Fig. 3: The time-integral and duration of BMP signaling correlate with cell fate at the single-cell level.

A Plot of 50 out of 369 signaling histories, population mean overlaid as a bold black line. B Separation of signaling histories along the first three principal components (PCs). Average of histories one standard deviation above or below the mean along each component are shown in red and blue, respectively. C Example signaling history with a sigmoidal fit to determine signaling features. D Scatterplot of duration vs. PC1 with and without denoising using MAGIC. E Signaling histories from A after denoising. F Correlation between signaling features and PCs across cells. G Correlation of fate marker expression across cells. H Mean signaling histories for amnion-like and pluripotent cells. I Heatmap of signaling histories sorted by log(ISL1 / NANOG). J Scatterplot of log(ISL1 / NANOG) against signaling integral for single cells, with and without denoising. P value calculated with the t-statistic in the MATLAB function corrcoef. K antibody stains for ISL1 and NANOG at different cell densities and BMP4 concentrations. L Mean signaling for amnion and pluripotent fate for each condition in K. M Heatmap of signaling histories sorted by log(ISL1 / NANOG). N Scatterplot of log(ISL1 / NANOG) against signaling integral for single cells, with and without denoising. Color is by condition, indicated with color borders around images in K. P value is as in J. O Heatmap of kernel density estimate after denoising of conditional distributions of log(ISL1 / NANOG) with respect to duration and signaling integral overlaid with a scatterplots of data points before (circles) and after denoising (dots). Dashed lines show separation of cells into amnion-like and pluripotent based on log(ISL1 / NANOG) or on signaling features. The percentage of cells in each quadrant is indicated, with correct assignments in the top right and bottom left quadrant of each heatmap. P Confusion matrix showing the performance of a neural network (NN) and a support vector machine (SVM) in classifying cells as amnion-like or pluripotent using the full signaling history. Source data are provided in a Source Data file.