Fig. 1 |. CM transcripts redefine the ischemic BZ.

a, Scientific question and experimental design. To define the ischemic BZ transcriptionally, we performed snRNA-seq of mouse hearts without injury and with ischemic injury, mapped the resulting transcriptomes to space using spatial transcriptomics and validated our findings using multiplex RNA FISH (Rebus Biosystems). b, Uniform manifold approximation and projection (UMAP) plots of clustered CMs (snRNA-seq) with high-resolution (left) and annotated clustering (right) based on spatial mapping and gene patterns. Representative data shown from Ctrl, 24 h post-MI and 72 h post-MI samples (n = 3 mice). c, UMAP plots of CMs split by condition. d, Quantification of CM composition by time after injury. e, Heatmap displaying DEGs as determined by clustering with the color bars above indicating cell cluster based on the annotation method (Wilcoxon signed-rank test, Bonferroni-adjusted P < 0.01). GO and motif enrichment terms are displayed to the right of each respective group. f, Representative spatial transcriptomic data of mouse heart cross-section after ischemic injury (Visium; 10X Genomics). g, Gene-set scores in space derived from snRNA-seq data with examples of expressed genes shown below. h, Trajectory analysis of representative genes from snRNA-seq data with direction of pseudotime indicated in b. i, Gene-set scores in space at the BZ from the box indicated in g. j, Gene-set scores as a function of space from the RZ toward the IZ as indicated by the arrow in i (data presented as mean values ± s.e.m.; n = 966 cells examined over one sample). k, Quantification of neighboring pixels, split by mapping classification (mean; box: 25th–75th percentile; whiskers: 2.5th–97.5th percentile; n = 966 cells examined over 1 sample). **P < 0.01, ****P < 0.0001; two-sided Mann–Whitney U-test. NS, not significant; min., minimum; max., maximum.