Figure 3.

Time Course Transcriptomic Analysis for E8, E6, and BA Samples at 6-h Intervals for 48 h

(A) Heatmap of differentially expressed genes, with hierarchical clustering sequentially grouping each BA time point.

(B) Principal component analysis showing the E8 and E6 samples clustering together, while the BA samples display an ordered trajectory.

(C) Genes differentially expressed in BA samples were clustered into paths based on similarity of temporal expression. Genes comprising each path were analyzed for enriched GO terms for upward trajectories (top row), downward trajectories (bottom row), and a trajectory with upward and downward components (bottom left panel).

(D) Enriched GO terms for genes upregulated (top row, red bars) and downregulated (bottom row, blue bars) in BA samples at 12-, 24-, and 48-h time points.

(E) List of enriched GO terms for genes upregulated at 48 h in BA samples, with terms related to mesoderm and endoderm differentiation highlighted.