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Under the influence of specific growth factors, adult stem cells differentiate and organize into 3D cultures named organoids. The molecular phenotyping of these structures is an essential step for validating an organoid model. However, the limited number of organoids generated in culture yields very low amounts of genetic material, making phenotyping difficult. Recently, digital PCR (dPCR) techniques have become available for the highly sensitive detection of genetic material at low concentrations. The aim of this work was to apply dPCR to the identification of the various cell populations expected to be present in murine duodenal organoids. 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Ootani","year":"2009","journal-title":"Nat Med"},{"issue":"5","key":"pone.0319701.ref026","doi-asserted-by":"crossref","first-page":"1762","DOI":"10.1053\/j.gastro.2011.07.050","article-title":"Long-term expansion of epithelial organoids from human colon, adenoma, adenocarcinoma, and Barrett\u2019s epithelium","volume":"141","author":"T Sato","year":"2011","journal-title":"Gastroenterology"},{"issue":"7","key":"pone.0319701.ref027","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1038\/s41580-020-0258-4","article-title":"COVID-19: organoids go viral","volume":"21","author":"H Clevers","year":"2020","journal-title":"Nat Rev Mol Cell Biol"},{"issue":"3","key":"pone.0319701.ref028","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1016\/j.stemcr.2020.11.009","article-title":"The Organoid Platform: Promises and Challenges as Tools in the Fight against COVID-19","volume":"16","author":"MH Geurts","year":"2021","journal-title":"Stem Cell 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