Extended Data Fig. 1: Quality control of the scRNA-seq datasets.

a, Experimental workflow for the generation of cellular profiling of the uterus. In short, single-cell suspensions were obtained following two protocols: (i) collagenase treatment to enrich for the stromal fraction (ii) collagenase followed by trypsin to enrich for the glandular fraction. In addition, tissue blocks were processed for single-nuclei RNA sequencing (snRNA-seq) and Visium experiments. b, Single-cell RNA sequencing (ScRNA-seq) data analysis strategy. In short, quality control was performed at the cell and gene level on the matrices generated by STARsolo. To integrate data from distinct individuals, data was batch corrected by each sample using scVI. After defining cell clusters, those clusters containing a high proportion of low-quality cells and doublets (defined by scrublet) were excluded. Re-clustering was performed on epithelial, endothelial and immune cells. c, UMAP (uniform manifold approximation and projection) of scRNA-seq data from all tissue samples. Clusters corresponding to doublets, low QC cells and epithelial cells from the cervix were further excluded from the analysis. d, Dot plot showing log₂-transformed expression of specific markers for the population labelled as ‘cervix’, absent in organ donor samples. Contamination from the cervix is possible due to the biopsy procedure. e, UMAP representations coloured by menstrual stage, biopsy type, menstrual day, tissue type, donor ID and cell cycle phase. f, UMAP of sub-clustered endothelial populations. g, Dot plot showing log₂-transformed expression of selected genes that distinguish the main cell populations. h, Dot plot showing log₂-transformed expression of selected immune cell markers. uSMC = uterine smooth muscle cell; PV = perivascular; eS = non-decidualised endometrial stromal cells; dS = decidualised endometrial stromal cells; uM = uterine macrophages; uNK = uterine Natural Killer cells, T = T cells, ILC = Innate lymphoid cells, DC = Dendritic cells; scRNA-seq = single-cell RNA sequencing, IHC = Immunohistochemistry.