Extended Data Fig. 7: Identifying patterns of RNA–protein discordance across gastruloid development.

(a) The temporal dynamics of the HOX gene expression cluster. Rows indicate genes, while columns signify samples. Color scale represents the log2 fold change of transcripts normalized to each sample’s respective species mean. (b) Representative examples of RNA vs. protein abundance correlation for SOX2 (red) and LAMTOR2 (teal). (c) Distributions of RNA-protein correlations (r_Pearson) for 6,010 genes grouped by protein class (curated from Human Protein Atlas). (d) Scatterplot of RNA (x-axis) and protein (y-axis) abundance across stages of mouse or human gastruloid development. (e) Hierarchical clustering of patterns of RNA-protein discordance ratios across genes during mouse gastruloid development. (f) Protein complexes whose RNA abundances differ significantly from their protein abundances when comparing early vs. late mouse gastruloids. Significance determined two-sided standard t-test. (g) Median RNA-protein discordances of members of protein complexes at each stage of mouse gastruloid development. (h) Comparison of the RNA and protein log₂-scaled fold changes between early vs. late mouse gastruloids in the Mediator complex (left), intraflagellar transport complex B (middle), and mitochondrial Complex I of the oxidative phosphorylation pathway. Significance testing on RNA and protein distributions was performed using a two-sided standard t-test (NS. denotes not significant; *** denotes p < 0.001).