Extended Data Fig. 7: A high-resolution snATAC-seq cell atlas of the human retina.

a, Venn diagram showing the overlapped OCRs detected by retinal snATAC-seq and bulk ATAC-seq. b, Pie chart showing cell type specificity of OCRs identified from retinal snATAC-seq (left) and bulk ATAC-seq (right). The color codes the number of cell types where the OCRs were observed. c, Heatmap showing the chromatin accessibility of differential accessible regions (DARs) identified in major retinal cell classes. Rows represented chromatin regions and columns corresponded to cell classes. d, Genome track of the RHO locus showing the cell class-specific chromatin accessibility in the promoter and linked cis-regulatory elements of this gene. e, Heatmap showing chromatin accessibility (left) and gene expression (right) of 129,636 significantly linked CRE–gene pairs identified by the correlation between gene expression and OCR accessibility. Rows represent cis-regulatory element (CRE)–gene pairs, which are clustered into 25 groups using k-means clustering. Columns represent cell groups that were grouped using the K nearest neighbor (KNN) method. f, Density plot showing the activity (log₂(FC) value of comparison of the activities between a tested sequence and a basal CRX promoter) distribution of the tested sequences by MPRAs. IRD CREs, n = 1,714 (green); control CREs with a variety of activities, n = 20 (red); scrambled CREs, n = 300 (blue). g, Box plots showing phastCons20way score distribution of validated enhancers, silencers and inactive elements. P-values were calculated using a one-sided Wilcoxon rank-sum test to assess differences among groups (n = 1,714 CREs) without adjustment for multiple comparisons. Centerline represents the median phastCons20way score, upper and lower hinges represent the upper and lower quartiles, respectively, and whiskers represent 1.5× IQR. h, Box plots showing phyloP20way score distribution of validated enhancers, silencers and inactive elements. P-values were calculated using a one-sided Wilcoxon rank-sum test to assess differences among groups (n = 1,714 CREs) without adjustment for multiple comparisons. Centerline represents the median phyloP20way score, upper and lower hinges represent the upper and lower quartiles, respectively, and whiskers represent 1.5× IQR. i, Scatterplot showing eRegulon specificity score of each transcription factor (TF) regulon across cell classes. The top five TFs are highlighted in red.