ArticleNucleic acids research2023
OrganoidDB: a comprehensive organoid database for the multi-perspective exploration of bulk and single-cell transcriptomic profiles of organoids.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers, 1 of them a synthesis that pooled it.
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Who cites it
12 citing papers in PubMed, 1 synthesis or guideline pooled it, 19 citations in OpenAlex.
- A systematic review on the culture methods and applications of 3D tumoroids for cancer research and personalized medicine.Cellular oncology (Dordrecht, Netherlands) · 2025Pooled it
- EPB41L family serves as a prognostic biomarker for kidney renal clear cell carcinoma.Cell adhesion & migration · 2026Article
- A Shared Genetic Basis Underlying Myopia-Exotropia Comorbidity.Investigative ophthalmology & visual science · 2026Article
- Human organoids: Fit for drug discovery?Stem cell reports · 2026Review
- Article
- scGeneBank: cross-species screening of functional gene sets at single-cell resolution.Nucleic acids research · 2026Article
- Integrating polygenic signals and single-cell multiomics identifies cell-type-specific regulomes critical for immune- and aging-related diseases.Nature aging · 2026Article
- Review
- Advancing cancer research through organoid technology.Journal of translational medicine · 2024Review
- Identification of an immune-related eRNA prognostic signature for clear cell renal cell carcinoma.Aging · 2024Article
- DiSignAtlas: an atlas of human and mouse disease signatures based on bulk and single-cell transcriptomics.Nucleic acids research · 2024Article
- Tumor Organoid as a Drug Screening Platform for Cancer Research.Current stem cell research & therapy · 2024Review
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Registered trials
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