Fig. 1

Dynamics of the developing NC gene expression profile. a Schematic depicting the region dissected from T18, T20 and T21 lamprey embryos for DNT RNA-seq and the number of biologically independent samples analysed. b PCA of rlog-transformed gene expression count tables for 56,319 genes with non-zero read counts. PC1, which accounts for 90% of the variance is stage dependent (colours indicate stage as in a. c Volcano plot of differential expression analysis between T21 and T18 (p value < 0.05; green, enriched; red depleted at T21). Coloured dots and labels indicate genes previously known to be enriched or depleted in the developing NC. Dashed line indicates logFoldChange = 1/−1. d–f Clusters of highly correlated genes (grey lines) identified by WGCNA (d, downregulated after T18; e, upregulated at T20; f, upregulated at T21; black line is the mean profile), showing specific genes that are known to be downregulated (red) or upregulated (green) in the NC, as well as upregulated genes that have not been previously implicated in NC development (blue). g–h Heatmaps of the average variance stabilised normalised gene counts for selected genes from WGCNA clusters 2 and 3, showing increased expression at T21. Low-level (g) and high-level (h) expressing genes are shown. i Bubble plots summarising enrichment and p values for the most significant GO biological process terms associated with enriched genes at T18 relative to T21 and at T20 and T21 relative to T18 (only terms enriched more than three-fold are shown). j Whole-mount in situ hybridisation for the indicated genes at T21 and T23 (expression patterns observed in at least 3 embryos). Insets are magnifications of boxed regions. Dashed lines indicate approximate plane of sections in the adjacent panel. Scale bars in row 1 and row 3 are the same for images at equivalent stages. Scale bars for wholemount embryo images: 100 μm. Scale bars for sections: 50 μm