Extended Data Fig. 8: Second wave of fetal pre-granulosa.
a, Boxplots of the predicted probabilities (Y-axis) of the label transfer from human to mouse supporting cells (X-axis) in the ovaries around the time of the second wave of pre-granulosa cells (8-16 post-conceptional weeks (PCW) human, embryonic day (E) 12.5-E16.5 mouse, n = 10,042 cells; left) and around the time of folliculogenesis (17-21 PCW human, E18.5- postnatal day (P)5 mouse, n = 5,296 cells; right). The box extends from the lower to upper quartile values of the data, with a line at the median. The whiskers extend from the box to show the range of the data. Flyer points are those past the end of the whiskers. b, Heatmap reporting label transfer scores from human scRNA-seq to scATAC-seq somatic cell data of matched individuals. c, UMAP (uniform manifold approximation and projection) of somatic cells in the human scATAC-seq dataset labelled by the cell state identified in snRNA-seq data from the cell-coupled snRNA-seq/snATAC-seq profiling. d, Hierarchical clustering of z-scores for each cis-co-accessibility network (CCAN) identified in human ovarian supporting cells in the human scATAC-seq dataset. e, UMAP projections of somatic cells in the macaque scRNA-seq dataset re-analysed from Zhao et al., 2020 labelled by cell type and stage. f, Dot plots showing the variance-scaled, log-transformed expression of genes (X-axis) characteristic of ovarian supporting cells (Y-axis) in mouse (left) and macaque (right) scRNA-seq data. Top-layer groups marker genes by categories. g, (top) Diagram showing the information added in the updated version of CellPhoneDB database (CellPhoneDB v4), which includes: (i) 534 novel (1,852 total) ligand-receptor interactions; (ii) 194 novel interactions mediated by small molecules; (iii) 186 novel curated links between ligand-receptor and transcription factors (CellSign module). (bottom) Diagram showing the new statistical framework to infer active cell-cell interaction partners. It includes an additional step to indicate active ligand-receptor partners in our data based on the activation of downstream signals on the receiver cell (CellSign module). Downstream signals are calculated based on TF expression and TF activity from scRNA-seq and scATAC-seq data. h, Heatmap showing the expression of TF downstream the receptors (CellSign) upregulated in germ and supporting cells (shown in Fig. 4d). Colour proportional to scaled log-transformed expression. Symbols highlight TF status, as in (Fig. 4b). Specificity between receptors and the corresponding downstream TF are indicated with a symbol matching the upstream receptors in Fig. 4d. i, Dot plots showing scaled log- transformed expression of genes coding for interacting extra-cellular matrix (ECM) proteins in supporting (top) and germ (bottom) cells states. j, High-resolution imaging of representative gonadal section of a human fetal ovary (19PCW), with intensity proportional to smFISH signal for NTN1 (green, granulosa), FIGLA (yellow, oocytes), DCC (red, oocyte), FOXL2 (magenta, granulosa); n = 2. White dashed rectangles highlight follicles and the enlarged gonadal region. Scale bars = 100 µm and 10 µm in the magnified region. k, Schematic illustration of main TFs, receptors, ligands and extracellular molecules regulating germ cell differentiation influenced by the granulosa lineage. New molecules identified in our study are highlighted in green. CoelEpi = coelomic epithelium; E = embryonic day; ESGC = early supporting gonadal cells; FGC = fetal germ cells; Gi = gonadal interstitial; Oi = ovarian interstitial; OSE = ovarian surface epithelium; P = postnatal day; PCW = post-conceptional week; PGC = primordial germ cells; preGC = pre-granulosa cells; TF = transcription factor; Ti = testicular interstitial; sPAX8 = supporting PAX8.
