Evaluation of Stem-Cell Embryo Models by Integration with a Human Embryo Single-Cell Transcriptome Atlas

Single-cell RNA sequencing (scRNA-seq) revolutionized our understanding of the molecular processes of early development and provided us with the means to capture biological heterogeneity and assess the cellular composition in early embryos. Comparative analysis of the transcriptional landscapes of embryos with single-cell resolution allows us to better understand and improve stem-cell-based embryo models. However, proper comparison between different single-cell datasets acquired by different laboratories and through different technologies is imperative for adequate analysis and findings. In this chapter, we focus on the analysis of human blastoids, which model the blastocyst, and their integrative analysis with human embryo datasets and a 2D in vitro early development model system dataset, which models epiblast, extraembryonic mesoderm, and trophoblast cells.