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However, their properties have not yet been fully studied, which hinders their wide spread application. Here we report the development of differentiation systems for ventricular and atrial heart organoids, enabling the study of heart diseases with chamber defects. We show that our systems generate chamber-specific organoids comprising of the major cardiac cell types, and we use single cell RNA sequencing together with sample multiplexing to characterize the cells we generate. To that end, we developed a machine learning label transfer approach leveraging cell type, chamber, and laterality annotations available for primary human fetal heart cells. We then used this model to analyze organoid cells from an isogeneic line carrying an Ebstein\u2019s anomaly associated genetic variant in <jats:italic>NKX2-5<\/jats:italic>, and we successfully recapitulated the disease\u2019s atrialized ventricular defects. In summary, we have established a workflow integrating heart organoids and computational analysis to model heart development in normal and disease states.<\/jats:p>","DOI":"10.1038\/s42003-022-03346-4","type":"journal-article","created":{"date-parts":[[2022,4,29]],"date-time":"2022-04-29T10:03:45Z","timestamp":1651226625000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":61,"title":["Computational profiling of hiPSC-derived heart organoids reveals chamber defects associated with NKX2-5 deficiency"],"prefix":"10.1038","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5605-0811","authenticated-orcid":false,"given":"Wei","family":"Feng","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9459-5548","authenticated-orcid":false,"given":"Hannah","family":"Schriever","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shan","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5910-1306","authenticated-orcid":false,"given":"Abha","family":"Bais","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haodi","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1460-5487","authenticated-orcid":false,"given":"Dennis","family":"Kostka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8546-2364","authenticated-orcid":false,"given":"Guang","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,4,29]]},"reference":[{"key":"3346_CR1","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1038\/nprot.2012.150","volume":"8","author":"X Lian","year":"2013","unstructured":"Lian, X. et al. 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