{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,31]],"date-time":"2026-07-31T02:49:28Z","timestamp":1785466168467,"version":"3.56.0"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,10,22]],"date-time":"2022-10-22T00:00:00Z","timestamp":1666396800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Research Startup Funds of Chongqing Medical University"},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82104063"],"award-info":[{"award-number":["82104063"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004374","name":"Chongqing Medical University","doi-asserted-by":"publisher","award":["BJRC202214"],"award-info":[{"award-number":["BJRC202214"]}],"id":[{"id":"10.13039\/501100004374","id-type":"DOI","asserted-by":"publisher"}]},{"name":"University Innovation Research Group Project of Chongqing","award":["CXQT21016"],"award-info":[{"award-number":["CXQT21016"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Organoids, three-dimensional in vitro tissue cultures derived from pluripotent (embryonic or induced) or adult stem cells, are promising models for the study of human processes and structures, disease onset and preclinical drug development. An increasing amount of omics data has been generated for organoid studies. Here, we introduce OrganoidDB (http:\/\/www.inbirg.com\/organoid_db\/), a comprehensive resource for the multi-perspective exploration of the transcriptomes of organoids. The current release of OrganoidDB includes curated bulk and single-cell transcriptome profiles of 16 218 organoid samples from both human and mouse. Other types of samples, such as primary tissue and cell line samples, are also integrated to enable comparisons with organoids. OrganoidDB enables queries of gene expression under different modes, e.g. across different organoid types, between different organoids from different sources or protocols, between organoids and other sample types, across different development stages, and via correlation analysis. Datasets and organoid samples can also be browsed for detailed information, including organoid information, differentially expressed genes, enriched pathways and single-cell clustering. OrganoidDB will facilitate a better understanding of organoids and help improve organoid culture protocols to yield organoids that are highly similar to living organs in terms of composition, architecture and function.<\/jats:p>","DOI":"10.1093\/nar\/gkac942","type":"journal-article","created":{"date-parts":[[2022,10,22]],"date-time":"2022-10-22T09:59:09Z","timestamp":1666432749000},"page":"D1086-D1093","source":"Crossref","is-referenced-by-count":23,"title":["OrganoidDB: a comprehensive organoid database for the multi-perspective exploration of bulk and single-cell transcriptomic profiles of organoids"],"prefix":"10.1093","volume":"51","author":[{"given":"Qinfeng","family":"Ma","sequence":"first","affiliation":[{"name":"Center for Novel Target and Therapeutic Intervention, Institute of Life Sciences, Chongqing Medical University , Chongqing \u00a0400016,\u00a0 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0743-4499","authenticated-orcid":false,"given":"Haodong","family":"Tao","sequence":"additional","affiliation":[{"name":"Center for Novel Target and Therapeutic Intervention, Institute of Life Sciences, Chongqing Medical University , Chongqing \u00a0400016,\u00a0 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiang","family":"Li","sequence":"additional","affiliation":[{"name":"Center for Novel Target and Therapeutic Intervention, Institute of Life Sciences, Chongqing Medical University , Chongqing \u00a0400016,\u00a0 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhaoyu","family":"Zhai","sequence":"additional","affiliation":[{"name":"Center for Novel Target and Therapeutic Intervention, Institute of Life Sciences, Chongqing Medical University , Chongqing \u00a0400016,\u00a0 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuelu","family":"Zhang","sequence":"additional","affiliation":[{"name":"Center for Novel Target and Therapeutic Intervention, Institute of Life Sciences, Chongqing Medical University , Chongqing \u00a0400016,\u00a0 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhewei","family":"Lin","sequence":"additional","affiliation":[{"name":"Center for Novel Target and Therapeutic Intervention, Institute of Life Sciences, Chongqing Medical University , Chongqing \u00a0400016,\u00a0 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ni","family":"Kuang","sequence":"additional","affiliation":[{"name":"Center for Novel Target and Therapeutic Intervention, Institute of Life Sciences, Chongqing Medical University , Chongqing \u00a0400016,\u00a0 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6014-8160","authenticated-orcid":false,"given":"Jianbo","family":"Pan","sequence":"additional","affiliation":[{"name":"Center for Novel Target and Therapeutic Intervention, Institute of Life Sciences, Chongqing Medical University , Chongqing \u00a0400016,\u00a0 China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,10,22]]},"reference":[{"key":"2023010804341770900_B1","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1038\/s41578-021-00279-y","article-title":"Engineering organoids","volume":"6","author":"Hofer","year":"2021","journal-title":"Nat. Rev. Mater."},{"key":"2023010804341770900_B2","doi-asserted-by":"crossref","first-page":"1247125","DOI":"10.1126\/science.1247125","article-title":"Organogenesis in a dish: modeling development and disease using organoid technologies","volume":"345","author":"Lancaster","year":"2014","journal-title":"Science"},{"key":"2023010804341770900_B3","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1038\/s41580-020-0259-3","article-title":"Human organoids: model systems for human biology and medicine","volume":"21","author":"Kim","year":"2020","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"2023010804341770900_B4","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1038\/s41576-018-0051-9","article-title":"Progress and potential in organoid research","volume":"19","author":"Rossi","year":"2018","journal-title":"Nat. Rev. Genet."},{"key":"2023010804341770900_B5","doi-asserted-by":"crossref","first-page":"4492","DOI":"10.1038\/s41467-021-24746-w","article-title":"Development of a quantitative prediction algorithm for target organ-specific similarity of human pluripotent stem cell-derived organoids and cells","volume":"12","author":"Lee","year":"2021","journal-title":"Nat. Commun."},{"key":"2023010804341770900_B6","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1038\/s41587-020-00762-x","article-title":"The organoid cell atlas","volume":"39","author":"Bock","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"2023010804341770900_B7","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/j.copbio.2018.11.002","article-title":"High-throughput single-cell transcriptomics on organoids","volume":"55","author":"Brazovskaja","year":"2019","journal-title":"Curr. Opin. 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Biol."},{"key":"2023010804341770900_B39","doi-asserted-by":"crossref","first-page":"224","DOI":"10.3109\/21691401.2016.1138495","article-title":"Hepatogenic differentiation from human adipose-derived stem cells and application for mouse acute liver injury","volume":"45","author":"Guo","year":"2017","journal-title":"Artif. Cells Nanomed. Biotechnol."},{"key":"2023010804341770900_B40","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1002\/hep.31037","article-title":"Large-Scale production of LGR5-positive bipotential human liver stem cells","volume":"72","author":"Schneeberger","year":"2020","journal-title":"Hepatology"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/D1\/D1086\/48441609\/gkac942.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/D1\/D1086\/48441609\/gkac942.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,8]],"date-time":"2023-01-08T04:39:10Z","timestamp":1673152750000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/51\/D1\/D1086\/6769766"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,10,22]]},"references-count":40,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2022,10,22]]},"published-print":{"date-parts":[[2023,1,6]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkac942","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,1,6]]},"published":{"date-parts":[[2022,10,22]]}}}