Figure 3.

Comparative analysis of RPE induction between hESC-RPE, 3D EB differentiation, and human embryonic eye

(A) UMAP of 3D EB cultures at D14 (HS980 line).

(B and C) UMAPs showing signature scores for brain regions (B) and neural tube cell types (C) visualized on the EB D14 UMAP.

(D) Bar plots comparing cell type compositions in 2D and 3D cultures at D14 (top) and D28/30 (bottom).

(E) UMAP of 3D EB cultures at D28 colored by cell type.

(F) Projection of 2D D30 cells from all three cell lines onto the UMAP from (E) using pairwise correlation distances, colored by annotated cell type (see supplemental experimental procedures, cf. Figure 2H). Cells in gray are those from (E).

(G) UMAP of human embryonic optic cup cells at Carnegie stages 12, 13, 14, and 15 (week 5, W5), colored by cell type (left) or stage (right).

(H) Heatmap of enriched gene expression by cell type across all samples in (G).

(I) Heatmap showing signature scores of in vitro cell clusters at D7, D14, and D30 illustrating the correspondence to in vivo clusters from (G). Signature scores were obtained using the top 30 genes of the respective in vivo reference population.

See also Figure S3.