Single-cell RNA-seq Analysis of Zebrafish Heart

Cite: If you use this website, it would be very grateful if you could please cite: J Koth, X Wang and AC Killen et al.

Code: Scripts used to analysis this dataset is available at

Main content of the website:

UMAP: UMAP visualisation of the data

Violinplots: Violin plots of the selected gene

GeneAnno: Differential expression results and pathway analysis of gene lists

Study Design:


  • WT: 4665 cells

  • Injured: 4696 cells

  • Injured Runx1 Mutant: 6054 cells
  • Main visualisation:

    EC: Endothelial/Endocardial cells;

    EPI: Epicardial cells;

    CM: Cardiomyocytes;

    VC: Valve cells;

    MyoFibro: Myofibroblasts;

    Fibro: Fibroblasts;

    Neutro: Neutrophils;

    Mono: Monocytes;

    Macro: Macrophages;

    DC: Dendritic cells;

    Naive T: Naive T cells;

    HSC: Haematopoietic stem cells;

    Lympho: Lymphocytes;

    Erythro: Erythrocytes;

    Thrombo: Thrombocytes;

    Separated by samples


    Please click on a gene in the differential expression result table to plot the gene expression on UMAP