Veselinyová D, Mašlanková J, Kalinová K, Mičková H, Mareková M, Rabajdová M. Selected in situ hybridization methods: principles and application. Molecules. 2021;26:3874.

Article  PubMed  PubMed Central  Google Scholar 

Young AP, Jackson DJ, Wyeth RC. A technical review and guide to RNA fluorescence in situ hybridization. PeerJ. 2020;8:e8806.

Article  PubMed  PubMed Central  Google Scholar 

Choi HMT, Chang JY, Trinh LA, Padilla JE, Fraser SE, Pierce NA. Programmable in situ amplification for multiplexed imaging of mRNA expression. Nat Biotechnol. 2010;28:1208–12.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Choi HMT, Beck VA, Pierce NA. Next-generation in situ hybridization chain reaction: higher gain, lower cost, greater durability. ACS Nano. 2014;8:4284–94.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Choi HMT, Schwarzkopf M, Fornace ME, Acharya A, Artavanis G, Stegmaier J, et al. Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust. Development. 2018;145:dev165753.

Article  PubMed  PubMed Central  Google Scholar 

Kim DW, Place E, Chinnaiya K, Manning E, Sun C, Dai W, et al. Single-cell analysis of early chick hypothalamic development reveals that hypothalamic cells are induced from prethalamic-like progenitors. Cell Rep. 2022;38:110251.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Williams RM, Lukoseviciute M, Sauka-Spengler T, Bronner ME. Single-cell atlas of early chick development reveals gradual segregation of neural crest lineage from the neural plate border during neurulation. eLife. 2022;11:e74464.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Choi HMT, Calvert CR, Husain N, Huss D, Barsi JC, Deverman BE, et al. Mapping a multiplexed zoo of mRNA expression. Development. 2016;143:3632–7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Elagoz AM, Styfhals R, Maccuro S, Masin L, Moons L, Seuntjens E. Optimization of whole mount RNA multiplexed in situ hybridization chain reaction with immunohistochemistry, clearing and imaging to visualize octopus embryonic neurogenesis. Front Physiol. 2022;13:882413.

Article  PubMed  PubMed Central  Google Scholar 

Huss D, Choi HMT, Readhead C, Fraser SE, Pierce NA, Lansford R. Combinatorial analysis of mRNA expression patterns in mouse embryos using hybridization chain reaction. Cold Spring Harb Protoc. 2015;2015:pdb.prot083832.

Article  Google Scholar 

Kramer EE, Steadman PE, Epp JR, Frankland PW, Josselyn SA. Assessing individual neuronal activity across the intact brain: using hybridization chain reaction (HCR) to detect Arc mRNA localized to the nucleus in volumes of cleared brain tissue. Curr Protoc Neurosci. 2018;84:e49.

Article  PubMed  Google Scholar 

Ling ITC, Sauka-Spengler T. Early chromatin shaping predetermines multipotent vagal neural crest into neural, neuronal and mesenchymal lineages. Nat Cell Biol. 2019;21:1504–17.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Trivedi V, Choi HMT, Fraser SE, Pierce NA. Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos. Development. 2018;145:dev156869.

Article  PubMed  PubMed Central  Google Scholar 

Galton R, Fejes-Toth K, Bronner ME. Co-option of the piRNA pathway to regulate neural crest specification. Sci Adv. 2022;8:eabn1441.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Miao Y, Djeffal Y, De Simone A, Zhu K, Lee JG, Lu Z, et al. Reconstruction and deconstruction of human somitogenesis in vitro. Nature. 2023;614:500–8.

Article  CAS  PubMed  Google Scholar 

Monroy BY, Adamson CJ, Camacho-Avila A, Guerzon CN, Echeverria CV, Rogers CD. Expression atlas of avian neural crest proteins: neurulation to migration. Dev Biol. 2022;483:39–57.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pajanoja C, Hsin J, Olinger B, Schiffmacher A, Yazejian R, Abrams S, et al. Maintenance of pluripotency-like signature in the entire ectoderm leads to neural crest stem cell potential. Nat Commun. 2023;14:5941.

Chinnaiya K, Burbridge S, Jones A, Kim DW, Place E, Manning E, et al. A neuroepithelial wave of BMP signalling drives anteroposterior specification of the tuberal hypothalamus. eLife. 2023;12:e83133.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Belle M, Godefroy D, Dominici C, Heitz-Marchaland C, Zelina P, Hellal F, et al. A simple method for 3D analysis of immunolabeled axonal tracts in a transparent nervous system. Cell Rep. 2014;9:1191–201.

Article  CAS  PubMed  Google Scholar 

Kirst C, Skriabine S, Vieites-Prado A, Topilko T, Bertin P, Gerschenfeld G, et al. Mapping the fine-scale organization and plasticity of the brain vasculature. Cell. 2020;180:780–795.e25.

Article  CAS  PubMed  Google Scholar 

Kolesová H, Olejníčková V, Kvasilová A, Gregorovičová M, Sedmera D. Tissue clearing and imaging methods for cardiovascular development. iScience. 2021;24:102387.

Article  PubMed  PubMed Central  Google Scholar 

Moreno-Bravo JA, Roig Puiggros S, Mehlen P, Chédotal A. Synergistic activity of floor-plate- and ventricular-zone-derived netrin-1 in spinal cord commissural axon guidance. Neuron. 2019;101:625–634.e3.

Article  CAS  PubMed  Google Scholar 

Porter DDL, Morton PD. Clearing techniques for visualizing the nervous system in development, injury, and disease. J Neurosci Methods. 2020;334:108594.

Article  PubMed  PubMed Central  Google Scholar 

Vieites-Prado A, Renier N. Tissue clearing and 3D imaging in developmental biology. Development. 2021;148:dev199369.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Klingberg A, Hasenberg A, Ludwig-Portugall I, Medyukhina A, Männ L, Brenzel A, et al. Fully automated evaluation of total glomerular number and capillary tuft size in nephritic kidneys using lightsheet microscopy. J Am Soc Nephrol. 2017;28:452–9.

Article  CAS  PubMed  Google Scholar 

Giovannone D, Ortega B, Reyes M, El-Ghali N, Rabadi M, Sao S, et al. Chicken trunk neural crest migration visualized with HNK1. Acta Histochem. 2015;117:255–66.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Holmes G, Niswander L. Expression of slit-2 and slit-3 during chick development. Dev Dyn. 2001;222:301–7.

Article  CAS  PubMed  Google Scholar 

De Bellard ME, Rao Y, Bronner-Fraser M. Dual function of Slit2 in repulsion and enhanced migration of trunk, but not vagal, neural crest cells. J Cell Biol. 2003;162:269–79.

Article  PubMed  PubMed Central  Google Scholar 

Jia L, Cheng L, Raper J. Slit/Robo signaling is necessary to confine early neural crest cells to the ventral migratory pathway in the trunk. Dev Biol. 2005;282:411–21.

Article  CAS  PubMed  Google Scholar 

Hargrave M, Karunaratne A, Cox L, Wood S, Koopman P, Yamada T. The HMG box transcription factor gene Sox14 marks a novel subset of ventral interneurons and is regulated by sonic hedgehog. Dev Biol. 2000;219:142–53.

Article  CAS  PubMed  Google Scholar 

Agarwala S, Aglyamova GV, Marma AK, Fallon JF, Ragsdale CW. Differential susceptibility of midbrain and spinal cord patterning to floor plate defects in the talpid2 mutant. Dev Biol. 2005;288:206–20.

Article  CAS  PubMed  Google Scholar 

Thompson H, Blentic A, Watson S, Begbie J, Graham A. The formation of the superior and jugular ganglia: insights into the generation of sensory neurons by the neural crest. Dev Dyn. 2010;239:439–45.

Article  PubMed  Google Scholar 

Yuan S, Schoenwolf GC. Islet-1 marks the early heart rudiments and is asymmetrically expressed during early rotation of the foregut in the chick embryo. Anat Rec. 2000;260:204–7.

Article  CAS  PubMed  Google Scholar 

Leconte L, Lecoin L, Martin P, Saule S. Pax6 interacts with cVax and Tbx5 to establish the dorsoventral boundary of the developing eye. J Biol Chem. 2004;279:47272–7.

Article  CAS  PubMed  Google Scholar 

Jacob J, Kong J, Moore S, Milton C, Sasai N, Gonzalez-Quevedo R, et al. Retinoid acid specifies neuronal identity through graded expression of Ascl1. Curr Biol. 2013;23:412–8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Le Dréau G, Garcia-Campmany L, Rabadán MA, Ferronha T, Tozer S, Briscoe J, et al. Canonical BMP7 activity is required for the generation of discrete neuronal populations in the dorsal spinal cord. Development. 2012;139:259–68.

Article  PubMed