Fig. 5: Modification of differentiation cytokines produces dendritic cells.

a (left) Schematic illustration of the in vitro differentiation protocol from iPSC to dendritic cells highlighting the time points when samples were collected for scRNAseq profiling. (right) Computational workflow diagram for cell-type annotation. b UMAP projections of the scRNAseq data labelled by cell type (left) and time point (right). In vivo data sets supporting the cell type annotation and the area under the curve (AUC) for the best performing LR model are listed. *In vivo data set LR model of the AUC shown. c Dot plot of canonical marker genes expression for each cell type. d Transcription factor (TF) activities computed with DoRothEA for the identified cell types present at day21 of the in vitro differentiation protocol and matched cell types in the in vivo yolk sac data set⁶ and foetal liver, skin and kidney data set²². Relevant TFs are in bold. e TF activities computed with DoRothEA for cDC2 identified at the last 4 time points of the differentiation protocol (step 3). Relevant TFs are in bold, asterisks highlight significantly different activity vs day31, Bonferroni adjusted p < 0.05. f Stacked area plot showing the proportions of the major cell types from day31 + 1 to day31 + 7. g Flow cytometry histograms showing the protein levels of cDC2 marker genes and CD14 as a negative marker in non-adherent cells at the end of the DC differentiation phase (day31 + 7), matched unstained controls are shown in grey. h Flow cytometry histograms for BODIPY™ FL DQ-ovalbumin processing by non-adherent cells at the end of the DC differentiation phase (day31 + 7) incubated for 15, 45 and 60 min at 37 °C. In grey are matched samples kept at 4 °C as a negative control. i Flow cytometry histograms for a T cell activation assay, peaks with lower CFSE signal than unstimulated T cell negative control (in grey) correspond to proliferative/activated T cells by the presence of anti-CD28, iPSC-derived macrophages or iPSC-derived DCs. Plots shown are representative of two donors and two independent experiments. Source data are provided in the Source data file.