Extended Data Fig. 9: Fibroblasts in the ME.
(a) Heatmap of differentially expressed genes between ME pericyte- and fibroblast-enriched areas of interest from GeoMX whole transcriptome profiling. (log2 fold-change greater than |1| and FDR < 0.05). Differential expression was determined by linear mixed model analysis and significance assessed by false discovery rate (FDR). (b) Upset plot showing overlap between ME fibroblast-enriched regions from GeoMx whole transcriptome profiling and fibroblasts from choroid plexus in Dani et al.31. (c) 3D reconstructions of fibroblasts in the ME and cortex are shown in red (based on Pdgra-CreER:Ai14 Tomato expression). Immunostaining for CD31 is shown in white. Scale bar 15 µm. (d) Another 3D view of (g) showing the ___location of fibroblasts below ME blood vessels. Scale bar 5 µm. (e) UMAP plot of 714 fibroblast transcriptomes. Fibroblast subtype clusters were identified with an unbiased analysis. The number of cells identified for each subtype is indicated in the plot legend. (f) UMAP plot in (a) colored by sample region. (g) VlnPlot showing the expression of Cola1a, Dcn and Pdgfra in fibroblast subclusters. (h) Heatmap illustrating the top 5 genes differentiating each fibroblast subcluster. Differentially expressed genes were determined by two-sided Wilcoxon test in Seurat comparing each subcluster to all other mural cell subclusters with min.pct=0.25 and log2_FC > 0.6 thresholds. (i) Table showing overlap of fibroblasts 1 and 4 subtypes with fibroblast topics from Dani et al.31. Differentially expressed genes were determined by two-sided Wilcoxon test in Seurat comparing the fibroblast 1 subcluster to the fibroblast 4 subcluster, with min.pct =0.25 and log2_FC > 0.6 thresholds. (j) Co-immunostaining for fibroblast-enriched protein, DECORIN (white) and Tomato in cortex and ME. Blood vessels labelled with Tomato using Cdh5-CreERT2:Ai14 mice. Scale bar 20 µm.
