Extended Data Fig. 9: Spatial patterning of the gut tube at E8.75.

a, Plots showing individual Phenograph cluster densities of the E8.75 gut tube cells ordered along the anterior–posterior pseudo-space (left) and in force-directed layouts (middle). ISH of representative differentially expressed genes in each cluster on whole E8.75 embryos (n > 3 for each gene) or micro-dissected E8.75 gut tubes (n > 3 for each gene) (right). Arrowheads point to expression of representative gene for each particular cluster. Scale bars, 200 μm (except for Nkx2-1, 100 μm). no, notochord. b, Density of E8.75 cells along the anterior–posterior pseudo-space axis. c, Comparison of empirical anterior–posterior pseudo-space axis and the predicted anterior–posterior pseudo-space, using expression of transcription factors. Each dot represents the anterior–posterior pseudo-space of a cell computed by all genes, versus pseudo-space prediction by the selected transcription factors alone. d, Plot showing the ranking of different transcription factors according to their predictive power, on the basis of the regression model. e, Heat map showing the coefficients for the top transcription factors when different proportions of cells are subsampled for the regression (total cells, 24,990). f, Heat map showing the Pearson’s correlation of transcription factor coefficients in e, highlighting the robustness of transcription factor coefficients in regression.