Tam, P.P.L. & Behringer, R.R. Mice Gastrulation: Formation of a Body Plan in Mammals. Mech. dev. 68, 3-25 (1997).
Loh, K. M. et al. Mapping paired choices ranging from pluripotency to bones, heart and other types of human mesodermal cells. Cell 166451-467 (2016).
Viotti, M., Nowotschin, S. and Hadjantonakis, A.-K. SOX17 connects the morphogenesis of the endoderm in the intestine and the segregation of the germinal layer. Nat. Biol cell. 161146-1156 (2014).
Lescroart, F. et al. Define the first step of the segregation of the cardiovascular lineage by unicellular RNA-seq. Science 3591177-1181 (2018).
Ibarra-Soria, X. et al. Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating the formation of blood progenitors. Nat. Biol cell. 20127-134 (2018).
Downs, K.M. & Davies, T. Staging of mouse embryos undergoing gastrulation with the aid of morphological landmarks under a dissecting microscope. Development 1181255-1266 (1993).
Koch, F. et al. Antagonist activities Sox2 and Brachyury control the choice to become neuro-mesodermal progenitors. Dev. Cell 42, 514-526.e7 (2017).
Tzouanacou, E., Wegener, A., Wymeersch, J., Wilson, V., and Nicolas, J.-F. Redefine the progression of lineage segregations during mammalian embryogenesis by clonal analysis. Dev. Cell 17365-376 (2009).
Kwon, G.S., Viotti, M. & Hadjantonakis, A.-K. The endoderm of the mouse embryo is formed by a generalized dynamic intercalation of embryonic and extraembryonic lineages. Dev. Cell 15509-520 (2008).
Finley, K.R., Tennessen, J. and Shawlot, W. The mouse Protein 5 related to frizz The gene is expressed in the anterior visceral endoderm and intestinal endoderm at the beginning of post-implantation development. Gene Expr. The reasons 3681 to 684 (2003).
Makover, A., Soprano, D.R., Wyatt, M.L. and Goodman, D.S. In situ hybridization study of messenger RNA localization of retinol-binding protein and transthyretin during fetal development in rats. Differentiation 40, 17-25 (1989).
Martinez Barbera, J.P. et al. The homeobox gene hex is required in definitive endodermal tissue for normal formation of the forebrain, liver and thyroid. Development 1272433-2445 (2000).
Bosse, A. et al. Identification of the family of Iroquois homeobox genes in vertebrates with overlapping expression during early development of the nervous system. Mech. dev. 69169-181 (1997).
Osipovich, A.B. et al. INSM1 promotes the differentiation of endocrine cells by modulating the expression of a gene network comprising Neurog3 and Ripply3. Development 1412939-2949 (2014).
Haghverdi, L., Büttner, M., Wolf, F. A., Buettner, F. & Theis, F. J. Dissemination. The pseudotime robustly reconstructs the branching of the lineage. Nat. The methods 13845-848 (2016).
Schiebinger, G. et al. Reconstructing development landscapes by analyzing optimal transport of monocellular gene expression allows for better understanding of cell reprogramming. Preprint to https://www.bioRxiv.org/content/early/2017/09/27/191056 (2017).
Viotti, M., Foley, A.C. and Hadjantonakis, A.K. Gutsy moves in mice: cellular and molecular dynamics of endoderm morphogenesis. Phil Trans. R. Soc. Lond. B 36920130547 (2014).
Deschamps, J. & Duboule, D. Embryonic synchronization, axial stem cells, chromatin dynamics and Hox clock. Genes Dev. 311406-1416 (2017).
Palis, J. Hematopoiesis independent of J. Hematopoietic stem cells: emergence of erythroid, megakaryocyte and myeloid potential in mammalian embryo. FEBS Lett. 5903965 to 3974 (2016).
McGrath, K.E. et al. Separate sources of hematopoietic progenitors emerge before HSCs and provide functional blood cells in the mammalian embryo. Cell reports 11, 1892-1904 (2015).
Downs, K. M., S. Gifford, M. Blahnik, M. & Gardner, R. L. The vasculature of the murine allantoin occurs by vasculogenesis without erythropoiesis. Development 1254507-4520 (1998).
Patan, S. in Angiogenesis in brain tumors (eds Kirsch, M. & Black, P.M.) 3-32 (Springer, Boston, MA, 2004).
Picelli, S. et al. Smart-seq2 for the sensitive profiling of complete transcriptome in single cells. Nat. The methods ten1096-1098 (2013).
Palis, J., S. Robertson, M. Kennedy, Wall, C. and Keller, G. Development of erythroid and myeloid progenitors in the yolk sac and the embryo proper of the mouse. Development 1265073-5084 (1999).
Tober, J. et al. The megakaryocyte lineage is derived from hemangioblast precursors and is an integral part of primitive and definitive hematopoiesis. Some blood 1091433-1441 (2007).
Xu, M.-j. et al. Proof of the presence of murine primary megakaryocytopoiesis in the first yolk sac. Some blood 972016-2022 (2001).
Hoeffel, G. et al. C-Myb+ Fetal monocytes derived from erythro-myeloid progenitors give rise to macrophages residing in adult tissues. Immunity 42, 665-678 (2015).
Gomez Perdiguero, E. et al. The origin of macrophages residing in the tissues: when an erythro-myeloid progenitor is an erythro-myeloid progenitor. Immunity 431023-1024 (2015).
Bennett, M.L. et al. New tools for the study of microglia in the central nervous system of mice and humans. Proc. Natl Acad. Sci. United States 113, E1738 – E1746 (2016).
Ginhoux, F. et al. The analysis of the mapping of fate reveals that the microglia of the adult derives from primitive macrophages. Science 330841-845 (2010).
Shivdasani, R.A., Mayer, E.L. and Orkin, S.H. Absence of blood formation in mice lacking the tal-1 / SCL oncoprotein of T cell leukemia. Nature 373432-434 (1995).
Robb, L. et al. the scl The gene product is necessary for the generation of all hematopoietic lineages in adult mice. EMBO J. 154123-4129 (1996).
Van Handel, B. et al. Scl suppresses cardiomyogenesis in the endothelium and endocardial hemogenic potential. Cell 150590-605 (2012).
Huber, T. L., Kouskoff, V., Fehling, H.J., Palis, J. and Keller, G. The hemangioblast is initiated in the primitive streak of the mouse embryo. Nature 432625-630 (2004).
Briggs, J.A. et al. The dynamics of gene expression in embryogenesis of vertebrates at the single-cell resolution. Science 360eaar5780 (2018).
Farrell, J.A. et al. Monocellular reconstruction of developmental trajectories during zebrafish embryogenesis. Science 360eaar3131 (2018).
Wagner, D.E. et al. Monocellular mapping of gene expression landscapes and lineage in the zebrafish embryo. Science 360, 981-987 (2018).
Pijuan-Sala, B., Guibentif, C. and Göttgens, B. The single-cell transcriptional profile: a window on the specification of the embryonic cell type. Nat. Rev. Mol. Biol cell. 19399 to 412 (2018).
Srinivas, S. et al. Cre reporter strains produced by targeted insertion of EYFP and ECFP in the ROSA26 place. BMC Dev. Biol. 14 (2001).
Nichols, J. & Jones, K. Derivation of mouse embryonic stem cell (ES) cell lines with the aid of small molecule inhibitors Erk and Gsk3 signaling (2i). Harb Spring Spring. protoc. 2017, https://doi.org/10.1101/pdb.prot094086 (2017).
Ying, Q.-L. et al. The fundamental state of self-renewal of embryonic stem cells. Nature 453519-523 (2008).
Wray, J. et al. The inhibition of glycogen synthase kinase-3 attenuates Tcf3 repression of the pluripotency network and increases the resistance of embryonic stem cells to differentiation. Nat. Biol cell. 13838-845 (2011).
Ran, F.A. et al. Genome engineering using the CRISPR-Cas9 system. Nat. protocols 82281-2308 (2013).
Bin, G.C. et al. Oct4 is necessary to prime the lineage in the developing inner cell mass of the mouse blastocyst. Development 1411001-1010 (2014).
Lun, A. et al. Distinguish cells from empty droplets in droplet-based single-cell RNA sequencing data. Preprint to https://www.bioRxiv.org/content/early/2018/04/04/234872 (2018).
Lun, A.T.L., McCarthy, D.J. and Marioni, J.C. A step-by-step workflow for low level analysis of single-cell RNA data with bioconductors. F1000Res. 52122 (2016).
Wu, T. D. & Nacu, S. Rapid and Tolerant SNP Detection of Complex Variants and Splicing in Short Reads. bioinformatics 26, 873-881 (2010).
Anders, S., Pyl, P.T. and Huber, W. HTSeq: a Python framework for working with high throughput sequencing data. bioinformatics 31166-169 (2015).
Wolf, F. A., Angerer, P. and Theis, F. J. SCANPY: Large-scale analysis of single-cell gene expression data. Genome Biol. 1915 (2018).
Bastian, M., Heymann, S. and Jacomy, M. Gephi: an open source software for network exploration and manipulation. In Third International AAAI Conference on Weblogs and Social Media (AAAI, 2009).
Jacomy, M., T. Venturini, S. Heymann and S. Bastian, M. ForceAtlas2, a continuous graph layout algorithm for practical network visualization designed for the Gephi software. PLoS One 9, 98679 (2014).
Wolf, F. A. et al. Graph abstraction reconciles clustering with trajectory inference through a map preserving unique cell topology. Preprint to https://www.bioRxiv.org/content/early/2017/10/25/208819 (2017).
Robinson, M.D., McCarthy, D.J. & Smyth, G.K. edgeR: a bioconductive software package for the analysis of differential expression of digital gene expression data. bioinformatics 26139-140 (2010).
Dong, J. et al. Analysis of unique RNA-seq cells reveals a predominant epithelial / mesenchymal hybrid state during organogenesis in mice. Genome Biol. 1931 (2018).
Brennecke, P. et al. Consideration of technical noise in unicellular RNA-seq experiments. Nat. The methods ten1093-1095 (2013).
Kinder, S.J. et al. The ordered assignment of mesodermal cells to extraembryonic structures and to the anteroposterior axis during gastrulation of the mouse embryo. Development 1264691-4701 (1999).