Extended Data Fig. 6: Mesenchymal patterning and mesenchymal-epithelial interaction along the differentiating Müllerian and Wolffian ducts.

a, Batch corrected t-distributed Stochastic Neighbour Embedding (t-SNE) of downsampled Müllerian-derived mesenchymal cells from female samples > 10 PCW profiled with scATAC-seq (n = 5370 cells after downsampling) 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 mesenchymal 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 of downsampled Wolffian-derived mesenchymal cells from male samples > 10 PCW profiled with scATAC-seq (n = 5469 cells after downsampling) 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 mesenchymal 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, Schematic illustration showing the bidirectional cell-cell communication between the mesenchyme and epithelium of the differentiating Müllerian and Wolffian ducts along their rostro-caudal axes in female and male samples > 10 PCW. f, (left) Hematoxylin and eosin (H&E) image of a representative 13 PCW female sample profiled with In Situ Sequencing (ISS) alongside (right) measured expression of ALDH1A1 and WIF1 (n = 3 biologically independent samples). Scale bar: 100 μm. g, Heatmap showing the min-max normalised expression measured in scRNA-seq data of epithelial partners of the spatially variable mesenchymal ligand/receptors (x-axis) along the binned imputed Müllerian rostro-caudal axis (y-axis). h, Network representation of the gene regulatory network for HOX code TFs only including targets that were identified as spatially-variable in the Müllerian-derived mesenchyme. i, Heatmap showing the min-max normalised expression measured in 10x Visium data of prioritised spatially variable mesenchymal ligands or receptors (x-axis) along the binned measured Wolffian rostro-caudal axis (y-axis). Interacting partners for each spatially variable mesenchymal ligand/receptor are reported on the x-axis below the activatory or inhibitory arrows. A dot in a bin indicates that the interacting partner of the spatially variable mesenchymal ligand/receptor is expressed in at least 20% of epithelial cells in that bin. j, Heatmap showing the min-max normalised expression measured in 10x Visium data of epithelial partners of the spatially variable mesenchymal ligand/receptors (x-axis) along the binned measured Wolffian rostro-caudal axis (y-axis). k, Heatmap showing the min-max normalised expression measured in scRNA-seq data of prioritised spatially variable epithelial TFs (x-axis) along the binned imputed Müllerian rostro-caudal axis (y-axis). CE: cervix; FT: fallopian tube; LV: lower vagina; UT: uterus; UV: upper vagina. Illustrations in e created by A. García.