Extended Data Fig. 4: Ontology, migration and regression of the Müllerian duct.

a, Dotplot showing the log-transformed, min-max normalised expression of Wolffian ligands and Müllerian receptors (y-axis) in each cell type (x-axis). Interacting ligands and receptors are connected with an arrow. b, Haematoxylin and eosin (H&E) stained image and high-resolution, large-area imaging of a representative section of a Carnegie Stage (CS) 23 sample with smFISH signal for KLK11 (green, coelomic epithelium), FGF20 (red, migrating Müllerian duct epithelium), GDNF (cyan, caudal migrating Müllerian duct epithelium), CALCA (yellow, caudal migrating Müllerian duct epithelium) (n = 3 biologically independent samples). Scale bar: 1000 μm. c, H&E image and ISS data of a representative section of a CS19 sample showing the measured expression of TMEM163 in the Müllerian duct mesenchyme (n = 3 biologically independent samples). Scale: 500 μm. d, High-resolution, large-area imaging of a representative section of a (left) CS22 male sample and (right) CS23 female sample with smFISH signal for WNT7A (red, Müllerian duct epithelium) and TMEM163 (green, migrating Müllerian duct mesenchyme) (n = 4 biologically independent samples, 2 males and 2 females). Scale bar: 200 μm (left panel), 500 μm (right panel). e, H&E image and ISS data of a representative section of a 10 PCW male sample showing the measured expression of WNT7A, WNT9B, SP7, WIF1, NOTUM, and NKD1 (n = 1 biologically independent sample). Scale bar: 1000 μm. f, High-resolution, large-area imaging of a representative section of a CS23 female sample with smFISH signal for WNT7A (red, Müllerian duct epithelium), SP7 (yellow, regressing Müllerian duct mesenchyme), WIF1 (cyan, regressing Müllerian duct mesenchyme), WNT9B (yellow, Wolffian duct epithelium), NOTUM (green, regressing Müllerian duct mesenchyme), NKD1 (cyan, regressing Müllerian duct mesenchyme) (n = 2 biologically independent samples). Scale bar: 500 μm. g, Batch corrected t-distributed Stochastic Neighbour Embedding (t-SNE) embedding of downsampled 6-8 PCW scATAC-seq cells (n = 1220) from the coelomic epithelium, Müllerian duct epithelium and Müllerian duct mesenchyme coloured by developmental stage (measured in PCW) and cell type. h, Heatmap showing the inferred regulon activity (from both scRNA-seq and scRNA-seq data 6-8 PCW samples) of the TFs (x-axis) involved in the formation of the Müllerian duct in each relevant cell type (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. i, Schematic illustration summarising the putative mechanisms underpinning the formation of the human Müllerian duct as found in our analysis. AG: adrenal gland; G: gonad, K: kidney; UGS: urogenital sinus. Illustrations in i created by A. García.