Study: A Cell Atlas Of the Chick Retina Based on Single Cell Transcriptomics 35026 cells

Retinal structure and function have been studied in many vertebrate orders, but molecular characterization has been largely confined to mammals. Here, we used single-cell RNA sequencing (scRNA-seq) to generate a cell atlas of the chick retina. From ~40000 single cell transcriptomes, we identified ~150 cell types distributed among the six classes conserved across vertebrates – photoreceptor, horizontal, bipolar, amacrine, retinal ganglion and glial cells.  To match molecular profiles to morphology, we adapted a method for CRISPR-based integration of reporters into selectively expressed genes. For Müller glia, we found that transcriptionally distinct cells were regionally localized along the anterior-posterior, dorsal-ventral and central-peripheral retinal axes.  We also identified immature photoreceptor, horizontal cell and oligodendrocyte types that persist into late embryonic stages. Finally, we analyzed relationships among chick, mice and primate retinal cell types. Taken together, our results provide a foundation for anatomical, physiological, evolutionary, and developmental studies of the avian visual system.