Fig. 1: iPSC macrophage differentiation produces a range of foetal myeloid and stromal cells.

a Schematic illustration of the in vitro differentiation protocol from iPSC to macrophages highlighting the time points sampled for scRNAseq and scATACseq profiling. Full culture well/plate was collected at each time point and at day31 the non-adherent fraction of the culture was also processed independently (day31 Non-adh). The protocol was repeated twice to generate the Discovery and Validation data sets. b Computational workflow diagram for cell-type annotation. Briefly, LR models were used to annotate the Discovery scRNAseq data set based on publicly available in vivo data sets of human gastrulation (Gas)²³, yolk sac (YS)⁶, foetal liver (including skin and kidney) (FLi)²², foetal thymus (FTh)²¹ and placenta (Pla)²⁰. Then, annotations were transferred to the scRNAseq and scATACseq Validation data sets. c UMAP projections of the Discovery scRNAseq data labelled by cell type. 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. (right) UMAP projections of the Discovery data set labelled by time point. d Dot plot showing canonical markers expression for each of the cell types. Colours depict the mean gene expression and dot size the percentage of expressing cells. e UMAP projections of the scRNAseq Validation data set (n = 62,000) labelled by cell type. f UMAP projections of the scATACseq Validation data set (n = 71,000) labelled by cell type. g Heatmap showing the mean logistic regression models’ predicted probabilities of the YS hematopoietic cell types⁶ for each of the cell types in the Discovery scRNAseq data set. h UMAP projections of the scRNAseq Discovery data coloured by the LR models’ predicted probabilities of the YS hematopoietic cell types⁶. iPSC induced pluripotent stem cell, EB embryoid body, Mac macrophage, LR logistic regression, UMAP uniform manifold approximation and projection, AUC area under the curve, ATAC assay for transposase-accessible chromatin, YS yolk sac, YSMP yolk sac myeloid-biased progenitors. Source data are provided in the Source data file.