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USA"},{"key":"10.1016\/j.cell.2026.09.050_bib68","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1006\/dbio.2001.0214","article-title":"Notochord Patterning of the Endoderm","volume":"234","author":"Cleaver","year":"2001","journal-title":"Dev. Biol."},{"key":"10.1016\/j.cell.2026.09.050_bib69","first-page":"68","article-title":"Clonal analysis of the origin of primordial germ cells in the mouse","volume":"182","author":"Lawson","year":"1994","journal-title":"Ciba Found.. Symp."},{"key":"10.1016\/j.cell.2026.09.050_bib70","doi-asserted-by":"crossref","DOI":"10.1101\/cshperspect.a008375","article-title":"Primordial germ cells in mice","volume":"4","author":"Saitou","year":"2012","journal-title":"Cold Spring Harb.. Perspect. Biol."},{"key":"10.1016\/j.cell.2026.09.050_bib71","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1016\/0959-437X(95)90055-L","article-title":"The role of the notochord and floor plate in inductive interactions","volume":"5","author":"Placzek","year":"1995","journal-title":"Curr. Opin. Genet. Dev."},{"key":"10.1016\/j.cell.2026.09.050_bib72","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1242\/dev.112.2.615","article-title":"Fate mapping and cell lineage analysis of Hensen\u2019s node in the chick embryo","volume":"112","author":"Selleck","year":"1991","journal-title":"Development"},{"key":"10.1016\/j.cell.2026.09.050_bib73","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1002\/aja.1002010310","article-title":"Prospective fate map of the mouse primitive streak at 7.5 days of gestation","volume":"201","author":"Smith","year":"1994","journal-title":"Dev. 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Res."},{"key":"10.1016\/j.cell.2026.09.050_bib79","doi-asserted-by":"crossref","DOI":"10.1126\/science.abb2986","article-title":"Characterization of a common progenitor pool of the epicardium and myocardium","volume":"371","author":"Tyser","year":"2021","journal-title":"Science"},{"key":"10.1016\/j.cell.2026.09.050_bib80","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-022-29311-7","article-title":"Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma","volume":"13","author":"Prummel","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.cell.2026.09.050_bib81","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-025-63599-5","article-title":"The pericardium forms as a distinct structure during heart formation","volume":"16","author":"Moran","year":"2025","journal-title":"Nat. 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Biol."},{"key":"10.1016\/j.cell.2026.09.050_bib93","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1387\/ijdb.160408gv","article-title":"Trunk neural crest cells: formation, migration and beyond","volume":"61","author":"Vega-Lopez","year":"2017","journal-title":"Int. J. Dev. Biol."},{"key":"10.1016\/j.cell.2026.09.050_bib94","doi-asserted-by":"crossref","DOI":"10.12703\/r\/10-38","article-title":"Neural crest multipotency and specification: power and limits of single cell transcriptomic approaches","volume":"10","author":"Artinger","year":"2021","journal-title":"Fac. 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