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Fig. 1 ATAC-seq analysis reveals dynamic chromatin accessibility in epicardial cells during heart regeneration. (A) Schematic for experimental design. Partial resection injuries were carried out in tcf21:nucEGFP animals. Ventricles were collected at 3 or 7 dpa, as were those of uninjured clutchmates (Ctrl). Areas of epicardial activation are labeled in green. Ventricles were dissociated, EGFP+ epicardial cells were isolated by FACS, and bulk RNA-seq and ATAC-seq were performed. (B) FACS-isolated cells in a culture dish to examine survival, morphology and EGFP signals. Arrows indicate EGFP+ cells. (C) MA plots of Log2 fold changes (Log2FC) over average normalized ATAC-seq signals. Pink dots indicate peaks with significantly changed chromatin accessibility with the numbers of differential peaks labeled in the corners (FDR<0.05). (D) Heat map of differential chromatin accessibility across three groups with four replicates each. Three clusters (increased, mixed and decreased) are indicated on the left. Increased, peaks with increased accessibility in both 3 and 7 dpa samples; decreased, peaks with decreased chromatin accessibility in both 3 and 7 dpa samples compared with the uninjured control; mixed, peaks with different trends in 3 and 7 dpa samples, compared with the control. (E) Violin plots of differential peaks of three clusters across samples, showing the distribution pattern of chromatin accessibility across samples. (F) Heat map shows the signals of ATAC-seq within ±5 kb of the peak centers. The blue, cyan and yellow lines at the top represent mean read densities of the corresponding ATAC-seq peaks at increased, mixed and decreased chromatin accessibility, respectively. (G) Genomic distributions of all ATAC-seq peaks in three groups. (H) Genomic distributions of the differential and unchanged regions in pair-wise comparisons (top, 3 dpa versus Ctrl; bottom, 7 dpa versus Ctrl).