is a Data Source.
ArrayExpress is EMBL-EBI's archive of functional genomics experiments, holding raw and processed data and MIAME/MINSEQE-compliant metadata from microarray and high-throughput sequencing studies, including bulk and single-cell RNA-seq. Since 2021 it has been served as a collection within BioStudies, and its accessions keep the E-XXXX-n form. It is the European counterpart of NCBI GEO and supplies the experiments reanalyzed by Expression Atlas.
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| arrayexpress.portal | ArrayExpress Web Interface | arrayexpress | Graphical Interface | http | Searchable web interface for browsing... |
| arrayexpress.api | ArrayExpress Search API | search | Programming Interface | http | BioStudies REST API endpoint for sear... |
| arrayexpress.ftp | ArrayExpress FTP Archive | biostudies | Product | mixed | FTP/HTTPS archive of ArrayExpress stu... |
| arrayexpress.annotare | Annotare Submission Tool | annotare | Graphical Interface | http | Annotare, the web-based submission to... |
| ID | Name | URL | Category | Format | Relation | Description |
|---|---|---|---|---|---|---|
| europepmc.textmined-terms | Europe PMC Text-Mined Database Accession Links | TextMinedTerms | Mapping | csv | had primary source | CSV files, one per database, linking ... |
| organoiddb.all-organoid-samples | OrganoidDB all organoid samples | all_org_samples (3.1 MB) | Product | csv | had primary source | Sample metadata for every organoid sa... |
| organoiddb.organoid-specificity-samples | OrganoidDB organoid specificity samples | org_specificity_samples (251.6 KB) | Product | csv | had primary source | Sample metadata for the organoid samp... |
| organoiddb.general-samples | OrganoidDB general samples | general_samples (91.8 KB) | Product | csv | had primary source | Sample metadata for the primary tissu... |
| expressionatlas.ftp-bulk | Expression Atlas FTP (Bulk Data) | experiments | Product | http | had primary source | FTP archive containing processed expr... |
| expressionatlas.experiment-downloads | Expression Atlas Experiment Downloads | download | Product | tsv | had primary source | Individual experiment data downloads ... |
| expressionatlas.r-objects | Expression Atlas R Data Objects | ExpressionAtlas | Product | mixed | had primary source | Normalized gene expression data and r... |
| expressionatlas.baseline-summary | Expression Atlas Baseline Summary | experiments | Product | tsv | had primary source | Baseline expression summary data acro... |
| expressionatlas.differential-results | Expression Atlas Differential Results | experiments?experimentType=differential | Product | tsv | had primary source | Differential gene expression results ... |
| biostudies.ftp | BioStudies FTP Archive | biostudies | Product | mixed | had primary source | FTP/HTTPS archive of BioStudies study... |
| omicsdi.portal | OmicsDI Portal | www.omicsdi.org | Graphical Interface | http | had primary source | Web portal for searching and browsing... |
| omicsdi.api | OmicsDI API | index.html | Programming Interface | http | had primary source | Swagger-documented web service for pr... |
| open-tggates.arrayexpress-rat-in-vitro | Open TG-GATEs in ArrayExpress (Rat In Vitro) | E-MTAB-797 | Product | http | had primary source | ArrayExpress record E-MTAB-797, Open ... |
| open-tggates.arrayexpress-human-in-vitro | Open TG-GATEs in ArrayExpress (Human In Vitro) | E-MTAB-798 | Product | http | had primary source | ArrayExpress record E-MTAB-798, Open ... |
| open-tggates.arrayexpress-rat-single-dose | Open TG-GATEs in ArrayExpress (Rat In Vivo Single Dose) | E-MTAB-799 | Product | http | had primary source | ArrayExpress record E-MTAB-799, Open ... |
| open-tggates.arrayexpress-rat-repeat-dose | Open TG-GATEs in ArrayExpress (Rat In Vivo Repeated Dose) | E-MTAB-800 | Product | http | had primary source | ArrayExpress record E-MTAB-800, Open ... |
ArrayExpress is EMBL-EBI’s archive of functional genomics experiments. It holds raw and processed data and MIAME/MINSEQE-compliant metadata from microarray and high-throughput sequencing studies, including bulk and single-cell RNA-seq. It is the European counterpart of NCBI GEO and supplies the experiments reanalyzed by Expression Atlas.
Since 2021 ArrayExpress has been served as a collection within BioStudies. Accessions
keep the E-XXXX-n form (for example E-MTAB-17130). The BioStudies API reported
80,947 ArrayExpress studies on 2026-10-03.
https://www.ebi.ac.uk/biostudies/api/v1/studies/<accession>/infoE-MTAB-/130/E-MTAB-17130/Files/ holds the IDF, SDRF and processed data for
E-MTAB-17130)The site links the EMBL-EBI Terms of Use. Individual studies may carry their own terms; no single data license is stated.
Created: October 03, 2026 | Last modified: October 03, 2026