Fig. 2: Validation of in vitro signatures of the TS cell model in single cell datasets from human placental samples.

UMAP plots of single cell expression values (normalized, scaled, and natural-log transformed) depicting cell clustering from two publicly available, independent, single-cell RNA sequencing (scRNA-Seq) datasets from first-trimester placentas^27,28 for (a) all cell types inferred using marker genes published previously²⁸ as decidual macrophages (dM), fetal (Endo f) and maternal endothelial cells (Endo m), epithelial glandular cells (Epi), extravillous trophoblast cells (EVT), fetal fibroblasts (FB), Hofbauer cells (HB), syncytiotrophoblast and villous cytotrophoblast (SCT/VCT) and cells not determined (ND) and (b) EVT cell-specific genes detected using an in vitro model (red color scale of expression values thresholded at the 5th and 95th percentiles). c–e Plots depicting gene set enrichment analysis using three genes sets (each N = 250) of genes significantly upregulated in (c) SCT/VCT cells or (d), EVT cells or (e) genes not differently expressed between SCT/VCT and EVT cells from scRNA-Seq data sets and tested for enrichment for expression pattern in stem state (phenotype 1, CT27) and EVT cells (phenotype 0, CT27) from the in vitro TS cell model. Enrichment score (ES) reflects the degree of which each gene set is overrepresented at the extremes (top or bottom) of genes expressed in phenotype 0 (EVT cells) versus phenotype 1 (stem state cells). Estimated significance of ES were accounted for multiple testing and corresponded to (b) Phenotype 0; FDR q value = NS; Phenotype 1; FDR q value = 0.00190 (c) Phenotype 0; FDR q value = 0.00196; Phenotype 1; FDR q value = NS and (d) Phenotype 0; FDR q value = NS; Phenotype 1; FDR q value = 0.0016. FDR = false discovery rate; NS = not significant.