Fig. 1. Reversible pausing in ESCs but not in TSCs.
a, Experimental setup: ESCs and TSCs were paused via mTORi for a total of 7 days (samples collected only within the first 48 h), then released. Three biological replicates were collected at the indicated timepoints for proteomics analysis. Representative images of ESC and TSC cultures are shown. Scale bar, 100 µm. b, PC analysis of ESC and TSC proteomics data. The colour scale indicates the timepoint during entry into pausing or release from pausing. c,d, Pseudotime analysis of ESCs (c) or TSCs (d), showing the computed pseudotime against the biological time (in hours, +1 for imputation) with a regression curve in the black dotted line and 95% confidence interval around it. The pseudotime analysis indicates reversibility of pausing of the ESC proteome. e, Divergent KEGG pathways during entry into pausing in ESCs and TSCs. The pathway score was computed on the basis of mean expression of pathway proteins over time (Methods). Selected pathways with a divergence score of >0.0075 are displayed (see Supplementary Table 5 for the full list). SNARE, soluble N-ethylmaleimide-sensitive factor attachment protein receptor. f, Line plots of log2FC of mean protein expression (mTORi/control t = 0) of selected divergent pathways.