Extended Data Fig. 8: Spatial transcriptomics on mechanical injury models.

(a) H&E sections at low magnification (lower panel) and high magnification (top panel). Representative of at least 2 separate experiments. (b) Clustering results of spatial transcriptomic data based on integrated dataset as shown in Extended Data Fig. 3. (c) Hif1 scores applied to representative 72 hrs post-MI sample (left) and NP (right) with quantifications plotted per pixel in (d). In comparison to post-MI hearts, needle pass injuries have a significantly lower Hif1 score compared to the positive control (72 hr MI) samples and is unchanged from negative controls in sham samples. (e) Experimental design of fluorescent dye assay to assess regional perfusion. Wheat germ agglutinin (WGA) conjugated to AlexaFluor 488 was injected directly into LV 10 min or 72 hrs post NP injury and hearts were harvested 20 minutes after injection for imaging and quantification (data presented as mean values ± SEM n = 3 biologically independent samples). The representative image in the left panel designates the visualization of the needle pass area designated as the negative control and the reference site designated as neighbors, and the right panel represents a positive control area remote from the site of injury. Quantification of samples harvested 30 minutes and 72 hrs post-NP injury reveal that in both time courses, Neighbors and Positive controls are significantly increased as compared to the Negative Control (Needle pass) sites and are not different from each other (f) Representative H&E-stained sections of NP injuries highlighting area of injury in dash lines and directions of adjacent myocyte bundles in arrows used to quantify gene expression. Representative of 2 separate experiments, each of which had tissue sections aligned with the long axis of the needle insertion. (g) Anisotropy ratios in each sample with non-injured area (right) showing no significant anisotropy in the borderzones of needle pass injuries (n = 2 biologically independent samples). Data presented as mean values ± SEM. *P-value < 0.05, **P-value < 0.01, ***P-value < 0.001, ****P-value < 0.0001; One-way ANOVA with Tukey’s post-hoc analysis.