Figure 2.

Gene Expression and Chromatin Accessibility of iPSC-RPE and Other Eye Samples

(A) tSNE plot based on the first 30 principal components of RNA-seq using 10,000 of the most variable genes. Samples include iPSCs, iPSC-CMs, iPSC-RPE, and fetal RPE data generated for this paper, and RPE and retina samples from external public data sources (see legend in B, inset).

(B) tSNE plot based on the first 30 principal components of RNA-seq using 10,000 of the most variable genes. In this case only samples related to RPE and retina are included.

(C) Heatmap showing expression levels of RPE signature genes (Strunnikova et al., 2010) in fetal RPE, iPSC-RPE, iPSC, and iPSC-derived cardiomyocytes. Genes are labeled by their gene group as annotated in Liao et al. (2010).

(D) Scatterplot showing RNA-seq TPM for an iPSC-RPE (iPSCORE_1_14) compared with the fetal RPE sample for RPE signature genes. Points are color coded according to their classification in Liao et al. (2010) and lines indicate linear regression best fits.

(E) Heatmap showing six iPSCORE iPSC-RPE (iPSCORE_42_1, 17_1, 29_1, 1_14, and 87_1) and human fetal RPE ATAC-seq peaks show stronger Jaccard similarity to native RPE ATAC-seq peaks than retina ATAC-seq peaks from adult eyes with and without AMD (Wang et al., 2018). Columns are color coded according to their AMD type and cell type. Three RPE and three Retina samples from the same subject with late AMD were not similar with respect to the other RPE and Retina samples and were labeled as “Late AMD Outlier.”

(F) Heatmap showing similarity of transcription factor (TF) binding site enrichment in ATAC-seq peaks across samples. Color indicates the TF's rank of enrichment within each sample with red indicating stronger enrichment. Columns are color coded according to their AMD type and cell type.

See also Figure S1.