Extended Data Fig. 6: Dynamics of maturation of enterocytes during intestinal homeostasis.

a, Velocity field projected on a 2D t-SNE plot. The clusters are labelled and coloured as in the original publication¹¹ to facilitate comparison (n = 2,683). Velocity analysis revealed a transition related to the maturation of distal and proximal enterocytes. No consistent velocity was observed in the part of the manifold occupied by stem cells and transit amplifying (TA) cells, suggesting that stem cell dynamics are more difficult to capture either for their slower rate or a more stochastic nature. The small velocities of transit amplifying cells were likely to be driven by the cell cycle. b, A selection of the cell cycle genes that were removed from the analysis is plotted on the t-SNE. Despite the removal of the genes annotated as cell cycle genes, we still observed important segregation by cell cycle, illustrating the difficulty of disentangling cell cycle phase from the cell state. c, A selection of phase portraits that show genes underlying the observed velocity field. Markers of endocrine, goblet and tuft cells displayed no detectable velocity. Velocity towards and from stem cell states was detectable for a limited set of genes (such as the stem cell marker Lgr5), however, on the genome-wide level, the exact dynamics of this process was probably confounded by the high correlation with cell cycle.