The main public repositories for microarray and functional genomics data — where to find, download and submit expression datasets. Both major repositories now also host RNA-seq and other high-throughput data.
Major repositories
- GEO (Gene Expression Omnibus, NCBI) — the largest public functional-genomics repository: microarray and sequencing series, samples and platforms, with the GEO2R tool for on-the-fly differential expression.
- ArrayExpress (EMBL-EBI, via BioStudies) — functional genomics experiments archived at EBI; many datasets are cross-referenced with GEO.
Related expression resources
- Expression Atlas (EBI) — curated, reanalysed expression across tissues and conditions.
- SRA — raw sequencing reads underlying RNA-seq datasets.
How to use them
- Search GEO or ArrayExpress by gene, condition or accession (GSE/E-MTAB).
- Download processed matrices, or use GEO2R / Expression Atlas for ready-made comparisons.
- For raw reads behind a study, follow the links to SRA.
Frequently asked questions
Where can I find public gene expression data?
GEO (NCBI) and ArrayExpress (EBI) are the two main repositories; both host microarray and RNA-seq datasets.
How do I analyse a GEO dataset without coding?
Use GEO2R on the dataset’s GEO page for differential expression, or Expression Atlas for curated comparisons.
What is a GSE accession?
A GEO Series accession (e.g. GSE12345) identifying one experiment’s samples and data.
