OrganoidDB: a comprehensive organoid database for the multi-perspective exploration of bulk and single-cell transcriptomic profiles of organoids

作者全名："Ma, Qinfeng; Tao, Haodong; Li, Qiang; Zhai, Zhaoyu; Zhang, Xuelu; Lin, Zhewei; Kuang, Ni; Pan, Jianbo"

作者地址："[Ma, Qinfeng; Tao, Haodong; Li, Qiang; Zhai, Zhaoyu; Zhang, Xuelu; Lin, Zhewei; Kuang, Ni; Pan, Jianbo] Chongqing Med Univ, Ctr Novel Target & Therapeut Intervent, Inst Life Sci, Chongqing 400016, Peoples R China"

通信作者："Pan, JB (通讯作者)，Chongqing Med Univ, Ctr Novel Target & Therapeut Intervent, Inst Life Sci, Chongqing 400016, Peoples R China."

来源：NUCLEIC ACIDS RESEARCH

ESI学科分类：BIOLOGY & BIOCHEMISTRY

WOS号：WOS:000871031400001

JCR分区：Q1

影响因子：14.9

年份：2022

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期号：　

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文献类型：Article; Early Access

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摘要："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."

基金机构：Research Startup Funds of Chongqing Medical University; National Natural Science Foundation of China [82104063]; project of the top-notch talent cultivation program for the graduate students of Chongqing Medical University [BJRC202214]; University Innovation Research Group Project of Chongqing [CXQT21016]; High-Level Innovation Platform Project of Chongqing

基金资助正文：Research Startup Funds of Chongqing Medical University; National Natural Science Foundation of China [82104063]; project of the top-notch talent cultivation program for the graduate students of Chongqing Medical University [BJRC202214]; University Innovation Research Group Project of Chongqing [CXQT21016]; High-Level Innovation Platform Project of Chongqing (No. 14). Funding for open access charge: the Research Startup Funds of Chongqing Medical University.