Extended Data Figure 8: Transcriptional perturbation in Hand2-null embryos.

a, Heatmap of marker genes of populations from Fig. 3a. Statistics for differential gene expression tests were applied to n = 13,185 cells. b, Heatmap of differentially expressed genes between WT and Hand2-null OFT and c, RV cells captured at E7.75 and E8.25. Statistics were applied to n = 253 OFT cells/genotype at E7.75, n = 276 OFT cells/genotype at E8.25, n= 132 RV cells/genotype at E7.75, and n=331 RV cells/genotype at E8.25. Scale indicates Z-scored expression values. d, Quantification of fluorescence signal for indicated genes in Fig. 3h–j and Extended Data Fig. 8f. n=3 independent embryos per genotype. The mean +/− s.e.m is indicated. Two-tailed t-test. *P<0.05 and **P<0.01. e, Violin plots showing expression of Smyd1 and Sema3c in WT and Hand2-null E8.25 AHF cells. f, Expression of Hoxb1 in WT and Hand2-null embryos at E9.25 by whole mount in situ hybridization in right lateral view. Arrowheads indicate expanded anterior Hoxb1 expression in Hand2-null embryos. Scale bar, 500 μm. n=3 independent experiments with similar results. g, Proportion of WT and Hand2-null cells from each population captured at E7.75. n = 5 WT embryos and n = 3 Hand2-null embryos. The mean +/− s.e.m is indicated. Two-tailed t-test. *P<0.05 and **P<0.01. h, Violin plots showing expression of Nppa and Nppb in E8.25 WT and Hand2-null RV cells. All genes in a, b, c, e, h have a Bonferroni correction adjusted p-value < 1×10–4 (Wilcoxon rank sum test, two-sided). Violin plot summary statistics: center white line represents median gene expression and central black rectangle spans the first to third quartile of the data distribution. The whiskers indicate value at 1.5x interquartile range above the third quartile or below the first quartile.