A unicellular molecular map of mouse gastrulation and early organogenesis

  • 1.

    Tam, P.P.L. & Behringer, R.R. Mice Gastrulation: Formation of a Body Plan in Mammals. Mech. dev. 68, 3-25 (1997).

  • 2

    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).

  • 3

    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).

  • 4

    Lescroart, F. et al. Define the first step of the segregation of the cardiovascular lineage by unicellular RNA-seq. Science 3591177-1181 (2018).

  • 5

    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).

  • 6

    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).

  • 7.

    Koch, F. et al. Antagonist activities Sox2 and Brachyury control the choice to become neuro-mesodermal progenitors. Dev. Cell 42, 514-526.e7 (2017).

  • 8

    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).

  • 9

    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).

  • ten.

    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).

  • 11

    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).

  • 12

    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).

  • 13

    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).

  • 14

    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).

  • 15

    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).

  • 16

    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).

  • 17

    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).

  • 18

    Deschamps, J. & Duboule, D. Embryonic synchronization, axial stem cells, chromatin dynamics and Hox clock. Genes Dev. 311406-1416 (2017).

  • 19

    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).

  • 20

    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).

  • 21

    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).

  • 22

    Patan, S. in Angiogenesis in brain tumors (eds Kirsch, M. & Black, P.M.) 3-32 (Springer, Boston, MA, 2004).

  • 23

    Picelli, S. et al. Smart-seq2 for the sensitive profiling of complete transcriptome in single cells. Nat. The methods ten1096-1098 (2013).

  • 24

    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).

  • 25

    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).

  • 26.

    Xu, M.-j. et al. Proof of the presence of murine primary megakaryocytopoiesis in the first yolk sac. Some blood 972016-2022 (2001).

  • 27

    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).

  • 28

    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).

  • 29

    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).

  • 30

    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).

  • 31.

    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).

  • 32

    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).

  • 33

    Van Handel, B. et al. Scl suppresses cardiomyogenesis in the endothelium and endocardial hemogenic potential. Cell 150590-605 (2012).

  • 34

    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).

  • 35

    Briggs, J.A. et al. The dynamics of gene expression in embryogenesis of vertebrates at the single-cell resolution. Science 360eaar5780 (2018).

  • 36

    Farrell, J.A. et al. Monocellular reconstruction of developmental trajectories during zebrafish embryogenesis. Science 360eaar3131 (2018).

  • 37

    Wagner, D.E. et al. Monocellular mapping of gene expression landscapes and lineage in the zebrafish embryo. Science 360, 981-987 (2018).

  • 38

    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).

  • 39

    Srinivas, S. et al. Cre reporter strains produced by targeted insertion of EYFP and ECFP in the ROSA26 place. BMC Dev. Biol. 14 (2001).

  • 40

    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).

  • 41

    Ying, Q.-L. et al. The fundamental state of self-renewal of embryonic stem cells. Nature 453519-523 (2008).

  • 42

    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).

  • 43

    Ran, F.A. et al. Genome engineering using the CRISPR-Cas9 system. Nat. protocols 82281-2308 (2013).

  • 44

    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).

  • 45

    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).

  • 46

    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).

  • 47

    Wu, T. D. & Nacu, S. Rapid and Tolerant SNP Detection of Complex Variants and Splicing in Short Reads. bioinformatics 26, 873-881 (2010).

  • 48.

    Anders, S., Pyl, P.T. and Huber, W. HTSeq: a Python framework for working with high throughput sequencing data. bioinformatics 31166-169 (2015).

  • 49

    Wolf, F. A., Angerer, P. and Theis, F. J. SCANPY: Large-scale analysis of single-cell gene expression data. Genome Biol. 1915 (2018).

  • 50

    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).

  • 51.

    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).

  • 52.

    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).

  • 53

    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).

  • 54

    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).

  • 55.

    Brennecke, P. et al. Consideration of technical noise in unicellular RNA-seq experiments. Nat. The methods ten1093-1095 (2013).

  • 56.

    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).

  • Source link