Fig. 2: PEMP display transcriptomic and phenotypic diversity.

A UMAP visualisation of 210 single-cell transcriptomes from 2 early placental samples. Cells are coloured by cluster identity. Bottom panels, cells are coloured by gate used for FACS isolation (left) and by donor (right). Mega: Megakaryocyte progenitors. B Dotplot heatmap displaying scaled log-normalised gene expression of key marker genes across the observed clusters. Dot size represents fraction of cells with nonzero expression. C Heatmap of selected inferred transcription factor activities (regulon scores) across the observed clusters, calculated via SCENIC analysis³⁰. The number of genes associated with each regulon is listed in parentheses. D Heatmap showing mean prediction scores (transcriptomic similarity) of single cells within observed placental clusters using a human foetal liver atlas dataset as a reference²⁸. Scores were calculated using the FindTransferAnchors function in Seurat (see Methods). MEMP (Megakaryocyte-Erythroid-Mast cell progenitors). E Left, Diffusion map embedding of PEMP scRNAseq data with PEMP-1 – PEMP-2 slingshot trajectory overlain (Black arrow). Right, Heatmap of smoothed normalized gene expression of differentially expressed genes across PEMP-1 – PEMP-2 slingshot trajectory. F Left, Diffusion map embedding of PEMP scRNAseq data with PEMP-1 – PEMP-3 slingshot trajectory overlain (Black arrow). Right, Heatmap of smoothed normalized gene expression of differentially expressed genes across PEMP-1 – PEMP-3 slingshot trajectory. G Diffusion map embedding of PEMP scRNAseq data with heatmap overlay of haematopoietic stem cells stemness gene signature enrichment scores. H Quantification of single-cell enrichment scores across PEMP subsets. P values calculated by two-tailed Mann–Whitney test. *p ≤ 0.05 (exact p value = 0.0457), ***p ≤ 0.001 (exact p value = 0.0001). Boxplot centre lines represent the median, with box limits showing the upper and lower quartiles, and whiskers denoting minimum and maximum values. Cells from n = 2 biologically independent placental samples. I Violin plot of CSF2RB log-normalised gene expression across observed clusters. J Analysis of CD131 and CD45RA expression within PEMP via flow cytometry revealing three populations: CD45RA⁻CD131⁻ PEMP (blue), CD45RA⁺ PEMP (green) and CD131⁺ PEMP (purple). K Quantification of PEMP populations via flow cytometry (n = 4 donors) (left panel) and scRNAseq (n = 2 donors) clusters within the PEMP gate (right panel). P values calculated by two-tailed Mann–Whitney test. Flow cytometry quantification data are presented as mean ± SEM, scRNAseq quantification data are presented as mean alone.