Figure 4.

Zone 3 in the SEAM whole-eye colonies is composed of cells expressing ocular surface ectoderm gene profile

(A) Schematic of SEAM culture differentiation and lineages of each SEAM zone. hESC-derived SEAM organoids were differentiated for 55 days, then processed for immunohistochemical analysis single-cell RNA-seq (n = 1 biological replicate). Unbiased clustering of SEAM culture was conducted using the Seurat package (Satija et al., 2015) in R.

(B) Cells possessing ocular surface ectoderm annotation were further clustered, presented as UMAP and principal-component analysis (PCA).

(C) Heatmap of genes distinguishing each cluster by relative expression.

(D) Expression pattern of genes associated with ocular surface ectoderm clusters.

(E) Violin plots of known markers of corneal, limbal, conjunctival, and epidermal lineages.

See also Figures S6 and S7.