Extended Data Fig. 7: Epithelial regionalisation along the differentiating Müllerian and Wolffian ducts and within the fallopian tube and epididymis.

a, Batch corrected t-SNE embedding of downsampled Müllerian-derived epithelial cells (n = 2502 cells after downsampling) from female samples > 10 PCW profiled with scATAC-seq coloured by stage (measured in PCW) and cell type. b, Heatmap showing the inferred regulon activity (from both scRNA-seq and scRNA-seq data > 10 PCW female samples) of the TFs (x-axis) involved in the establishment of cellular diversity in the Müllerian duct-derived epithelial cells (y-axis). The colour scale is proportional to the expression of the TF while the size of the dot reflects the importance of the TF regulon in each cell type. c, Batch corrected t-SNE embedding of Wolffian-derived epithelial cells (n = 1502 cells after downsampling) from male samples > 10 PCW profiled with scATAC-seq coloured by stage (measured in PCW) and cell type. d, Heatmap showing the inferred regulon activity (from both scRNA-seq and scRNA-seq data > 10 PCW male samples) of the TFs (x-axis) involved in the establishment of cellular diversity in the Wolffian duct-derived epithelial cells (y-axis). The colour scale is proportional to the expression of the TF while the size of the dot reflects the importance of the TF regulon in each cell type. e, (left) Hematoxylin and eosin (H&E) image of a representative 17 PCW fallopian tube sample profiled with 10x Visium alongside (right) measured expression of LGR5 and TSPAN8 in each spot (n = 6 biologically independent samples). Scale bar: 500 μm. f, High-resolution, large-area imaging of a representative section of a 13 PCW female sample with smFISH signal for EPCAM (red, epithelium), LGR5 (yellow, fallopian tube mesenchyme and uterocervical epithelium), LYPD1 (magenta, middle fallopian tube epithelium), FOXL2 (cyan, fallopian and uterocervical mesenchyme) (n = 3 biologically independent samples). Scale bar: 1000 μm. g, Schematic illustration summarising the mesenchymal-epithelial signalling present along the differentiating Müllerian and Wolffian ducts found in our analysis. h, Schematic illustration of the derivation of the fallopian axis in female samples > 10 PCW (this is part of the Müllerian rostro-caudal axis shown in Fig. 3a–d). i, Schematic illustration of the derivation of the epididymal axis in male samples > 10 PCW (this is part of the Wolffian rostro-caudal axis shown in Extended Data Fig. 5b). j, High-resolution, large-area imaging of a representative section of a 21 PCW female sample with smFISH signal for EPCAM (blue, epithelium), LGR5 (red, fallopian tube mesenchyme and uterine epithelium), LYPD1 (yellow, middle fallopian tube epithelium), FOXL2 (cyan, fallopian tube and uterine mesenchyme) (n = 3 biologically independent samples). Scale bar: 1000 μm. k, Normalised, log-transformed expression of (left) PNOC and (right) MUC6 in each 10x Visium spot of capture areas in Fig. 3k. Scale bars: 500 μm. l, Heatmap showing the min-max normalised expression measured in 10x Visium data of selected spatially variable non-ciliated epithelial genes (x-axis) along the binned epididymal axis (y-axis). m, High-resolution, large-area imaging of a representative section of a 21 PCW male sample with smFISH signal for WNT9B (red, caudal epididymal epithelium), GATA3 (yellow, caudal epididymal epithelium), WIF1 (cyan, epididymal mesenchyme) (n = 3 biologically independent samples). Scale bar: 1000 μm. Illustrations in g–i created by A. García.