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Fig. 4 Cell death of retinal neurons in the smarce1-mutants. (A) Confocal sections of 72 hpf and 5 dpf retinas stained with methyl green. Pyknotic nuclei representing apoptotic cells exhibit enhanced fluorescence (examples marked with an asterisk). Scale bar: 40 μm. (B and D). Quantification of the total number of pyknotic nuclei in WT (Ctrl) and smarce1-/- (Mut) retinas at 72 hpf (B) and 5 dpf (D). At 72 hpf, n = 8 for both, control and smarce1-/- mutants; at 5 dpf, n = 8 for control and n = 11 for mutant retinas. A Welch́s t-test was performed showing a significant increase in pyknotic nuclei in smarce-/- samples compared to Ctrl. At 72 hpf (t6 = 4.11, p** = 0.0058); at 5 dpf (U = 0,*** p = 0.0004). (C and E). Quantification of the number of pyknotic nuclei per layer in the smarce1-/- retinas at 72 hpf (C) and 5 dpf (E). PR: photoreceptors, INL: inner nuclear layer, GC, ganglion cell layer. (F) KEGG enrichment results show the upregulation of the apoptosis pathway (red), the most significant 20 KEGG upregulated pathways were selected for display. The x-axis represents the ratio of the number of differential genes linked with the KEGG pathway to the total number of differential genes; the y-axis lists the KEGG pathway. The size of a point represents the number of genes annotated to a specific KEGG pathway. The color from red to purple represents the significant level of enrichment. (G) Heatmap showing the top upregulated genes of the Apoptosis Term. The bar shows the average FPKM value of three replicates. Yellow color indicates a high expression level, and black color indicates a low expression level. Genes are organized according to their Padj value from small to large (range 1.72e-93 to 0.021). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)