Fig. 3: Endometrial stromal cell heterogeneity and stromal–epithelial cell crosstalk across the menstrual cycle.

a, Dot plot showing normalized, log-transformed and variance-scaled expression of genes (x axis) characteristic of the identified stromal cell states (y axis) in scRNA-seq data. b, Visium spatial transcriptomics data and an H&E image of the same tissue section are shown. Spot color indicates estimated cell state density for a specific cell population in each Visium spot as computed by cell2location. Spatial mapping of the eStromal, dStromal early and dStromal mid cell populations is shown in a section of a whole-uterus biopsy from donor A13 (top panel, proliferative phase; a representative image of n = 2 independent samples from the same donor), a section of a superficial biopsy from donor FX0033 (middle panel, early secretory phase; a representative image of n = 2 biologically independent samples) and a section of a whole-uterus biopsy from donor A30 (bottom panel, mid secretory phase; a representative image of n = 2 independent samples from the same donor). Mapping of menstrual cycle phase-relevant epithelial cell populations is also shown in the niche composition panel. Scale bars, 1 mm. c, Dot plot showing normalized, log-transformed and variance-scaled expression of genes coding for ligands involved in TGFβ, insulin, retinoic acid and WNT signaling (x axis) in epithelial and mesenchymal cell states (y axis) in scRNA-seq data. d, Schematic illustration of the temporal complexity of endometrial stromal cells and signaling pathways across the proliferative and secretory phases. RA, retinoic acid.