Extended Data Fig. 2: Spatial transcriptomic quality controls.
From: Single-cell profiling of the human endometrium in polycystic ovary syndrome
a) From the top, spatial maps of haematoxylin and eosin (H&E) staining of adjacent sections, genes per bin30, Uniform manifold approximation and projections (UMAP) of UMAP label transfer-based cell type labelling and prediction scores of the cell type labelling of six samples: 2 controls, 2 PCOS, 1 PCOS-metformin and 2 PCOS-lifestyle. b) Bar plot of cell type proportions of bin30 after labelling by UMAP label transfer. c) Violin plots of the immunolabeled spatial bin30 of PAEP expression per sample and of log-transformed PAEP expression in the single nuclei immune cluster in the control, PCOS, PCOS-metformin and PCOS-lifestyle groups in uNK 1–3 and uM 1-2. Statistics: DEG analysis by two-sided MAST between log-transformed gene expression between groups. Benjamini-Hochberg (BH) adjusted P < 0.05 and a log2-foldchange >0.5 is considered significant. ***, BH adjusted P < 0.001 in DEG analysis. d) Violin plots of immunolabeled spatial bin30 of PAEP expression per sample.
