is a Data Source.
It is part of the NAMs collection.
OrganoidDB is a database of curated bulk and single-cell transcriptome profiles of organoids. It holds 16,218 organoid samples (12,911 human and 3,307 mouse) collected from GEO and ArrayExpress and organized into 1,069 datasets, 145 of them single-cell RNA-seq. Primary tissue and cell line samples are included so that organoids can be compared against them, with GTEx and the Human Protein Atlas linked as references. The web interface supports gene expression search across organoid types, culture sources and protocols, sample types and developmental stages, plus correlation analysis, and datasets can be browsed with culture details, differentially expressed genes, enriched pathways and single-cell clusters. It is run by the Intelligent Bioinformatics Research Group at the Institute of Life Sciences, Chongqing Medical University.
Unknown
No external IDs available
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| organoiddb.portal | OrganoidDB web portal | genes | Graphical Interface | http | Web interface for searching gene expr... |
| organoiddb.all-organoid-samples | OrganoidDB all organoid samples | all_org_samples (3.1 MB) | Product | csv | Sample metadata for every organoid sa... |
| organoiddb.organoid-specificity-samples | OrganoidDB organoid specificity samples | org_specificity_samples (251.6 KB) | Product | csv | Sample metadata for the organoid samp... |
| organoiddb.general-samples | OrganoidDB general samples | general_samples (91.8 KB) | Product | csv | Sample metadata for the primary tissu... |
OrganoidDB is a database of curated bulk and single-cell transcriptome profiles of organoids. It holds 16,218 organoid samples (12,911 human and 3,307 mouse) collected from GEO and ArrayExpress and organized into 1,069 datasets, 145 of them single-cell RNA-seq.
Primary tissue and cell line samples are included so that organoids can be compared against them, with GTEx and the Human Protein Atlas linked as references. The web interface supports gene expression search across organoid types, culture sources and protocols, sample types and developmental stages, plus correlation analysis. Sample metadata can be downloaded as CSV.
OrganoidDB is run by the Intelligent Bioinformatics Research Group at the Institute of Life Sciences, Chongqing Medical University.
Created: October 02, 2026 | Last modified: October 19, 2026