Fig. 3: Evaluation of the macrophage phase.

a Schematic illustration of the in vitro differentiation protocol and cell-type annotation analysis, steps before the macrophage differentiation phase are hidden. Additional experimental conditions (alternative cytokines, top, and media experiment, bottom) are highlighted in red, standard protocol conditions are in black. b (right) UMAP projections of the macrophage phase labelled by cell type and time points. All experiments are pooled. (right) UMAP projections highlighting the cells included in each experiment. c Stacked area plot of the cell type percentages in each time point. Only samples from the time points experiment (M-CSF) were included. d (left) UMAP projection highlighting macrophages from the time points experiment (M-CSF only) and coloured by time point. (right) Heatmap of the transcription factor activity scores calculated using DoRothEA across time points, relevant TFs are in bold, asterisks highlight significantly different activity vs day31, Bonferroni adjusted p < 0.05. e TF motif enrichment values in macrophage ATAC open peaks at day31 + 7 vs day31 plotted against TF transcriptional activity score at day31 + 1 (left) or day31 + 7 (right). Pearson correlation’s r and exact p values are shown. f (left) UMAP projection highlighting macrophages from the cytokines experiment and coloured by time point and cytokine cocktail used. (right) Heatmap of the TF activity scores across time points and cytokines, relevant TFs are in bold, asterisks highlight significantly different activity vs day31, Bonferroni adjusted p < 0.05. iPSC induced pluripotent stem cells, TF transcription factor, ATAC assay for transposase-accessible chromatin. Source data are provided in the Source data file.