Extended Data Fig. 8: Mural cells associated with cortex and ME blood vessels show distinct morphology and transcriptomic differences.

(a) Representative cross section images of (i) vessel 1 and (ii) vessel 2 reconstruction by serial TEM. Pseudocolors show reconstructed regions: blood vessel lumen (L, red); EC (green); and pericyte cell (blue). White arrows indicate EC tight junctions (purple), and white boxes highlight ‘peg and socket’ pericyte-EC interactions. Scale bar represents 1 µm. (b) Representative image of cortex vessel 4 from serial TEM dataset. Scale bar represents 1 µm. (c) Immunostaining for PDGFRβ (white, left panels) and Imaris 3D reconstruction of pericytes (white, middle and right panels) in cortex and ME. Co-staining for Glut1 (green) and Emcn (red) to mark capillaries in the cortex and ME, respectively. Scale bar 10 µm. (d) High magnification images of reconstructed pericytes (PDGFRβ, white) in contact with capillaries (Glut1, green and Emcn, red) in cortex and ME. Arrows point at ME pericyte protrusions not in contact with capillaries. Scale bar 5 µm. (e) Violin plots showing expression of published markers of brain pericytes in both ME and cortex areas of interest from GeoMX whole transcriptome profiling. (f) Heatmap of differentially expressed genes (log₂ fold-change greater than |1| and FDR < 0.05) between cortex and ME pericyte-enriched regions of interest from GeoMX whole transcriptome profiling (also shown in Fig. 5h). Differential expression was determined by linear mixed model analysis and significance assessed by false discovery rate (FDR). (g) Immunostaining for CD31 (green) and SLC12A7 (red) in ME and cortex in coronal tissue sections. Scale bar 10 µm. (h) Upset plot showing overlap between human pericyte cell type signatures and differentially expressed genes in ME and cortex pericyte-enriched regions. (i) Upset plot showing overlap between human brain pericyte cell type signatures and ME and cortex pericyte-enriched differentially expressed genes (Fig. 5h). (j) Upset plot showing overlap between human pericyte cell type signatures and pericyte marker genes from our scRNAseq dataset (calculated by two-sided Wilcoxon test in Seurat comparing pericytes to other mural cells, with min.pct=0.25 and logFC>0.6).