Extended Data Fig. 10: Gene regulation in the differentiation of pigment and notochord cells.
a, UMAP projection of all pigment cells colored by one progenitor population and three pigment subtypes. b, Genome browser tracks of aggregate chromatin accessibility profiles for each cell type of pigment cells at selected marker gene loci that were used for cell cluster annotation. c, Heatmap summary of cell-type-specific cCRE-to-gene linkages where chromatin accessibility is highly correlated with gene activity score (Pearson’s r > 0.5) in pigment cells. Rows in the left heatmap represent peaks and are colored by accessibility while rows in the right heatmap represent genes and are colored by gene activity score. The top Zebrafish Wild-type Expression terms for cCREs of four cell-type-specific modules were listed on the right (GREAT ontology enrichment analysis with the binomial distribution test). d, UMAP projection of notochord cells colored by gene activity scores of several selected marker genes. e, UMAP projection of single-cell RNA-seq data from Wagner DE, et al.8 and Farnsworth DR, et al.6, colored by developmental stages. Notochord cells are in silico extracted, colored by gene expression of several selected marker genes. f, UMAP projection of a recently released single-cell RNA sequencing time-course dataset of zebrafish development (Zebrahub, https://zebrahub.ds.czbiohub.org/), colored by developmental stages. Notochord cells are in silico extracted, colored by gene expression of several selected marker genes. g, Heatmap summary of cell-type-specific cCRE-to-gene linkages where chromatin accessibility is highly correlated with gene activity score (correlation > 0.7) in notochord cells. Rows in the left heatmap represent peaks and are colored by accessibility while rows in the right heatmap represent genes and are colored by gene activity score. h, Distribution of the number of genes mapped per peak (median = 1; left). Distribution of the number of peaks mapped per gene (median = 2; right). Source numerical data are provided as source data.
