Fig. 5: BMP signaling may be integrated by SOX2.

A Normalized expression of SOX2, GATA3, and ISL1 over time for different signaling levels, measured with time-series IF. Data presented as mean +/− standard deviation (SD) across N = 6 images. A box outlined in black shows the data points corresponding to image data in D. B Average nuclear SMAD4 signaling level for each treatment condition in A, determined using SMAD4 dynamics measured in the same conditions and shown in Supplementary Fig. 5B. C Cross section of A showing SOX2 and GATA3 expression at 12 hours, plotted against SMAD4 signaling integral. D Example IF image data for SOX2 in each treatment condition at 36 hours, corresponding to the points boxed in A. Scale bar 50um. E Heatmap of time-series bulk RNA seq data (normalized counts per million) with genes on the y-axis ordered by hierarchical clustering. The cluster dendrogram is shown to the left, with lines colored for discrete cluster assignment, and white lines are drawn on the heatmap to separate clusters. The location in the heatmap of genes also measured with IF is indicated to the right. F Example bulk RNA seq dose-response data is shown for SOX2 with a linear least squares fit of SOX2 with respect to SMAD4 signaling level. The slope of the least squares fit and the correlation coefficient between SOX2 and SMAD4 signaling level are indicated. G Scatterplot of the slope of each gene with respect to SMAD4 signaling and that gene’s correlation with SMAD4 signaling in the dose-response bulk RNA seq data, as determined in F. Locations in the scatterplot of genes for which we also have IF data are indicated. Transcription factors are marked in blue, other transcripts in gray. Source data are provided in a Source Data file.