Fig. 2: Spatiotemporal complexity of epithelial cells.
From: An integrated single-cell reference atlas of the human endometrium
a, Dot plot showing normalized, log-transformed and variance-scaled expression of genes (x axis) for epithelial cell states (y axis) in scRNA-seq data. b, Visium spatial transcriptomics data and an H&E image of the same tissue section. Spot color indicates cell2location-estimated cell density for the SOX9 basalis (CDH2+) population in sections of whole-uterus biopsies (n = 2 biologically independent samples) from donors A13 (proliferative phase) and A30 (secretory phase). c, High-resolution multiplexed smFISH of a section of a whole-uterus biopsy from donor A13 stained for DAPI (white, nuclei), EPCAM (magenta, epithelium), SOX9 (yellow, epithelium) and CDH2 (red, basalis epithelium) (n = 2 biologically independent samples). The dotted line highlights the basalis endometrium where signals for all markers co-localize within the basalis glands. The inset shows a representative magnified area. Scale bars, 100 µm. d, Dot plot showing normalized, log-transformed and variance-scaled expression of CXCR4 and CXCL12 (x axis) in a selection of epithelial and mesenchymal cells (y axis) in scRNA-seq data. Asterisk denotes a significant cell–cell interaction identified through CellPhoneDB analyses. e, Left, high-resolution multiplexed smFISH of a section of a superficial biopsy from donor FX1233 showing the expression of DAPI (white, nuclei), EPCAM (magenta, epithelium), CBR3 (cyan, preGlandular cells) and OPRK1 (yellow, preGlandular cells) (n = 2 biologically independent samples). Top right, a magnified image of the luminal region with low OPRK1 and CBR3 signal. Bottom right, a magnified image of the glandular region with high and co-localized OPRK1 and CBR3 signal. Scale bars, 100 µm. f, Visium spatial transcriptomics data and an H&E image of the same tissue section. Spot color indicates cell2location-estimated cell density for the preLuminal, Luminal, preGlandular and Glandular populations in a section of a superficial biopsy from donor FX0028 (early secretory phase; n = 2 biologically independent samples) and a section of a whole-uterus biopsy from donor A30 (mid secretory phase; n = 1). Scale bars, 1 mm. g, Schematic illustration of the spatiotemporal complexity of the endometrial epithelium across the proliferative and secretory phases.
