clusters of unknown cells were removed from downstream analysis. Ext indicates cells that expressed multiple excitatory markers and could not be assigned to a specific layer. X- and Y-axis values in a and b reflect pixel positions. (c) Fold change of elderly and adult MERFISH cells of 9 ribosomal proteins (left) and 10 nuclear-encoded mitochondrial proteins (right) in excitatory and L2/3 neurons (Two-sided Wilcoxon rank-sum test, elderly N = 3, adult N = 3). (d,e) Log₂ fold change of elderly vs. adult nuclear-encoded mitochondrial genes by snRNA-seq (Two-sided T-Test, elderly N = 7, adult N = 9) (d) and MERFISH (Two-sided Wilcoxon rank-sum test, elderly N = 3, adult N = 3) (e). Genes shown in both d and e are colour-coded. All box plots depict median, and first and third quartile. Whiskers show 1.5 × IQR beyond the first and third quartiles. Points beyond whiskers are outliers. (*, p < 0.05; **, p < 0.01).