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. 2019 Dec 23;8:e50163. doi: 10.7554/eLife.50163

Figure 3. Pseudo time analysis reveals dedifferentiation and metabolic changes in border zone cardiomyocytes.

(a) Bar plot of StemID scores for the cardiomyocyte clusters (clusters #2, 1, 4 and 7) calculated by the formula: number of significant links for each cluster multiplied by the median transcriptome entropy across all cells in a cluster. (b) Cardiomyocyte clusters from adult injured heart. Arrow indicates the dedifferentiation path derived from the StemID scores. (c) Pseudo time analysis. Left; one-dimensional SOM of z-score transformed expression profiles along the differentiation trajectory incurred by StemID analysis. Y-axis represents the fourteen modules with differentially expressed genes. X-axis represents the pseudo time in which the cells were ordered. Middle; expression profiles of representative genes of the major modules. Y-axis shows transcript counts. X-axis represents the pseudo time. Right; Major gene ontology terms derived from all genes expressed in the module with p-values.

Figure 3—source data 1. List of genes that are differentially upregulated in the respective modules identified in the pseudo timeline analysis (related to Figure 3c).

Figure 3.

Figure 3—figure supplement 1. Induction of hexokinase1 expression precedes expression of myomesin1b.

Figure 3—figure supplement 1.

In situ hybridization for the glycolysis gene hexokinase1 (a,b) and the embryonic cardiac gene myomesin1b (c,d) on sections of injured zebrafish hearts at 3 dpi (a,c) and 7 dpi (b,d). While hk1 expression in border zone cardiomyocytes was visible at 3 dpi and 7 dpi, myom1b expression was visible at 7 dpi but undetectable at 3dpi. (a’,b’,c’ and d’) show zoom-in of boxed areas in corresponding panels. Dashed line indicates the injury site.