Wennekamp, S., Mesecke, S., Nédélec, F. & Hiiragi, T. A self-organization framework for symmetry breaking in the mammalian embryo. Nat. Rev. Mol. Cell Biol. 14, 452–459 (2013).
Tanaka, S., Kunath, T., Hadjantonakis, A. K., Nagy, A. & Rossant, J. Promotion of trophoblast stem cell proliferation by FGF4. Science 282, 2072–2075 (1998).
Ying, Q.-L. et al. The ground state of embryonic stem cell self-renewal. Nature 453, 519–523 (2008).
van den Brink, S. C. et al. Symmetry breaking, germ layer specification and axial organisation in aggregates of mouse embryonic stem cells. Development 141, 4231–4242 (2014).
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).
Rai, A. & Cross, J. C. Three-dimensional cultures of trophoblast stem cells autonomously develop vascular-like spaces lined by trophoblast giant cells. Dev. Biol. 398, 110–119 (2015).
Rivron, N. C. et al. Tissue deformation spatially modulates VEGF signaling and angiogenesis. Proc. Natl Acad. Sci. USA 109, 6886–6891 (2012).
Vrij, E. et al. Directed assembly and development of material-free tissues with complex architectures. Adv. Mater. 28, 4032–4039 (2016).
Manejwala, F., Kaji, E. & Schultz, R. M. Development of activatable adenylate cyclase in the preimplantation mouse embryo and a role for cyclic AMP in blastocoel formation. Cell 46, 95–103 (1986).
Kemp, C., Willems, E., Abdo, S., Lambiv, L. & Leyns, L. Expression of all Wnt genes and their secreted antagonists during mouse blastocyst and postimplantation development. Dev. Dyn. 233, 1064–1075 (2005).
Ralston, A. & Rossant, J. Cdx2 acts downstream of cell polarization to cell-autonomously promote trophectoderm fate in the early mouse embryo. Dev. Biol. 313, 614–629 (2008).
McDole, K. & Zheng, Y. Generation and live imaging of an endogenous Cdx2 reporter mouse line. Genesis 50, 775–782 (2012).
Kubaczka, C. et al. Derivation and maintenance of murine trophoblast stem cells under defined conditions. Stem Cell Reports 2, 232–242 (2014).
Plusa, B., Piliszek, A., Frankenberg, S., Artus, J. & Hadjantonakis, A.-K. Distinct sequential cell behaviours direct primitive endoderm formation in the mouse blastocyst. Development 135, 3081–3091 (2008).
Simmons, D. G., Fortier, A. L. & Cross, J. C. Diverse subtypes and developmental origins of trophoblast giant cells in the mouse placenta. Dev. Biol. 304, 567–578 (2007).
Red-Horse, K. et al. Trophoblast differentiation during embryo implantation and formation of the maternal-fetal interface. J. Clin. Invest. 114, 744–754 (2004).
Latos, P. A. & Hemberger, M. From the stem of the placental tree: trophoblast stem cells and their progeny. Development 143, 3650–3660 (2016).
McConaha, M. E., Eckstrum, K., An, J., Steinle, J. J. & Bany, B. M. Microarray assessment of the influence of the conceptus on gene expression in the mouse uterus during decidualization. Reproduction 141, 511–527 (2011).
Ohnishi, Y. et al. Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages. Nat. Cell Biol. 16, 27–37 (2014).
Gotoh, N. et al. The docking protein FRS2alpha is an essential component of multiple fibroblast growth factor responses during early mouse development. Mol. Cell. Biol. 25, 4105–4116 (2005).
Saba-El-Leil, M. K. et al. An essential function of the mitogen-activated protein kinase Erk2 in mouse trophoblast development. EMBO Rep. 4, 964–968 (2003).
Arman, E., Haffner-Krausz, R., Chen, Y., Heath, J. K. & Lonai, P. Targeted disruption of fibroblast growth factor (FGF) receptor 2 suggests a role for FGF signaling in pregastrulation mammalian development. Proc. Natl Acad. Sci. USA 95, 5082–5087 (1998).
Papanayotou, C. & Collignon, J. Activin/Nodal signalling before implantation: setting the stage for embryo patterning. Phil. Trans. R. Soc. Lond. B 369, 1–8 (2014).
Mesnard, D. & Constam, D. B. Imaging proprotein convertase activities and their regulation in the implanting mouse blastocyst. J. Cell Biol. 191, 129–139 (2010).
Gardner, R. L. Flow of cells from polar to mural trophectoderm is polarized in the mouse blastocyst. Hum. Reprod. 15, 694–701 (2000).
Gardner, R. L., Papaioannou, V. E. & Barton, S. C. Origin of the ectoplacental cone and secondary giant cells in mouse blastocysts reconstituted from isolated trophoblast and inner cell mass. J. Embryol. Exp. Morphol. 30, 561–572 (1973).
Matsumoto, N. et al. Developmental regulation of yolk sac hematopoiesis by Kruppel-like factor 6. Blood 107, 1357–1365 (2006).
DiFeo, A. et al. E-cadherin is a novel transcriptional target of the KLF6 tumor suppressor. Oncogene 25, 6026–6031 (2006).
Tarkowski, A. K. & Wróblewska, J. Development of blastomeres of mouse eggs isolated at the 4- and 8-cell stage. J. Embryol. Exp. Morphol. 18, 155–180 (1967).
Tesar, P. J. et al. New cell lines from mouse epiblast share defining features with human embryonic stem cells. Nature 448, 196–199 (2007).
Rivron, N. C. In vitro generation of blastoids from trophoblast stem cells and embryonic stem cells. Protoc. Exch. (2018).
van de Wetering, M. et al. The β-catenin/TCF-4 complex imposes a crypt progenitor phenotype on colorectal cancer cells. Cell 111, 241–250 (2002).
Muraro, M. J. et al. A single-cell transcriptome atlas of the human pancreas. Cell Syst. 3, 385–394.e3. (2016).
Hashimshony, T. et al. CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome Biol. 17, 77 (2016).
Hashimshony, T., Wagner, F., Sher, N. & Yanai, I. CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Reports 2, 666–673 (2012).
Grün, D. et al. Single-cell messenger RNA sequencing reveals rare intestinal cell types. Nature 525, 251–255 (2015).
Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).
Dennis, G., Jr et al. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 4, 3 (2003).
Eden, E., Navon, R., Steinfeld, I., Lipson, D. & Yakhini, Z. GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 10, 48 (2009).
Vrij, E. J. et al. 3D high throughput screening and profiling of embryoid bodies in thermoformed microwell plates. Lab Chip 16, 734–742 (2016).
Nakamura, T. et al. SC3-seq: a method for highly parallel and quantitative measurement of single-cell gene expression. Nucleic Acids Res. 43, e60 (2015).
Kolodziejczyk, A. A. et al. Single cell RNA-sequencing of pluripotent states unlocks modular transcriptional variation. Cell Stem Cell 17, 471–485 (2015).
Qiu, D. et al. Klf2 and Tfcp2l1, two Wnt/β-catenin targets, act synergistically to induce and maintain naive pluripotency. Stem Cell Reports 5, 314–322 (2015).
Morgani, S. M. et al. Totipotent embryonic stem cells arise in ground-state culture conditions. Cell Rep. 3, 1945–1957 (2013).
Hussein, S. M., Duff, E. K. & Sirard, C. Smad4 and β-catenin co-activators functionally interact with lymphoid-enhancing factor to regulate graded expression of Msx2. J. Biol. Chem. 278, 48805–48814 (2003).
Labbé, E. et al. Transcriptional cooperation between the transforming growth factor-β and Wnt pathways in mammary and intestinal tumorigenesis. Cancer Res. 67, 75–84 (2007).