Extended Data Fig. 1: Temporal and spatial composition of human prenatal skin.

(a) Prenatal skin cells isolation by fluorescence-activated cell sorting into CD45⁺ and CD45⁻ fractions (n = 18); from the CD45⁻ fraction we further isolated all cells that were not within the CD34⁺/CD34⁺CD14⁻ gate (n = 4) to enrich for endothelial cells and keratinocytes. Representative data from n = 1 is shown as mean percentage +/− SD values. (b) Quality control plots showing frequency distribution of UMI counts (log1p-transformed) and percent of UMI counts in mitochondrial genes per sample fraction. (c) Dot plot showing variance-scaled, mean expression (dot colour) and percent of expressing cells (dot size) of defining genes for cell states corresponding to Fig. 1b. (d) Milo beeswarm plot showing differential abundance of neighbourhoods in prenatal skin across gestation time, annotated by refined cell labels. Red/blue neighbourhoods are significantly enriched in earlier/later gestation respectively. Colour intensity denotes degree of significance. (e) Bar plot showing cell type co-location, indicated by positive Pearson correlation coefficients calculated between per-spot normalised cell type abundances, for selected cell type pairs (macrophage and endothelial cells). Pearson correlation coefficients were calculated across all skin-covered spots of Visium samples; each sample is shown by an individual bar. (f) Bar plot showing cell type co-location, indicated by positive Pearson correlation coefficients calculated between per-spot normalised cell type abundances, for selected cell type pairs (pre-dermal condensate and immune cells: DC1, DC2, LTi and ILC3). Pearson correlation coefficients were calculated across all skin-covered spots of Visium samples; each sample is shown by an individual bar. ASDC, Axl⁺Siglec6⁺ dendritic cells; CD45en, CD45 negative fraction enriched for keratinocyte/endothelial cells, CD45N, CD45 negative; CD45NCD34N, CD45 negative-CD34 negative; CD45NCD34P, CD45 negative-CD34 positive; CD45P, CD45 positive; DC, dendritic cells; HSC, hematopoietic stem cells; LC, Langerhans cells; LTi, lymphoid tissue inducer cells; MEMP, megakaryocyte-erythroid-mast cell progenitor; pDC, plasmacytoid dendritic cells.