Figure 3.

Figure 3. Single-cell RNA sequencing of NRE-eGFP/HS5-mCherry retinal cells at 48 hpf.

(A) Cells from six sequenced libraries of NRE-eGFP/HS5-mCherry F1 embryos at 48 hpf, merged into one sample, and visualised on a Uniform Manifold Approximation and Projection plot created by Louvain clustering using Seurat (Butler et al, 2018). Retinal cell types are manually annotated to clusters depending on marker gene expression. (B) Dot plot showing average expression level and percentage of cells expressing key marker genes used to annotate cell-type clusters. (C) Schematic of cell types in the zebrafish retina. In the ciliary marginal zone, retinal stem cells undergo asymmetrical division to give rise to a rapidly proliferating pool of retinal progenitor cells (left), which divide and differentiate to form cells present in the retinal layers (right) (Richardson et al, 2017; Wan et al, 2016). (A) Colours correspond to the annotated cluster cell types in (A). RGC, retinal ganglion cell; GCL, ganglion cell layer; IPL, inner plexiform layer; INL, inner nuclear layer; OPL, outer plexiform layer; ONL, outer nuclear layer.