Database Commons
Database Commons

a catalog of worldwide biological databases

Database Profile

General information

Full name: Organoid Database
Description: OrganoidDB, a comprehensive transcriptome data (microarray, bulk RNA-seq and single-cell RNA-seq) resource of human and mouse organoids. 16,218 organoid samples were collected and labeled from GEO and ArrayExpress. Other types of sample are also integrated, including primary tissues and cell lines to enable comparisons to be made with organoids.
Year founded: 2021
Last update: 2022-07-18
Version: v1.0
Real time : Checking...
Country/Region: China

Classification & Tag

Data type:
Data object:
Database category:
Major species:

Contact information

University/Institution: Chongqing Medical University
Country/Region: China
Contact name (PI/Team): Jianbo Pan
Contact email (PI/Helpdesk):


OrganoidDB: a comprehensive organoid database for the multi-perspective exploration of bulk and single-cell transcriptomic profiles of organoids. [PMID: 36271792]
Qinfeng Ma, Haodong Tao, Qiang Li, Zhaoyu Zhai, Xuelu Zhang, Zhewei Lin, Ni Kuang, Jianbo Pan

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 (, 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.

Nucleic Acids Res. 2023:51(D1) | 0 Citations (from Europe PMC, 2023-09-16)



Community reviews

Not Rated
Data quality & quantity:
Content organization & presentation
System accessibility & reliability:

Word cloud

Related Databases

Cited by

Record metadata

Created on: 2023-08-22
Curated by:
Xinyu Zhou [2023-09-19]
Yuanyuan Cheng [2023-09-11]
Yuxin Qin [2023-09-05]
Yuanyuan Cheng [2023-08-22]