Fig. 1: A spatiotemporal transcriptomic and cellular transcriptomic atlas of the regenerating zebrafish heart.

a Schematic diagram of the experimental design. Hearts were harvested pre-injury (i.e., uninjured), 6 hpa, 12 hpa, 1 dpa, 3 dpa, 7 dpa, 14 dpa, and 28 dpa and subjected to Stereo-seq (3 sections per heart, 6 hearts per stage, 8 stages; 105 total sections analyzed) or scRNA-seq (3 or 6 libraries per stage, 27 total libraries, 7656 cells on average per library). b Documentation of key cellular responses across sequential stages of regeneration. Spatial distributions of major cell-type domains in representative cardiac sections from Stereo-seq. c UMAP clusters discovered by scRNA-seq including all 8 time-points of zebrafish heart across sequential regeneration stages. Pie charts represent the proportions of cell types at each stage. Single asterisks show newly appearing cell types at different time points, and double asterisks show cell types with significantly higher proportions at 1 dpa and 3 dpa compared to the uninjured group. d Scaled cell-type compositions within each domain. The color legend is shared with (b and c). e Directed acyclic graph showing inferred cellular trajectories during the stages of zebrafish heart regeneration. Each row corresponds to one cluster annotation, and each column corresponds to one regenerative stage. Nodes and their colors denote cell-type or cell-state annotations. The gray lines represent lineage relationships between different cell types or states. Speculated nodes and their relationships are shown using dashed nodes and lines. f, g Organ-wide spatial visualization of imputed expression patterns of genes cd63, hif1ab, acta1b, and mt-nd5 at the indicated regeneration stages. CM Cardiomyocyte, V Ventricle, A Atrium, comp. compact, activ. activation, dediff. dedifferentiation, prolif. proliferation, re-diff. re-differentiation, reg. pro-regenerative, BZm border zone myocardium, RZm remote zone myocardium, Vm Ventricular myocardium, Am Atrial myocardium, VAm Ventricular or Atrial myocardium, ECs Endothelial cells, SMC Smooth muscle cells, MC Macrophages, MFE Macrophages Fibroblasts and Endocardial cells, FB Fibroblasts, Epi Epicardium, RBC Red blood cells. Source data are provided as a Source Data file.