Fig. 5: Dynamic gene expression changes before and after eye opening.

a, Number of clusters and subclusters at each synchronized age. b, Quantification of changes of DE genes in each subclass across development, grouped by classes. For each sliding pair of adjacent synchronized ages, we calculated the sum of log₂[FC] of DE genes in each subclass, with positive and negative changes (later time minus earlier time) calculated separately (Methods). The box plots show repeated DE analysis 100 times for each pair of adjacent synchronized ages, each time randomly subsampling 70% of the selected cells in each subclass (Methods and Supplementary Table 3). The central line indicates the median value, the box spans the IQR range (25th–75th percentile), and the whiskers extend to 1.5× the IQR, with outliers individually plotted. Microglia are not represented in the P3–P4, P4–P5 and P25–P28 comparisons owing to an absence of this population in at least one group in each comparison. Similarly, VLMCs are absent across all comparisons from P1–P2 to P4–P5. Subclass colours of the curves are the same as subclass colours shown in c and d. c, UMAP representations of the neuronal and non-neuronal classes, coloured by subclass (left panels of each class) and synchronized age (before eye opening: P7–10; after eye opening: P11–15; right panels). d, DE genes between ages before and after eye-opening for all cell subclasses. Top, sum of log₂[FC] of all DE genes upregulated (blue) or downregulated (red) during eye opening. Middle, number of DE genes upregulated or downregulated during eye opening (coloured by class). Bottom, log₂[FC] of each DE gene (coloured by subclass).