ArrayExpress – functional genomics data

ArrayExpress Archive of Functional Genomics Data stores data from high-throughput functional genomics experiments, and provides these data for reuse to the research community.

Latest News

18 May 2018 - New single-cell submission and metadata guide
We are happy to announce the newest addition to our help pages: The single-cell submission guide!
This is a simple step-by-step guide which leads you through submitting single-cell sequencing submissions and lists the minimum required metadata to include. The guide starts by explaining the expected sample attributes dependent on the experiment design to help you correctly annotate your samples. The next section details the technical information that is required for single cell-specific procedures including pre/post analysis quality control or how single cells were generated. The library and sequencing information section helps you to understand the required information for the library construction protocols, how to include barcode information, and spike-in information where applicable. Lastly, how to prepare the raw data files for your submission.
We hope you find this useful to submit single-cell sequencing data!


Information about how to search ArrayExpress, understand search results, how to submit data and FAQ can be found in our Help section.

Find out more about the Functional Genomics group.

Tools and Access

Annotare: web-based submission tool for ArrayExpress.

ArrayExpress Bioconductor package: an R package to access ArrayExpress and build data structures.

Programmatic access: query and download data using web services or JSON.

FTP access: data can be downloaded directly from our FTP site.

Related Projects

Discover up and down regulated genes in numerous experimental conditions in the Expression Atlas.

Explore the Experimental Factor Ontology used to support queries and annotation of ArrayExpress data.