\bibitem{1} Berriz, G. F., Beaver, J. E., Cenik, C., Tasan, M. \& Roth, F. P. Next generation software for functional trend analysis. \textit{Bioinformatics} \textbf{25}, 3043--3044 (2009).
\bibitem{2} Hsu, S.-H. C. et al. Suppressor of fused (Sufu) mediates the effect of parathyroid hormone-like hormone (Pthlh) on chondrocyte differentiation in the growth plate. \textit{J. Biol. Chem}. \textbf{287}, 36222--36228 (2012).
\bibitem{3} Kozhemyakina, E., Lassar, A. B. \& Zelzer, E. A pathway to bone: signaling molecules and transcription factors involved in chondrocyte development and maturation. \textit{Development} \textbf{142}, 817--831 (2015).
\bibitem{4} Shea, K. L. et al. Sprouty1 Regulates Reversible Quiescence of a Self-Renewing Adult Muscle Stem Cell Pool during Regeneration. \textit{Cell Stem Cell} \textbf{6}, 117--129 (2010).
\bibitem{5} Sato, T., Rocancourt, D., Marques, L., Thorsteinsdóttir, S. \& Buckingham, M. A Pax3/Dmrt2/Myf5 Regulatory Cascade Functions at the Onset of Myogenesis. \textit{PLoS Genet}. \textbf{6}, e1000897 (2010).
\bibitem{6} Zakany, J. \& Duboule, D. The role of \textit{Hox} genes during vertebrate limb development. \textit{Curr. Opin. Genet. Dev}. \textbf{17}, 359--366 (2007).
\bibitem{7} Bensoussan-Trigano, V., Lallemand, Y., Saint Cloment, C. \& Robert, B. Msx1 and Msx2 in limb mesenchyme modulate digit number and identity. \textit{Dev. Dyn}. \textbf{240}, 1190--1202 (2011).
\bibitem{8} Krawchuk, D. et al. Twist1 activity thresholds define multiple functions in limb development. \textit{Dev. Biol}. \textbf{347}, 133--146 (2010).
\bibitem{9} Loebel, D. A. F. et al. Regionalized Twist1 activity in the forelimb bud drives the morphogenesis of the proximal and preaxial skeleton. \textit{Dev. Biol}. \textbf{362}, 132--140 (2012).
\bibitem{10} Maes, C. et al. Osteoblast Precursors, but Not Mature Osteoblasts, Move into Developing and Fractured Bones along with Invading Blood Vessels. \textit{Dev. Cell} \textbf{19}, 329--344 (2010).
\bibitem{11} Guntur, A. R., Rosen, C. J. \& Naski, M. C. N-cadherin adherens junctions mediate osteogenesis through PI3K signaling. \textit{Bone} \textbf{50}, 54--62 (2012).
\bibitem{12} Bandyopadhyay, A., Kubilus, J. K., Crochiere, M. L., Linsenmayer, T. F. \& Tabin, C. J. Identification of unique molecular subdomains in the perichondrium and periosteum and their role in regulating gene expression in the underlying chondrocytes. \textit{Dev. Biol.} \textbf{321}, 162--174 (2008).
\bibitem{13} Hojo, H., Ohba, S., He, X., Lai, L. P. \& McMahon, A. P. Sp7/Osterix Is Restricted to Bone-Forming Vertebrates where It Acts as a Dlx Co-factor in Osteoblast Specification. \textit{Dev. Cell} \textbf{37}, 238--253 (2016).
\bibitem{14} Hartmann, C. Transcriptional networks controlling skeletal development. \textit{Curr. Opin. Genet. Dev}. \textbf{19}, 437--443 (2009).
\bibitem{15} Terry, E. E. et al. Transcriptional profiling reveals extraordinary diversity among skeletal muscle tissues. \textit{eLife} \textbf{7}, e34613 (2018).
\bibitem{16} Buckingham, M. \& Rigby, P. W. J. Gene Regulatory Networks and Transcriptional Mechanisms that Control Myogenesis. \textit{Dev. Cell} \textbf{28}, 225--238 (2014).
\bibitem{17} Bladt, F., Riethmacher, D., Isenmann, S., Aguzzi, A. \& Birchmeier, C. Essential role for the c-met receptor in the migration of myogenic precursor cells into the limb bud. \textit{Nature} \textbf{376}, 768 (1995).
\bibitem{18} Goulding, M., Lumsden, A. \& Paquette, A. J. Regulation of \textit{Pax-3} expression in the dermomyotome and its role in muscle development. \textit{Dev. Camb. Engl}. \textbf{120}, 957--971 (1994).
\bibitem{19} Williams, B. A. \& Ordahl, C. P. \textit{Pax-3} expression in segmental mesoderm marks early stages in myogenic cell specification. \textit{Dev. Camb. Engl.} \textbf{120}, 785--796 (1994).
\bibitem{20} Bober, E., Franz, T., Arnold, H. H., Gruss, P. \& Tremblay, P. \textit{Pax-3} is required for the development of limb muscles: a possible role for the migration of dermomyotomal muscle progenitor cells. \textit{Dev. Camb. Engl.} \textbf{120}, 603--612 (1994).
\bibitem{21} Ishii, M. et al. A Stable Cranial Neural Crest Cell Line from Mouse. \textit{Stem Cells Dev.} \textbf{21}, 3069--3080 (2012).
\bibitem{22} Simoes-Costa, M. \& Bronner, M. E. Establishing neural crest identity: a gene regulatory recipe. \textit{Development} \textbf{142}, 242--257 (2015).
\bibitem{23} Mass, E. et al. Specification of tissue-resident macrophages during organogenesis. \textit{Science} \textbf{353}, aaf4238--aaf4238 (2016).
\bibitem{24} McKinney-Freeman, S. et al. The transcriptional landscape of hematopoietic stem cell ontogeny. \textit{Cell Stem Cell} \textbf{11}, 701--714 (2012).
\bibitem{25} Devic, E., Rizzoti, K., Bodin, S., Knibiehler, B. \& Audigier, Y. Amino acid sequence and embryonic expression of \textit{msr}/\textit{apj}, the mouse homolog of Xenopus \textit{X-msr} and human \textit{APJ}. \textit{Mech. Dev}. \textbf{84}, 199--203 (1999).
\bibitem{26} Kaipainen, A. The related FLT4, FLT1, and KDR receptor tyrosine kinases show distinct expression patterns in human fetal endothelial cells. \textit{J. Exp. Med}. \textbf{178}, 2077--2088 (1993).
\bibitem{27} Jeong, H.-W. et al. Transcriptional regulation of endothelial cell behavior during sprouting angiogenesis. \textit{Nat. Commun}. \textbf{8}, (2017).
\bibitem{28} Atit, R. et al. Beta-catenin activation is necessary and sufficient to specify the dorsal dermal fate in the mouse. \textit{Dev. Biol}. \textbf{296}, 164--176 (2006).
\bibitem{29} Gao, X. et al. HES6 acts as a transcriptional repressor in myoblasts and can induce the myogenic differentiation program. \textit{J. Cell Biol.} \textbf{154}, 1161--1172 (2001).
\bibitem{30} Gagan, J., Dey, B. K., Layer, R., Yan, Z. \& Dutta, A. Notch3 and Mef2c proteins are mutually antagonistic via Mkp1 protein and miR-1/206 microRNAs in differentiating myoblasts. \textit{J. Biol. Chem}. \textbf{287}, 40360--40370 (2012).
\bibitem{31} Buckingham, M. \& Relaix, F. PAX3 and PAX7 as upstream regulators of myogenesis. \textit{Semin. Cell Dev. Biol.} \textbf{44}, 115--125 (2015).
\bibitem{32} Schmidt, K., Glaser, G., Wernig, A., Wegner, M. \& Rosorius, O. Sox8 Is a Specific Marker for Muscle Satellite Cells and Inhibits Myogenesis. \textit{J. Biol. Chem.} \textbf{278}, 29769--29775 (2003).
\bibitem{33} Maeda, T., Chapman, D. L. \& Stewart, A. F. R. Mammalian Vestigial-like 2, a Cofactor of TEF-1 and MEF2 Transcription Factors That Promotes Skeletal Muscle Differentiation. \textit{J. Biol. Chem.} \textbf{277}, 48889--48898 (2002).
\bibitem{34} Mielcarek, M., Piotrowska, I., Schneider, A., G\"unther, S. \& Braun, T. VITO-2, a new SID domain protein, is expressed in the myogenic lineage during early mouse embryonic development. \textit{Gene Expr. Patterns GEP} \textbf{9}, 129--137 (2009).
\bibitem{35} Figeac, N. et al. Vgll3 operates via Tead1, Tead3 and Tead4 to influence myogenesis in skeletal muscle. \textit{J. Cell Sci.} jcs.225946 (2019). % doi:10.1242/jcs.225946
\bibitem{36} Li, Z., Chen, M. J., Stacy, T. \& Speck, N. A. Runx1 function in hematopoiesis is required in cells that express \textit{Tek}. \textit{Blood} \textbf{107}, 106--110 (2006).
\bibitem{37} Summerhurst, K., Stark, M., Sharpe, J., Davidson, D. \& Murphy, P. 3D representation of \textit{Wnt} and \textit{Frizzled} gene expression patterns in the mouse embryo at embryonic day 11.5 (Ts19). \textit{Gene Expr. Patterns} \textbf{8}, 331--348 (2008).
\bibitem{38} Auden, A. et al. Spatial and temporal expression of the Grainyhead-like transcription factor family during murine development. \textit{Gene Expr. Patterns GEP} \textbf{6}, 964--970 (2006).
\bibitem{39} Bazzi, H., Fantauzzo, K. A., Richardson, G. D., Jahoda, C. A. B. \& Christiano, A. M. Transcriptional profiling of developing mouse epidermis reveals novel patterns of coordinated gene expression. \textit{Dev. Dyn.} \textbf{236}, 961--970 (2007).
\bibitem{40} Yu, L. et al. Shox2 is required for chondrocyte proliferation and maturation in proximal limb skeleton. \textit{Dev. Biol.} \textbf{306}, 549--559 (2007).
\bibitem{41} Imamura, Y., Scott, I. C. \& Greenspan, D. S. The pro-alpha3(V) collagen chain. Complete primary structure, expression domains in adult and developing tissues, and comparison to the structures and expression domains of the other types V and XI procollagen chains. \textit{J. Biol. Chem.} \textbf{275}, 8749--8759 (2000).
\bibitem{42} Sp\"ath, S., Andrade, A. C., Chau, M., Baroncelli, M. \& Nilsson, O. Evidence That Rat Chondrocytes Can Differentiate Into Perichondrial Cells. \textit{JBMR Plus} \textbf{2}, 351--361 (2018).
\bibitem{43} Garc\'ia-Andr\'es, C. \& Torres, M. Comparative expression pattern analysis of the highly conserved chemokines SDF1 and CXCL14 during amniote embryonic development. \textit{Dev. Dyn.} \textbf{239}, 2769--2777 (2010).
\bibitem{44} Kimmel, R. A. et al. Two lineage boundaries coordinate vertebrate apical ectodermal ridge formation. \textit{Genes Dev.} \textbf{14}, 1377--1389 (2000).
\bibitem{45} McDonald, L. A., Gerrelli, D., Fok, Y., Hurst, L. D. \& Tickle, C. Comparison of Iroquois gene expression in limbs/fins of vertebrate embryos: \textit{Iroquois} gene expression. \textit{J. Anat.} \textbf{216}, 683--691 (2010).
\bibitem{46} Singh, M. K. et al. The T-box transcription factor Tbx15 is required for skeletal development. \textit{Mech. Dev.} \textbf{122}, 131--144 (2005).
\bibitem{47} Li, L., Cserjesi, P. \& Olson, E. N. Dermo-1: A Novel Twist-Related bHLH Protein Expressed in the Developing Dermis. \textit{Dev. Biol.} \textbf{172}, 280--292 (1995).
\bibitem{48} Gerety, S. S. \& Anderson, D. J. Cardiovascular ephrinB2 function is essential for embryonic angiogenesis. \textit{Dev. Camb. Engl.} \textbf{129}, 1397--1410 (2002).
\bibitem{49} Wei, G. et al. Ets1 and Ets2 are required for endothelial cell survival during embryonic angiogenesis. \textit{Blood} \textbf{114}, 1123--1130 (2009).
\bibitem{50} Feenstra, J. M. et al. Detection of genes regulated by Lmx1b during limb dorsalization: Lmx1b regulated genes in limb dorsalization. \textit{Dev. Growth Differ}. \textbf{54}, 451--462 (2012).
\bibitem{51} Zhao, H. et al. Foxp1/2/4 regulate endochondral ossification as a suppresser complex. \textit{Dev. Biol.} \textbf{398}, 242--254 (2015).
\bibitem{52} Gu, W. X. W. \& Kania, A. Identification of genes controlled by LMX1B in E13.5 mouse limbs. \textit{Dev. Dyn}. \textbf{239}, 2246--2255 (2010).
\bibitem{53} Wenstrup, R. J. et al. Regulation of Collagen Fibril Nucleation and Initial Fibril Assembly Involves Coordinate Interactions with Collagens V and XI in Developing Tendon. \textit{J. Biol. Chem.} \textbf{286}, 20455--20465 (2011).
\bibitem{54} Ito, Y. et al. The \textit{Mohawk} homeobox gene is a critical regulator of tendon differentiation. \textit{Proc. Natl. Acad. Sci.} \textbf{107}, 10538--10542 (2010).
\bibitem{55} Yin, Z. et al. Single-cell analysis reveals a nestin + tendon stem/progenitor cell population with strong tenogenic potentiality. \textit{Sci. Adv.} \textbf{2}, e1600874 (2016).
\bibitem{56} Grosch, M., Fuchs, J., B\"osl, M., Winterpacht, A. \& Tagariello, A. Selenoprotein M is expressed during bone development. \textit{EXCLI J.} \textbf{12}, 967--979 (2013).
\bibitem{57} Choi, J. et al. Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans. \textit{Nucleic Acids Res.} \textbf{47}, D780--D785 (2019).
\bibitem{58} Ferronha, T. et al. LMO4 is an Essential Cofactor in the Snail2-Mediated Epithelial-to-Mesenchymal Transition of Neuroblastoma and Neural Crest Cells. \textit{J. Neurosci.} \textbf{33}, 2773--2783 (2013).
\bibitem{59} Nishino, J. et al. Meteorin: a secreted protein that regulates glial cell differentiation and promotes axonal extension. \textit{EMBO J.} \textbf{23}, 1998--2008 (2004).
\bibitem{60} Choi, J., Djebbar, S., Fournier, A. \& Labrie, C. The co-chaperone DNAJC12 binds to Hsc70 and is upregulated by endoplasmic reticulum stress. \textit{Cell Stress Chaperones} \textbf{19}, 439--446 (2014).
\bibitem{61} Richter, K., Haslbeck, M. \& Buchner, J. The Heat Shock Response: Life on the Verge of Death. \textit{Mol. Cell} \textbf{40}, 253--266 (2010).
\bibitem{62} Wang, C.-H., Wu, S.-B., Wu, Y.-T. \& Wei, Y.-H. Oxidative stress response elicited by mitochondrial dysfunction: Implication in the pathophysiology of aging. \textit{Exp. Biol. Med.} \textbf{238}, 450--460 (2013).
\bibitem{63} Stephens, A. S. et al. Myocyte Enhancer Factor 2C, an Osteoblast Transcription Factor Identified by Dimethyl Sulfoxide (DMSO)-enhanced Mineralization. \textit{J. Biol. Chem.} \textbf{286}, 30071--30086 (2011).
\bibitem{64} Qiu, T. et al. PTH receptor signaling in osteoblasts regulates endochondral vascularization in maintenance of postnatal growth plate. \textit{J. Bone Miner. Res. Off. J. Am. Soc. Bone Miner. Res.} \textbf{30}, 309--317 (2015).
\bibitem{65} Schuster-Gossler, K., Cordes, R. \& Gossler, A. Premature myogenic differentiation and depletion of progenitor cells cause severe muscle hypotrophy in \textit{Delta1} mutants. \textit{Proc. Natl. Acad. Sci.} \textbf{104}, 537--542 (2007).
\bibitem{66} Yokoyama, S. et al. A Systems Approach Reveals that the Myogenesis Genome Network Is Regulated by the Transcriptional Repressor RP58. \textit{Dev. Cell} \textbf{17}, 836--848 (2009).
\bibitem{67} Majesky, M. W., Dong, X. R., Regan, J. N. \& Hoglund, V. J. Vascular Smooth Muscle Progenitor Cells: Building and Repairing Blood Vessels. \textit{Circ. Res.} \textbf{108}, 365--377 (2011).
\bibitem{68} Breland, A. et al. Smooth Muscle Transcriptome Browser: offering genome-wide references and expression profiles of transcripts expressed in intestinal SMC, ICC, and PDGFRa+ cells. \textit{Sci. Rep.} \textbf{9}, (2019).
\bibitem{69} Williams, H. C. et al. Role of Coronin 1B in PDGF-Induced Migration of Vascular Smooth Muscle Cells. \textit{Circ. Res.} \textbf{111}, 56--65 (2012).
\bibitem{70} McGrath, K. E., Fegan, K. H., Frame, J. M., Kingsley, P. D. \& Palis, J. Definitive Erythro-Myeloid Progenitors (EMP) Emerge in the Yolk Sac From Hemogenic Endothelium and Share Transcriptional Regulators with Adult Hematopoiesis. \textit{Blood} \textbf{118}, 910--910 (2011).
\bibitem{71} Bianchi, E., Norfo, R., Pennucci, V., Zini, R. \& Manfredini, R. Genomic landscape of megakaryopoiesis and platelet function defects. \textit{Blood} \textbf{127}, 1249--1259 (2016).
\bibitem{72} Wang, H. et al. MEIS1 Regulates Hemogenic Endothelial Generation, Megakaryopoiesis, and Thrombopoiesis in Human Pluripotent Stem Cells by Targeting TAL1 and FLI1. \textit{Stem Cell Rep.} \textbf{10}, 447--460 (2018).
\bibitem{73} Vallecillo-Garc\'ia, P. et al. Odd skipped-related 1 identifies a population of embryonic fibro-adipogenic progenitors regulating myogenesis during limb development. \textit{Nat. Commun.} \textbf{8}, (2017).
\bibitem{74} Amano, K., Densmore, M., Nishimura, R. \& Lanske, B. Indian Hedgehog Signaling Regulates Transcription and Expression of Collagen Type X via Runx2/Smads Interactions. \textit{J. Biol. Chem.} \textbf{289}, 24898--24910 (2014)
