Fig. 4: Transcriptome-wide changes in fibroblasts at different stages after ischemic injury suggest dynamic fibroblasts function during wound healing.
From: Single-cell transcriptomics following ischemic injury identifies a role for B2M in cardiac repair
a tSNE plot indicating transcriptomic similarities across fibroblasts obtained from all conditions. Different colors and numbers highlight the clusters as determined by k-medoids clustering of 1 −  Pearson’s correlation coefficient. b Bar graph showing the proportion of fibroblasts originating from the different conditions per cluster. c Heatmap showing expression of all genes significantly enriched in at least one cluster. Examples of genes enriched per cluster are depicted on the right side of the heatmap. d Bubble plot of gene ontology analysis on genes significantly enriched within a cluster. b–d Numbers highlighted in red depict clusters that mainly contain 1 dp IR (cluster 4) or 3 dp IR (cluster 3) fibroblasts. e, f, Cell trajectory analysis of fibroblasts, showing pseudotime on a color-coded scale (e) or highlighting the k-medoids cluster of each fibroblast in the trajectory plot (f). The branches in the trajectory plot that contain mostly cells from k-medoids cluster 1, 3 or 4 are highlighted by number. g RT-qPCR analysis on the infarcted cardiac tissue at different time points post IR for Ccl2 and Col1a1. Per time point post IR, expression levels are relative to the corresponding time point post sham surgery (n = 6 animals). Data are presented as mean ± SEM. *P < 0.05, **P < 0.01, ***P < 0.001, Two-sample t-test vs the corresponding time point post sham, with Holm–Sidak adjustment for multiple comparisons.
