Figure 4.

Figure 4. Assigning the identity of HS5 and NRE-active cells using the expression of eGFP and mCherry, and differential abundance analysis in cell-type clusters.

(A, B) Expression of eGFP and (B) mCherry in single cells visualised on UMAP plots (clustered as in Fig 3A). eGFP expression is enriched in amacrine and retinal stem cell clusters. (C) Dot plot showing average expression and percentage of cells expressing mCherry (HS5-active) and eGFP (NRE-active) in cell-type clusters. Enrichment is seen for eGFP expression in amacrine and retinal stem cell clusters, and for mCherry in Müller glia and retinal progenitor/stem cell clusters. (D) DAseq (Zhao et al, 2021) differential abundance analysis comparing the relative prevalence of cells from mCherry-enriched or eGFP-enriched samples. Cells are coloured by DAseq score and displayed on a UMAP plot. A score is calculated for each cell based on the abundance of cells from both populations in the cell’s neighbourhood. Positive (red) scores indicate an abundance of cells from mCherry-enriched samples; negative (blue) scores indicate an abundance of cells from eGFP-enriched samples.