Fig. 3
Transcriptomic analyses on control and Tet2/3-DKO embryonic heart tissues. a Scatter plot of the RNA-seq expression data to identify differentially expressed genes (DEGs) in embryonic heart tissues between the control and Tet2/3-DKO groups at the E12.5 (left) or E15.5 (right) developmental stages. DEGs were defined as q-value < = 0.05. Red and blue dots stand for up- and down-regulated genes, respectively, in the Tet2/3-DKO group when compared to control. b GSEA analysis of DEGs identified between control and Tet2/3-DKO embryonic heart tissues collected at E12.5 (top) and E15.5 (bottom). Benjamini–Hochberg corrected hypergeometric p-value were used. c (Left) Heatmap presentation of the cardiac development-associated DEGs in control and Tet2/3-DKO heart tissue collected at E12.5. (Right) Heatmap presentation of expression data for the same group of cardiac development-associated DEGs in embryonic heart tissues collected at different developmental stages (E10.5 to P0). RNA-seq data were obtained from ENCODE. d Percentages of cell types in E12.5 and E15.5 heart tissues collected from control and Tet2/3-DKO mice using single-cell RNA-seq (scRNA-seq) analysis. Numbers listed above each bar represent the total analyzed cell numbers. e Violin plot showing the distribution of normalized expression levels of selected DEGs at E12.5 and E15.5 heart tissues collected from the control and Tet2/3-DKO groups. CMs were selected based on the expression of cTnT in each cell. Each dot represents the expression levels of corresponding genes in single cells. f The 3D PCA plots (top) and Ttn expression levels (bottom) of individual cardiomyocytes based on scRNA-seq data in the E15.5 control (red) and Tet2/3-DKO (blue) groups. g Selected Ttn-expressing CMs from E15.5 control (red) and Tet2/3-DKO (blue) were displayed based on the expression levels of Hey2 and Tbx20 (left). The expression of Ttn in the corresponding cells were shown in the right panel
