Extended Data Fig. 6: Human-mouse comparison and trajectory inference of early gonadal somatic cells.

a, UMAP (uniform manifold approximation and projection) of gonadal somatic cells in the human (top) and mouse (bottom) scRNA-seq datasets coloured by sample of origin, sex and developmental stage (indicated in post-conceptional weeks (PCW) or embryonic (E) / postnatal (P) day). Dots from the same donor or sample share a colour. b, UMAP projections of the fate probabilities of each cell ending up in one of the terminal states (scRNA-seq). Coloured symbols indicate the initial and terminal cell states predicted by CellRank. Top UMAPs depict two human (7 post-conceptional weeks, PCW testis; 7.5 PCW ovary) gonadal samples while bottom UMAPs depict two mouse (E11.5 testis and E12.5 ovary) gonadal samples, analysed independently. c, t-SNE (t-distributed stochastic neighbour embedding) projection of somatic cells coloured by Palantir pseudo-time and probability of cells to progress from the gonadal coelomic epithelium GATA4+ in humans between 6-8.5 PCW (left) and mice at E10.5-E11.5 (right). Somatic cells are downsampled to account for 150 cells for each cell state in each sex in both species. d, (left) UMAP projections of the predicted probability of ESGC from our dataset onto Guo et al., 2021 somatic cells manifold using a Support Vector Machine (SVM) classifier. (right) UMAP projections on the validation dataset of human fetal testis, re-analysed from Guo et al., 2021, labelled by somatic cell state. e, Barplot showing the proportions of somatic cells in the Guo et al., 2021 dataset coloured by cell state and classified by PCW. f, Dot plots showing the variance-scaled, log-transformed expression of genes characteristic of human ESGC in the Guo et al., 2021 dataset of human fetal testis. g, Dot plot showing the variance-scaled, log-transformed expression of genes in the WNT4/RSPO1 pathway in ESGC (split in male and female), preGC-I and Sertoli cells in the human (top) and mouse (bottom) scRNA-seq dataset. h, Dot plots showing the variance-scaled, log-transformed expression of human-specific markers of ESGC in the mouse scRNA-seq dataset. i, High-resolution, imaging of representative human gonadal sections with intensity proportional to smFISH signal for RNA markers. (top) Carnegie stage 19 (CS19) ovary stained for LGR5 (red, ESGC), TSPAN8 (yellow, ESGC), RIMS4 (magenta, 1st wave somatic cells), OSR1 (cyan, preGC-I). The white dashed line outlines the ovary; the white dashed rectangle highlights the enlarged gonadal region. ESGCs nuclei have been marked with dashed circles. (bottom) CS19 testis stained for LGR5 (red, ESGC), TSPAN8 (yellow, ESGC), SRY (magenta, ESGC), SOX9 (cyan, Sertoli). The white dashed line outlines the testis. The white dashed rectangle highlights the enlarged gonadal region. White arrows in the magnified areas mark ESGC nuclei; n = 2. Scale bars = 100 µm and 10 µm in magnified regions. CoelEpi = coelomic epithelium; E = embryonic day; ESGC = early supporting gonadal cells; Gi = gonadal interstitial; P = postnatal day; PCW = post-conceptional week; preGC = pre-granulosa cells; sPAX8 = supporting PAX8; Ti = testicular interstitial.