Fig. 3: Benchmark of EVTs derived from primary-derived trophoblast organoids and TSCs.

a, Top, phase-contrast images of PTOs plated in a Matrigel droplet and exposed to TOM or EVTM. Scale bar, 1 mm. Representative image of n = 6 experiments. Below, phase-contrast images of TSCs exposed to TSCM or EVTM. Scale bar, 400 μm. Representative image of n = 2 experiments. b, UMAP plot of PTO (n = 26,852 cells) and TSC (n = 9957 cells) scRNA-seq data coloured by cell state. Annotation was performed as indicated in Extended Data Fig. 9b. c, Bar plot representing the proportion (%) of cell states assigned to the in vitro cell states (defined by markers) using a logistic regression classifier trained on the in vivo data. Red text indicates cell states that differ between the annotations given by the logistic regression classifier and the ones given by the expression of canonical markers. d, Dot plot showing normalized, log-transformed and variance-scaled expression of genes (x-axis) characteristic of VCT y-axis in PTOs (top) and TSCs (bottom). Red text indicates genes that differ from the in vivo observed expression pattern. e, Heat map showing z-scores of normalized, log-transformed and variance-scaled expression of transcription factor genes that are known to be upregulated in in vivo trophoblast invasion (see Fig. 2b). The y-axis indicates cell state and the x-axis shows transcription factor genes. f, Heat map showing z-scores of normalized, log-transformed and variance-scaled expression of transcription factor genes that are known to be downregulated in in vivo trophoblast invasion.