\bibitem{1} Peter, I. \& Davidson, E. H. \textit{Genomic Control Process: Development and Evolution}. (Academic Press, 2015).
\bibitem{2} Moore, J. et al. Expanded Encyclopedias of DNA Elements in the Human and Mouse Genomes. (2020).
\bibitem{3} Picelli, S. et al. Full-length RNA-seq from single cells using Smart-seq2. \textit{Nat. Protoc}. \textbf{9}, 171--181 (2014).
\bibitem{4} Marinov, G. K. et al. From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing. \textit{Genome Res}. \textbf{24}, 496--510 (2014).
\bibitem{5} Tabula Muris Consortium et al. Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris. \textit{Nature} \textbf{562}, 367--372 (2018).
\bibitem{6} Scialdone, A. et al. Resolving early mesoderm diversification through single-cell expression profiling. \textit{Nature} \textbf{535}, 289--293 (2016).
\bibitem{7} La Manno, G. et al. Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells. \textit{Cell} \textbf{167}, 566--580.e19 (2016).
\bibitem{8} Zeisel, A. et al. Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. \textit{Science} \textbf{347}, 1138--1142 (2015).
\bibitem{9} Cadwell, C. R. et al. Multimodal profiling of single-cell morphology, electrophysiology, and gene expression using Patch-seq. \textit{Nat. Protoc.} \textbf{12}, 2531--2553 (2017).
\bibitem{10} FANTOM Consortium. A promoter-level mammalian expression atlas. \textit{Nature} \textbf{507}, 462--470. (2014).
\bibitem{11} Cao, J. et al. The single-cell transcriptional landscape of mammalian organogenesis. \textit{Nature} \textbf{566}, 496--502 (2019).
\bibitem{12} Han, X. \textit{et al.} Mapping the Mouse Cell Atlas by Microwell-Seq. \textit{Cell} \textbf{172}, 1091--1107.e17 (2018).
\bibitem{13} Zhang, Y., An, L., Yue, F. \& Hardison, R. C. Jointly characterizing epigenetic dynamics across multiple human cell types. \textit{Nucleic Acids Res}. \textbf{44}, 6721--6731 (2016). 
\bibitem{14} Zhang, Y. \& Hardison, R. C. Accurate and reproducible functional maps in 127 human cell types via 2D genome segmentation. \textit{Nucleic Acids Res}. \textbf{45}, 9823--9836 (2017). 
\bibitem{15} Kajikhina, K., Tsuneto, M. \& Melchers, F. B-Lymphopoiesis in Fetal Liver, Guided by Chemokines. \textit{Adv. Immunol}. \textbf{132}, 71--89 (2016). 
\bibitem{16} Tsuneto, M. \textit{et al.} B-cell progenitors and precursors change their microenvironment in fetal liver during early development. \textit{Stem Cells} \textbf{31}, 2800--2812 (2013). 
\bibitem{17} DeKoter, R. P. \textit{et al.} Regulation of the interleukin-7 receptor alpha promoter by the Ets transcription factors PU.1 and GA-binding protein in developing B cells. \textit{J. Biol. Chem.} 282, 14194--14204 (2007). 
\bibitem{18} Nutt, S. L. \& Kee, B. L. The transcriptional regulation of B cell lineage commitment. \textit{Immunity} \textbf{26}, 715--725 (2007). 
\bibitem{19} Rahmanian, S. \textit{et al.} Dynamics of microRNA expression during mouse prenatal development. \textit{Genome Res.} \textbf{29}, 1900--1909 (2019). 
\bibitem{20} Soneson, C., Lilljebj\"orn, H., Fioretos, T. \& Fontes, M. Integrative analysis of gene expression and copy number alterations using canonical correlation analysis. \textit{BMC Bioinformatics} \textbf{11}, 191 (2010).
\bibitem{21} Brown, B. C., Bray, N. L. \& Pachter, L. Expression reflects population structure. \textit{PLoS Genet}. \textbf{14}, e1007841 (2018).
\bibitem{22} Hollenhorst, P. C., Shah, A. A., Hopkins, C. \& Graves, B. J. Genome-wide analyses reveal properties of redundant and specific promoter occupancy within the \textit{ETS} gene family. \textit{Genes Dev}. \textbf{21}, 1882--1894 (2007). 
\bibitem{23} Rozenberg, J. M. \textit{et al.} All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues. \textit{BMC Genomics} \textbf{9}, 67 (2008). 
\bibitem{24} Mukherjee, S., Brulet, R., Zhang, L. \& Hsieh, J. REST regulation of gene networks in adult neural stem cells. \textit{Nat. Commun.} \textbf{7}, 13360 (2016). 
\bibitem{25} Arnold, P. \textit{et al.} Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting. \textit{Genome Res.} \textbf{23}, 60--73 (2013). 
\bibitem{26} McGann, J. C. \textit{et al.} Polycomb- and REST-associated histone deacetylases are independent pathways toward a mature neuronal phenotype. \textit{eLife} \textbf{3}, e04235 (2014). 
\bibitem{27} Newman, A. M. \textit{et al.} Robust enumeration of cell subsets from tissue expression profiles. \textit{Nat. Methods} \textbf{12}, 453--457 (2015). 
\bibitem{28} Buckingham, M. \& Relaix, F. PAX3 and PAX7 as upstream regulators of myogenesis. \textit{Semin. Cell Dev. Biol.} \textbf{44}, 115--125 (2015). 
\bibitem{29} Goulding, M., Lumsden, A. \& Paquette, A. J. Regulation of \textit{Pax-3} expression in the dermomyotome and its role in muscle development. \textit{Development} \textbf{120}, 957--971 (1994). 
\bibitem{30} Williams, B. A. \& Ordahl, C. P. \textit{Pax-3} expression in segmental mesoderm marks early stages in myogenic cell specification. \textit{Development} \textbf{120}, 785--796 (1994). 
\bibitem{31} Seale, P. \textit{et al.} Pax7 is required for the specification of myogenic satellite cells. \textit{Cell} \textbf{102}, 777--786 (2000). 
\bibitem{32} Yin, H., Price, F. \& Rudnicki, M. A. Satellite Cells and the Muscle Stem Cell Niche. \textit{Physiol. Rev}. \textbf{93}, 23--67 (2013). 
\bibitem{33} Vallecillo--Garc\'ia, P. \textit{et al.} Odd skipped-related 1 identifies a population of embryonic fibroadipogenic progenitors regulating myogenesis during limb development. \textit{Nat. Commun.} \textbf{8}, (2017). 
\bibitem{34} Liu, N. \textit{et al.} A Twist2-dependent progenitor cell contributes to adult skeletal muscle. \textit{Nat. Cell Biol.} \textbf{19}, 202--213 (2017). 
\bibitem{35} Mathew, S. J. \textit{et al.} Connective tissue fibroblasts and Tcf4 regulate myogenesis. \textit{Development} \textbf{138}, 371--384 (2011). 
\bibitem{36} Mitchell, K. J. \textit{et al.} Identification and characterization of a non-satellite cell muscle resident progenitor during postnatal development. \textit{Nat. Cell Biol.} \textbf{12}, 257--266 (2010). 
\bibitem{37} Biressi, S. \textit{et al.} Intrinsic phenotypic diversity of embryonic and fetal myoblasts is revealed by genome-wide gene expression analysis on purified cells. \textit{Dev. Biol.} \textbf{304}, 633--651 (2007). 
\bibitem{38} Lagha, M. \textit{et al.} Transcriptome analyses based on genetic screens for Pax3 myogenic targets in the mouse embryo. \textit{BMC Genomics} \textbf{11}, 696 (2010). 	
\bibitem{39} Singh, A. J. \textit{et al.} FACS-Seq analysis of Pax3-derived cells identifies non-myogenic lineages in the embryonic forelimb. \textit{Sci. Rep.} \textbf{8}, 7670 (2018). 
\bibitem{40} Trapnell, C. \textit{et al.} Pseudo-temporal ordering of individual cells reveals dynamics and regulators of cell fate decisions. \textit{Nat. Biotechnol.} \textbf{32}, 381--386 (2014). 
\bibitem{41} Liu, C.-F., Samsa, W. E., Zhou, G. \& Lefebvre, V. Transcriptional control of chondrocyte specification and differentiation. \textit{Semin. Cell Dev. Biol.} \textbf{62}, 34--49 (2017). 
\bibitem{42} 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{43} Hartmann, C. Transcriptional networks controlling skeletal development. \textit{Curr. Opin. Genet. Dev.} \textbf{19}, 437--443 (2009). 
\bibitem{44} Shah, S., Lubeck, E., Zhou, W. \& Cai, L. seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus. \textit{Neuron} \textbf{94}, 752758.e1 (2017). 
\bibitem{45} Wang, G., Moffitt, J. R. \& Zhuang, X. Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy. \textit{Sci. Rep.} \textbf{8}, 4847 (2018). 
\bibitem{46} Rodriques, S. G. \textit{et al.} Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. \textit{Science} \textbf{363}, 1463--1467 (2019). 
\bibitem{47} Vickovic, S. \textit{et al.} High-definition spatial transcriptomics for in situ tissue profiling. \textit{Nat. Methods} \textbf{16}, 987--990 (2019). 
\bibitem{48} Fong, A. P. et al. Genetic and epigenetic determinants of neurogenesis and myogenesis. \textit{Dev. Cell} \textbf{22}, 721--735 (2012).
\bibitem{49} Visel, A., Minovitsky, S., Dubchak, I. \& Pennacchio, L. A. VISTA Enhancer Browser--a database of tissue-specific human enhancers. \textit{Nucleic Acids Res}. \textbf{35}, D88--92 (2007).
\bibitem{50} Gorkin, D. \textit{et al.} Systematic mapping of chromatin state landscapes during mouse development. \textit{bioRxiv} 166652 (2017) doi:10.1101/166652. 
\bibitem{51} He, Y. \textit{et al.} Spatiotemporal DNA Methylome Dynamics of the Developing Mammalian Fetus. \textit{bioRxiv} 166744 (2017) doi:10.1101/166744. 
\bibitem{52} Fulco, C. P. \textit{et al.} Systematic mapping of functional enhancer-promoter connections with CRISPR interference. \textit{Science} \textbf{354}, 769--773 (2016). 
\bibitem{53} Fulco, C. P. \textit{et al.} Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations. \textit{Nat. Genet.} \textbf{51}, 1664--1669 (2019). 
\bibitem{54} Xiang, G. et al. An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis. \textit{Genome Res}. \textbf{30}, 472--484 (2020)

\bibitem{55} van der Maaten, L. van der \& Hinton, G. Visualizing Data using $t$-SNE. \textit{J. Mach. Learn. Res.} \textbf{9}, 2579--2605 (2008).
\bibitem{56} Wolock, S. L., Lopez, R. \& Klein, A. M. Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data. \textit{Cell Syst}. \textbf{8}, 281--291.e9 (2019).
\bibitem{57} Pijuan-Sala, B. et al. A single-cell molecular map of mouse gastrulation and early organogenesis. \textit{Nature} \textbf{566}, 490--495 (2019).
\bibitem{58} Szklarczyk, D. et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. \textit{Nucleic Acids Res}. \textbf{47}, D607--D613 (2019).
\bibitem{59} Gansner, E. R. \& North, S. C. An open graph visualization system and its applications to software engineering. \textit{Softw. Pract. Exp}. \textbf{30}, 1203--1233 (2000).
\bibitem{60} Wolf, F. A., Angerer, P. \& Theis, F. J. SCANPY: large-scale single-cell gene expression data analysis. \textit{Genome Biol}. \textbf{19}, 15 (2018).
\bibitem{61} Bailey, T. L., Johnson, J., Grant, C. E. \& Noble, W. S. The MEME Suite. \textit{Nucleic Acids Res}. \textbf{43}, W39--49 (2015).
\bibitem{62} Weirauch, M. T. et al. Determination and inference of eukaryotic transcription factor sequence specificity. \textit{Cell} \textbf{158}, 1431--1443 (2014).
\bibitem{63} McLeay, R. C. \& Bailey, T. L. Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data. \textit{BMC Bioinformatics} \textbf{11}, 165 (2010).
\bibitem{64} Yee, S.-P. \& Rigby, P. W. J. The regulation of myogenin gene expression during the embryonic development of the mouse. \textit{Genes Dev}. \textbf{7}, 1277--1289 (1993).
