Extended Data Fig. 1: Single-cell RNA-sequencing datasets of the Human Endometrial Cell Atlas (HECA) and the cervix.
From: An integrated single-cell reference atlas of the human endometrium
a, UMAP projections of scRNA-seq data for HECA coloured by cell lineage, dataset, menstrual cycle, cell cycle phase and biopsy type. b, Dot plot showing normalised, log-transformed and variance-scaled expression of genes (x-axis) characteristic of the main cell lineages (y-axis) in the HECA. c, Dot plot showing normalised, log-transformed and variance-scaled expression of genes (x-axis) characteristic of mesenchymal and endothelial cells (y-axis) in the HECA. d, Bar plot showing the cellular composition of endometrial biopsies in the different menstrual cycle groups (y-axis). e, UMAP projection of a scANVI representation of the HECA coloured by the cell states identified. Red dotted-lined shapes outline the MUC5B, KRT5 and HOXA13 populations. f, UMAP projection of the Liu et al.30 scRNA-seq dataset of human cervix coloured by Liu’s clusters and the four main cell lineages. g, Dot plot showing normalised, log-transformed and variance-scaled expression of genes (x-axis) characteristic of the cell clusters identified in the Liu et al.30 cervix dataset by the authors (y-axis). Purple rectangles highlight the epithelial and mesenchymal clusters that expressed markers characteristic of the MUC5B, KRT5 and HOXA13 populations defined in the HECA. h, UMAP projection of the mapping of the Liu et al. 30 cervix dataset onto the scANVI representation of the HECA coloured by either the endometrial cell states identified in the HECA or the cervix cell states Liu et al.30 (grey). Red dotted-lined shapes outline the MUC5B, KRT5 and HOXA13 populations of the HECA. i, UMAP projection of the mapping of the Liu et al.30 cervix dataset onto the scANVI representation of the HECA coloured by the matched cervix cell clusters identified by Liu et al.30. Red dotted-lines outline the MUC5B, KRT5 and HOXA13 populations of the HECA. dStromal, decidualised stromal cells; ePV, endometrial perivascular cells; eStromal, endometrial stromal cells specific to proliferative phase; HECA, human endometrial cell atlas; MMPs, matrix metalloproteinases; NK, natural killer cells; scRNA-seq, single-cell RNA-sequencing; scANVI, single-cell ANnotation using Variational Inference; T, T cells; UMAP, uniform manifold approximation and projection; uSMCs, uterine smooth muscle cells.
