Rossant, J. & Tam, P. P. L. New insights into early human development: lessons for stem cell derivation and differentiation. Cell Stem Cell 20, 18–28 (2017).
Thomson, J. A. et al. Embryonic stem cell lines derived from human blastocysts. Science 282, 1145–1147 (1998).
Takahashi, K. et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131, 861–872 (2007).
Fu, J., Warmflash, A. & Lutolf, M. P. Stem-cell-based embryo models for fundamental research and translation. Nat. Mater. 20, 132–144 (2021).
Harrison, S. E., Sozen, B., Christodoulou, N., Kyprianou, C. & Zernicka-Goetz, M. Assembly of embryonic and extraembryonic stem cells to mimic embryogenesis in vitro. Science 356, eaal1810 (2017).
Sozen, B. et al. Self-assembly of embryonic and two extra-embryonic stem cell types into gastrulating embryo-like structures. Nat. Cell Biol. 20, 979–989 (2018).
Rivron, N. C. et al. Blastocyst-like structures generated solely from stem cells. Nature 557, 106–111 (2018).
Zhang, S. et al. Implantation initiation of self-assembled embryo-like structures generated using three types of mouse blastocyst-derived stem cells. Nat. Commun. 10, 496 (2019).
Sozen, B. et al. Self-organization of mouse stem cells into an extended potential blastoid. Dev. Cell 51, 698–712 (2019).
Li, R. et al. Generation of blastocyst-like structures from mouse embryonic and adult cell cultures. Cell 179, 687–702 (2019).
Liu, X. et al. Reprogramming roadmap reveals route to human induced trophoblast stem cells. Nature 586, 101–107 (2020).
Blakeley, P. et al. Defining the three cell lineages of the human blastocyst by single-cell RNA-seq. Development 142, 3613 (2015).
Petropoulos, S. et al. Single-cell RNA-seq reveals lineage and X chromosome dynamics in human preimplantation embryos. Cell 165, 1012–1026 (2016).
Shahbazi, M. N. et al. Self-organization of the human embryo in the absence of maternal tissues. Nat. Cell Biol. 18, 700–708 (2016).
Xiang, L. et al. A developmental landscape of 3D-cultured human pre-gastrulation embryos. Nature 577, 537–542 (2020).
Qin, H. et al. YAP induces human naive pluripotency. Cell Rep. 14, 2301–2312 (2016).
Liu, L. et al. An integrated chromatin accessibility and transcriptome landscape of human pre-implantation embryos. Nat. Commun. 10, 364 (2019).
Durruthy-Durruthy, J. et al. Spatiotemporal reconstruction of the human blastocyst by single-cell gene-expression analysis informs induction of naive pluripotency. Dev. Cell 38, 100–115 (2016).
Fogarty, N. M. E. et al. Genome editing reveals a role for OCT4 in human embryogenesis. Nature 550, 67–73 (2017).
Niakan, K. K. & Eggan, K. Analysis of human embryos from zygote to blastocyst reveals distinct gene expression patterns relative to the mouse. Dev. Biol. 375, 54–64 (2013).
Deglincerti, A. et al. Self-organization of the in vitro attached human embryo. Nature 533, 251–254 (2016).
Roode, M. et al. Human hypoblast formation is not dependent on FGF signalling. Dev. Biol. 361, 358–363 (2012).
Kovacic, B., Vlaisavljevic, V., Reljic, M. & Cizek-Sajko, M. Developmental capacity of different morphological types of day 5 human morulae and blastocysts. Reprod. Biomed. Online 8, 687–694 (2004).
Posfai, E. et al. Evaluating totipotency using criteria of increasing stringency. Nat. Cell Biol. 23, 49–60 (2021).
Okae, H. et al. Derivation of human trophoblast stem cells. Cell Stem Cell 22, 50–63 (2018).
Tyser, R. C. V., Mahammadov, E., Nakanoh, S. & Vallier, L. A spatially resolved single cell atlas of human gastrulation. Preprint at https://doi.org/10.1101/2020.07.21.213512 (2020).
Chen, D. et al. Human primordial germ cells are specified from lineage-primed progenitors. Cell Rep. 29, 4568–4582 (2019).
West, R. C. et al. Dynamics of trophoblast differentiation in peri-implantation-stage human embryos. Proc. Natl Acad. Sci. USA 116, 22635–22644 (2019).
Alpha Scientists in Reproductive Medicine and ESHRE Special Interest Group of Embryology. The Istanbul consensus workshop on embryo assessment: proceedings of an expert meeting. Hum. Reprod. 26, 1270–1283 (2011).
Hyun, I., Munsie, M., Pera, M. F., Rivron, N. C. & Rossant, J. Toward guidelines for research on human embryo models formed from stem cells. Stem Cell Rep. 14, 169–174 (2020).
Warnock—report of the committee of inquiry into human fertilisation and embryology. Ir. Nurs. News 5, 7–8 (1985).
Guo, G. et al. Naive pluripotent stem cells derived directly from isolated cells of the human inner cell mass. Stem Cell Rep. 6, 437–446 (2016).
Tan, J. P., Liu, X. & Polo, J. M. Generation of human blastocyst-like structures by somatic cell reprogramming. Protoc. Exch. https://doi.org/10.21203/rs.3.pex-1347/v1 (2021).
Liu, X. et al. Comprehensive characterization of distinct states of human naive pluripotency generated by reprogramming. Nat. Methods 14, 1055–1062 (2017).
Zhou, F. et al. Reconstituting the transcriptome and DNA methylome landscapes of human implantation. Nature 572, 660–664 (2019).
Paynter, J. M., Chen, J., Liu, X. & Nefzger, C. M. Propagation and maintenance of mouse embryonic stem cells. Methods Mol. Biol. 1940, 33–45 (2019).
Rostovskaya, M., Stirparo, G. G. & Smith, A. Capacitation of human naïve pluripotent stem cells for multi-lineage differentiation. Development 146, dev172916 (2019).
Boroviak, T. et al. Single cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development. Development 145, dev167833 (2018).
Lim, H. Y. G. et al. Keratins are asymmetrically inherited fate determinants in the mammalian embryo. Nature 585, 404–409 (2020).
Gerri, C. et al. Initiation of a conserved trophectoderm program in human, cow and mouse embryos. Nature 587, 443–447 (2020).
Aberkane, A. et al. Expression of adhesion and extracellular matrix genes in human blastocysts upon attachment in a 2D co-culture system. Mol. Hum. Reprod. 24, 375–387 (2018).
Bankhead, P. et al. QuPath: Open source software for digital pathology image analysis. Sci. Rep. 7, 16878 (2017).
Lam, A. Q. et al. Rapid and efficient differentiation of human pluripotent stem cells into intermediate mesoderm that forms tubules expressing kidney proximal tubular markers. J. Am. Soc. Nephrol. 25, 1211–1225 (2014).
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Huang, Y., McCarthy, D. J. & Stegle, O. Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference. Genome Biol. 20, 273 (2019).
Wickham, H. et al. dplyr: a grammar of data manipulation. R version 1.0.5 https://CRAN.R-project.org/package=dplyr (2021).
Butler, A., Hoffman, P., Smibert, P., Papalexi, E. & Satija, R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat. Biotechnol. 36, 411–420 (2018).
Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888–1902 (2019).
Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2016).
Kolde, R. & Vilo, J. GOsummaries: an R package for visual functional annotation of experimental data. F1000Res. 4, 574 (2015).
Hafemeister, C. & Satija, R. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome Biol. 20, 296 (2019).
Scialdone, A. et al. Computational assignment of cell-cycle stage from single-cell transcriptome data. Methods 85, 54–61 (2015).
Linneberg-Agerholm, M. et al. Naïve human pluripotent stem cells respond to Wnt, Nodal and LIF signalling to produce expandable naïve extra-embryonic endoderm. Development 146, dev180620 (2019).
