Extended Data Fig. 8: Immune cells in scRNA-seq and snRNA-seq data.

a, UMAP projections of scRNA-seq data for immune cells coloured by dataset, menstrual cycle group, cell cycle phase and biopsy type. b, UMAP projections of snRNA-seq data for immune cells coloured by menstrual cycle group and cell cycle phase. c, UMAP projection of snRNA-seq data for immune cells coloured by the probability of assigning the immune cell types identified in the scRNA-seq data. Support Vector Machine (SVM) classifier was trained using the immune cell scRNA-seq data and the predicted cell type annotations were then projected onto the snRNA-seq data with the probability shown. d, Dot plot showing normalised, log-transformed and variance-scaled expression of genes (x-axis) characteristic of the identified immune cell states (y-axis) in the scRNA-seq data. e, Dot plot showing normalised, log-transformed and variance-scaled expression of genes (x-axis) characteristic of the identified immune cell states (y-axis) in the snRNA-seq data. f, Beeswarm plot of the distribution of log fold change across the menstrual cycle (proliferative and secretory phases) in neighbourhoods containing immune cells from different cell type clusters in snRNA-seq data. Differentially abundant neighbourhoods at log fold change > 2.5 and spatial FDR < 0.1 are coloured. g, Visium spatial transcriptomics data for donors A13 (proliferative phase) and A30 (secretory phase) (n = 2 biologically independent samples) are shown. Spot colour indicates estimated cell state density for a specific population of perivascular cells (mPV, ePV-1a, ePV-1b and ePV-2) in each Visium spot, as computed by cell2location. h, Dot plot showing normalised, log-transformed and variance-scaled expression of genes (x-axis) characteristic of the identified endothelial, perivascular and stromal cells (y-axis) in the scRNA-seq data. cDC, conventional dendritic cells; eStromal, endometrial stromal cells specific to proliferative phase; ePV, endometrial perivascular cells; FDR, false discovery rate; ILC3, innate lymphoid cell type 3; mPV, myometrial perivascular cells; pDC, plasmacytoid dendritic cells; RBC, red blood cells; scRNA-seq, single-cell RNA-sequencing; snRNA-seq, single-nucleus RNA-sequencing; SVM, support vector machine; T Reg, T regulatory cells; uM, uterine macrophages; UMAP, uniform manifold approximation and projection; uNK, uterine natural killer cells.