Fig. 5: Spatiotemporal atlas of the infarcted heart.

a Experimental scheme of generating the spatial transcriptomic time series. Voxels are colored by clusters after data integration across time points, with clusters 3 and 4 annotated as infarct-1 (I1) and infarct-2 (I2), respectively. Confocal images of serial sections complementing each dataset are presented and include stainings for NG2 (red) and CD31 (gray), along with endogenous Pdgfra-EGFP (green) signals. Dotted lines delineate the infarct zone. b K-means clustering of temporally regulated genes representing general patterns of gene expression. Elbow plot of within-cluster-sum of squared errors (WSS) against number of clusters indicated the inflection point at four clusters (C1-4). Heatmap depicts the relative average expression of cluster-specific genes per zone and time point. Segment-dot plots display the top 10 biological processes associated with each pattern. The length of segment and dot color intensity represent log-transformed adjusted P-values and the relative number of genes mapped to the pathway, respectively. c–e Assessment of temporally regulated genes associated with “inflammatory response” (c), “ECM organization” (d), and “blood vessel development” (e) per zone and time point. Strip plots display the average scaled expression of genes with means taken to generate the trend lines split by zone. Heatmaps represent the relative average normalized expression of genes of interest. f Relative information flow of all active pathways scaled by signaling strengths across time points. g, h Directionality and signaling strength of ligands associated with matrix remodeling (g) and vascular development (h). Dot color intensity reflects the sum of communication probabilities of each ligand, and the digit adjacent to each dot indicates the number of unique receptors associated with the ligand. Source data are provided as a Source Data file.