Fig. 2: Shifts in broad spatial transcriptional profiles across time post-stroke.

A Visium d2, d10, and d21 brain sections (columns) with overlaid NMF-identified factors (rows) that specifically localized to the injury area at d2 (factor 1, top row) or d10 (factor 2, middle row). No factor localized to the injury area at d21, instead a factor that follows the pattern of cortical neuronal layering was observed (factor 3, bottom row). Values plotted are spatial autocorrelation values of the factors per spot. B Table of select genes (dark blue) driving each of the factors in (A) and the pathways associated with the genes (light blue). Pathways were obtained by running the genes through EnrichR and adjusted p-values are shown in parentheses. C Visium d2 (top), d10 (middle) and d21 (bottom) sections with overlaid genes from (B) that drive factors 1, 2, and 3 from (A). The value represents the summed SCT normalized expression values corresponding genes from (B). D UMAP plot of all the spots from Visium d2, d10, and d21 sections in a UMAP-reduced dimension. Colors for clusters remain constant through (E–G). E Visium d2, d10 and d21 sections overlaid with all clusters from (D) are shown in the top row. Overlay of individual clusters associated with the d2 injury space and d10 injury space are shown in the middle and bottom rows, respectively. Spots bordering these clusters (grey spots in the middle row, navy blue in the bottom row) were isolated for differential gene expression. F, G Heatmaps representing the differential gene expression between the injured clusters in d2 (F) and d10 (G) and their neighboring border spots (colors correspond to spot colors in E). Expression represents SCT normalized expression values where high is bright yellow and low is dark purple. Source data are provided as a Source Data file.