Etzrodt, M., Endele, M. & Schroeder, T. Quantitative single-cell approaches to stem cell research. Cell Stem Cell 15, 546–558 (2014).
Fischer, D. S. et al. Inferring population dynamics from single-cell RNA-sequencing time series data. Nat. Biotechnol. 37, 461–468 (2019).
Haas, S., Trumpp, A. & Milsom, M. D. Causes and consequences of hematopoietic stem cell heterogeneity. Cell Stem Cell 22, 627–638 (2018).
Laurenti, E. & Göttgens, B. From haematopoietic stem cells to complex differentiation landscapes. Nature 553, 418–426 (2018).
Nowotschin, S. et al. The emergent landscape of the mouse gut endoderm at single-cell resolution. Nature 569, 361–367 (2019).
Zaret, K. S. & Grompe, M. Generation and regeneration of cells of the liver and pancreas. Science 322, 1490–1494 (2008).
Zorn, A. M. & Wells, J. M. Vertebrate endoderm development and organ formation. Annu. Rev. Cell Dev. Biol. 25, 221–251 (2009).
Slack, J. M. W. Origin of stem cells in organogenesis. Science 322, 1498–1501 (2008).
Larsen, H. L. et al. Stochastic priming and spatial cues orchestrate heterogeneous clonal contribution to mouse pancreas organogenesis. Nat. Commun. 8, 605 (2017).
Treutlein, B. et al. Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature 509, 371–375 (2014).
Baron, C. S. & van Oudenaarden, A. Unravelling cellular relationships during development and regeneration using genetic lineage tracing. Nat. Rev. Mol. Cell Biol. 20, 753–765 (2019).
Pei, W. et al. Polylox barcoding reveals haematopoietic stem cell fates realized in vivo. Nature 548, 456–460 (2017).
Rulands, S. & Simons, B. D. Tracing cellular dynamics in tissue development, maintenance and disease. Curr. Opin. Cell Biol. 43, 38–45 (2016).
Prior, N. et al. Lgr5+ stem and progenitor cells reside at the apex of a heterogeneous embryonic hepatoblast pool. Development 146, dev174557 (2019).
Tremblay, K. D. & Zaret, K. S. Distinct populations of endoderm cells converge to generate the embryonic liver bud and ventral foregut tissues. Dev. Biol. 280, 87–99 (2005).
Li, L.-C. et al. Single-cell transcriptomic analyses reveal distinct dorsal/ventral pancreatic programs. EMBO Rep. 19, e46148 (2018).
Spence, J. R. et al. Sox17 regulates organ lineage segregation of ventral foregut progenitor cells. Dev. Cell 17, 62–74 (2009).
Zhou, Q. et al. A multipotent progenitor domain guides pancreatic organogenesis. Dev. Cell 13, 103–114 (2007).
Sosa-Pineda, B., Wigle, J. T. & Oliver, G. Hepatocyte migration during liver development requires Prox1. Nat. Genet. 25, 254–255 (2000).
Raue, A. et al. Lessons learned from quantitative dynamical modeling in systems biology. PLoS ONE 8, e74335 (2013).
Rodríguez-Seguel, E. et al. Mutually exclusive signaling signatures define the hepatic and pancreatic progenitor cell lineage divergence. Genes Dev. 27, 1932–1946 (2013).
Ober, E. A. & Lemaigre, F. P. Development of the liver: Insights into organ and tissue morphogenesis. J. Hepatol. 68, 1049–1062 (2018).
Liu, J. et al. Non-parallel recombination limits Cre-LoxP-based reporters as precise indicators of conditional genetic manipulation. Genesis 51, 436–442 (2013).
Danielian, P. S., Muccino, D., Rowitch, D. H., Michael, S. K. & McMahon, A. P. Modification of gene activity in mouse embryos in utero by a tamoxifen-inducible form of Cre recombinase. Curr. Biol. 8, 1323–1326 (1998).
Lotto, J. et al. Single-cell transcriptomics reveals early emergence of liver parenchymal and non-parenchymal cell lineages. Cell 183, 702–716.e14 (2020).
Hebrok, M. Hedgehog signaling in pancreas development. Mech. Dev. 120, 45–57 (2003).
Bangs, F. & Anderson, K. V. Primary cilia and mammalian hedgehog signaling. Cold Spring Harb. Perspect. Biol. 9, a028175 (2017).
Dessaud, E., McMahon, A. P. & Briscoe, J. Pattern formation in the vertebrate neural tube: a sonic hedgehog morphogen-regulated transcriptional network. Development 135, 2489–2503 (2008).
Martínez-Frías, M. L. et al. Tracheoesophageal fistula, gastrointestinal abnormalities, hypospadias, and prenatal growth deficiency. Am. J. Med. Genet. 44, 352–355 (1992).
Mitchell, J. et al. Neonatal diabetes, with hypoplastic pancreas, intestinal atresia and gall bladder hypoplasia: search for the aetiology of a new autosomal recessive syndrome. Diabetologia 47, 2160–2167 (2004).
Heij, H. A. & Niessen, G. J. Annular pancreas associated with congenital absence of the gallbladder. J. Pediatr. Surg. 22, 1033 (1987).
Park, E. J. et al. System for tamoxifen-inducible expression of cre-recombinase from the Foxa2 locus in mice. Dev. Dyn. 237, 447–453 (2008).
Hingorani, S. R. et al. Preinvasive and invasive ductal pancreatic cancer and its early detection in the mouse. Cancer Cell 4, 437–450 (2003).
Perl, A.-K. T., Wert, S. E., Nagy, A., Lobe, C. G. & Whitsett, J. A. Early restriction of peripheral and proximal cell lineages during formation of the lung. Proc. Natl Acad. Sci. USA 99, 10482–10487 (2002).
Snippert, H. J. et al. Intestinal crypt homeostasis results from neutral competition between symmetrically dividing Lgr5 stem cells. Cell 143, 134–144 (2010).
Abe, T. et al. Establishment of conditional reporter mouse lines at ROSA26 locus for live cell imaging. Genesis 49, 579–590 (2011).
Gong, S. et al. A gene expression atlas of the central nervous system based on bacterial artificial chromosomes. Nature 425, 917–925 (2003).
Means, A. L., Xu, Y., Zhao, A., Ray, K. C. & Gu, G. A CK19(CreERT) knockin mouse line allows for conditional DNA recombination in epithelial cells in multiple endodermal organs. Genesis 46, 318–323 (2008).
Gu, G., Dubauskaite, J. & Melton, D. A. Direct evidence for the pancreatic lineage: NGN3+ cells are islet progenitors and are distinct from duct progenitors. Development 129, 2447–2457 (2002).
Madisen, L. et al. A robust and high-throughput Cre reporting and characterization system for the whole mouse brain. Nat. Neurosci. 13, 133–140 (2010).
Gong, S., Yang, X. W., Li, C. & Heintz, N. Highly efficient modification of bacterial artificial chromosomes (BACs) using novel shuttle vectors containing the R6Kgamma origin of replication. Genome Res. 12, 1992–1998 (2002).
Petzold, K. M. & Spagnoli, F. M. A system for ex vivo culturing of embryonic pancreas. J. Vis. Exp. (66), e3979 (2012). https://doi.org/10.3791/3979.
Preibisch, S., Saalfeld, S. & Tomancak, P. Globally optimal stitching of tiled 3D microscopic image acquisitions. Bioinformatics 25, 1463–1465 (2009).
Dewitz, C. et al. Nuclear organization in the spinal cord depends on motor neuron lamination orchestrated by catenin and afadin function. Cell Rep. 22, 1681–1694 (2018).
Husson, F., Josse, J. & Pagès, J. Principal component methods-hierarchical clustering-partitional clustering: why would we need to choose for visualizing data? Applied Mathematics Department, 1–10 (2010).
Charrad, M., Ghazzali, N., Boiteau, V. & Niknafs, A. NbClust: An R package for determining the relevant number of clusters in a data set. J. Stat. Softw. 61, 1–36 (2014).
Raue, A. et al. Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems. Bioinformatics 31, 3558–3560 (2015).
Picelli, S. et al. Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat. Methods 10, 1096–1098 (2013).
Lun, A. T. L., McCarthy, D. J. & Marioni, J. C. A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor. F1000Res 5, 2122 (2016).
McCarthy, D. J., Campbell, K. R., Lun, A. T. L. & Wills, Q. F. Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R. Bioinformatics 33, 1179–1186 (2017).
Lun, A. T., Bach, K. & Marioni, J. C. Pooling across cells to normalize single-cell RNA sequencing data with many zero counts. Genome Biol. 17, 75 (2016).
Amezquita, R. A. et al. Orchestrating single-cell analysis with Bioconductor. Nat. Methods 17, 137–145 (2020).
Trapnell, C. et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat. Biotechnol. 32, 381–386 (2014).
Escot, S., Willnow, D., Naumann, H., Di Francescantonio, S. & Spagnoli, F. M. Robo signalling controls pancreatic progenitor identity by regulating Tead transcription factors. Nat. Commun. 9, 5082 (2018).
Palaria, A., Angelo, J. R., Guertin, T. M., Mager, J. & Tremblay, K. D. Patterning of the hepato-pancreatobiliary boundary by BMP reveals heterogeneity within the murine liver bud. Hepatology 68, 274–288 (2018).
Sanders, E. J., Varedi, M. & French, A. S. Cell proliferation in the gastrulating chick embryo: a study using BrdU incorporation and PCNA localization. Development 118, 389–399 (1993).
van den Berg, G. et al. A caudal proliferating growth center contributes to both poles of the forming heart tube. Circ. Res. 104, 179–188 (2009).
Clevers, H. & Watt, F. M. Defining adult stem cells by function, not by phenotype. Annu. Rev. Biochem. 87, 1015–1027 (2018).
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