Fig. 2: Meta-analysis of retinal cells with different donors and species.

a Highlighted region of the eye was selected for single-cell analyses. b tSNE plot visualisation of cells obtained from human retina. Ten transcriptionally distinct clusters were observed in the neural retina of the eye. c RAB41 colocalisation with OPN1SW using RNA FISH. INL inner nuclear layer, ONL outer nuclear layer, GCL ganglion cell layer. Scale bar = 20 µm. n = 2 technical replicates. d, e Representative RNA FISH images of the novel markers TRDN (e) and NIF3L1 (d) for different regions of the eye. MALAT1 was used as an internal control, while PKCA was immuno-stained with NIF3L1 and TRDN with VIM. Scale bar = 20 µm. n = 2 technical replicates. f Patterns of gene expression as determined by scCoGAPS algorithm in retinal cell types of the human eye (see Supplementary Information). The correlation of each pattern to human retinal cell types was colour-coded. g Pattern 17 showed a high correlation to Muller glial cells across species. h Bubble plot showing expression levels of the top 20 genes by gene weight of pattern 17. The size of each circle is proportional to the percentage of cells expressing the gene, and its intensity depicts the average transcript count within expressing cells. i Correlation of human pattern 17 with resting Muller glial cells and Muller glial cells activated after injury in zebrafish. j The patterns of gene expression in zebrafish Muller glial cells which were activated after injury. k Respective GO of the patterns in Fig. 2j. Metascape calculated the statistical significance of each GO term enrichment (p-value) based on the accumulative hypergeometric distribution. The grey colour indicated a lack of significance. l List of genes that were common between human pattern 17 and zebrafish pattern 78.