The cornea, limbus, and sclera form the ocular surface, a critical interface that protects the eye, maintains visual function, and provides structural support. The cornea serves as the primary refractive surface and barrier against external pathogens. The limbus, located at the corneal-scleral junction, houses limbal stem cells essential for the regeneration of the corneal epithelium. The sclera provides structural integrity, protects the eye, and serves as the attachment site for extraocular muscles. Together, these three components play integral roles in sustaining ocular function and homeostasis. To capture the major cell types and subclasses of the ocular surface, we generated large-scale datasets using scRNA-seq and snRNA-seq technologies from healthy human donors spanning a wide range of ages, genders, and ethnicities. Additionally, publicly available datasets were integrated to expand the scope of the atlas. In total, the atlas includes over 1 million cells and nuclei from 102 donors. We identified 10 major cell classes and 31 types in the atlas, including rare populations such as limbal progenitor cells, Schlemn’s canel endothelium, and specific immune subtypes. The atlas also captures the full trajectory of epithelial differentiation. To further enhance our understanding of gene regulation, we generated a snATAC-seq atlas, profiling over 362k nuclei from 26 donors, including 8 developmental samples, facilitating the characterization of cell type-specific chromatin accessibility landscapes and regulatory elements. All datasets underwent a unified preprocessing pipeline and data integration to ensure consistency and quality. The atlas is publicly accessible through CELLxGENE, enabling interactive exploration of gene expression and regulatory landscapes. As part of the Human Cell Atlas initiative, this comprehensive ocular surface atlas marks a significant advance in understanding ocular tissue physiology and provides a valuable resource for studying ocular surface development, aging, and diseases such as corneal dystrophies, limbal stem cell deficiency, and scleral remodeling.
This atlas is an integrated collection of over 147k cells, derived from single-nuclei RNA-seq data of human ocular surface, including cornea, limbus, and anterior sclera. These cells have been categorized into 10 major cell classes and 26 types.
This atlas is an integrated collection of over 815k cells, derived from single-cell RNA-seq data of human ocular surface, including cornea, limbus, and anterior sclera. These cells have been categorized into 10 major cell classes and 31 types.
