Fig. 5: Reprogramming heterogeneity induced by TFs.

a,b, Adiposcore (a; Methods) and expression level of adipogenesis-related genes (b) in CEBPA cells at different doses and batch-paired control cells (dose = 0). c,d, KLF4 and batch-paired control cells colored by Klf4 dose (c, left), cluster (c, right), category (d, top) or batch (d, bottom). Fitted model = LOESS. e, Dose distribution of KLF4 cells in each cluster shown in c (right). f, Heatmap displaying log-normalized expression (z score scaled by gene) of the top differentially expressed genes of KLF4 clusters (shown in c (right) and d (top)). Colored outlines indicate marker genes for respective clusters from e. g, Top ten unique biological process terms identified by GO enrichment analysis on the substantially differentially expressed genes of each KLF4 cluster (shown in c (right)). h, RNAscope images showing DAPI, WPRE (proxy for TF dose), Postn and Glul expression in control and KLF4 cells. Representative images of two independent experiments. Red and purple outlines indicate the cell boundary and expanded cell boundary, respectively. Scale bar = 100 µm. i, Scatterplot showing the expression of Glul (top) or Postn (bottom) in KLF4 cells (colored by the clusters shown in c (right)) and batch-paired control cells in function of Klf4 dose. j, Single-cell quantification of RNAscope (as shown in h) showing the log-normalized mean fluorescence intensity of WPRE (proxy for TF dose) versus Glul or Postn in KLF4 and control cells. Fitted model = GAM. k, UMAP plots of MEIS2 and batch-paired control cells colored by Meis2 dose (top) or cluster (bottom). l, Violin plot showing the dose distribution of MEIS2 cells in each cluster shown in k. m, Dose–response curves for the scores of five distinct gene expression modules regulated by MEIS2. Each module represents the substantially differentially expressed genes from the individual MEIS2 clusters in k. The same color scheme used for the clusters in k is applied to the corresponding modules here. Fitted model = GAM. See Supplementary Table 5 and Methods for statistics and exact P values (Extended Data Figs. 5–7). Ctr, clusters containing fewer than 60% TF cells; GAM, generalized additive model; norm., normalized; pos. reg., positive regulation.