Extended Data Fig. 1: Mapping the dynamics of gastruloid development using multi-omics.

(a) Timeline and conditions for human and mouse ESC culturing and gastruloid induction. (b) Total numbers of proteins quantified across all human or mouse samples. Protein identifications were filtered to a 1% FDR and required summed TMTpro reporter ion signal-to-noise ratios >100 for quantitation. (c) Scatterplots comparing the RNA counts between biological replicates for each sample. (d,e) All-by-all sample similarity matrices of pairwise Pearson correlation coefficients (r_Pearson) calculated from summed protein (d) or phosphosite intensities (e) across human (top) or mouse (bottom) samples. Biological replicates were highly correlated across each data type (RNA: r > 0.98; protein: r > 0.93; phosphosite: r > 0.97). (f) PCA plots of PC1 vs. PC2 using RNA (top), protein (middle) or phosphosite (bottom) data across human (left) or mouse (right) samples. (g) Fraction of proteins assigned to each of 34 subcellular localizations by the Human Protein Atlas that were successfully detected here. Numbers within brackets indicate the total numbers of proteins within each class shown. (h) Representative images highlighting the morphology (left) and the SOX2-mCitrine expression across the stages of gastruloid development. Scale bar: 200 μm. The experiments were independently reproduced five times with similar results.