Cell alterations of the ischemic macaque retina were generated through droplet-based scRNA-seq following 6 hours of ophthalmic artery occlusion by operation (
Fig. 1A). A total of 9495 cells from four retinas, two from the ischemic group and two from the control group, were collected for high-quality cell atlases following quality inspection. The initial analysis of the single-cell transcriptome data involved categorizing similar individual cells into specific cell subpopulations based on their gene expression profiles, utilizing the uniform manifold approximation and projection (UMAP) technique.
11 The cells were categorized into 13 primary classes using the widely recognized retina cell types and the firmly established gene signatures specific to each class
12,13 (
Figs. 1B,
1C). In this study, we have assigned cell identities to various cell types with the retina based on the expression of hallmark genes, including rod photoreceptors (PDE6A, GNGT1, RHO), cone photoreceptors (ARR3, PDE6H, GUCA1C), bipolar cells (VSX2, LRTM1, TRPM1), horizontal cells (LAMP5, SLC6A9, CPLX3), amacrine cells (GAD1, C1QL2, AMIGO2), retinal ganglion cells (SNCG, NEFM, SLC17A6), microglia (C1QA, C1QB, CD163), astrocytes (GPX3, WIF1, FRZB), Müller cells (TTR, RDH5, ENPP2), pericytes (RGS5, CALD1, ACTA2), endothelial cells (CLDN5, ITM2A, RNASE1), neutrophils (S100A8, S100A9, CSF3R), and T cells (GZMB, CCL5, CD3D). The expression of these selected marker genes is depicted in dot plots (
Fig. 1D).