# ArrayExpress update – from bulk to single-cell expression data

Article · Awais Athar, Anja Füllgrabe, Nancy George, Haider Iqbal, Laura Huerta, Ahmed Yousif Ali, Catherine Snow, Nuno A. Fonseca, Robert Petryszak, Irene Papatheodorou, Uğis Sarkans, Alvis Brāzma

- Archive id: doi:10.1093/nar/gky964
- Published: 2018-10-10
- Venue: Nucleic Acids Research
- DOI: https://doi.org/10.1093/nar/gky964
- PMID: 30357387
- Citations: 606
- Source URL: https://doi.org/10.1093/nar/gky964
- PDF: https://academic.oup.com/nar/article-pdf/47/D1/D711/27436407/gky964.pdf
- Provenance: openalex

## Abstract

ArrayExpress (https://www.ebi.ac.uk/arrayexpress) is an archive of functional genomics data from a variety of technologies assaying functional modalities of a genome, such as gene expression or promoter occupancy. The number of experiments based on sequencing technologies, in particular RNA-seq experiments, has been increasing over the last few years and submissions of sequencing data have overtaken microarray experiments in the last 12 months. Additionally, there is a significant increase in experiments investigating single cells, rather than bulk samples, known as single-cell RNA-seq. To accommodate these trends, we have substantially changed our submission tool Annotare which, along with raw and processed data, collects all metadata necessary to interpret these experiments. Selected datasets are re-processed and loaded into our sister resource, the value-added Expression Atlas (and its component Single Cell Expression Atlas), which not only enables users to interpret the data easily but also serves as a test for data quality. With an increasing number of studies that combine different assay modalities (multi-omics experiments), a new more general archival resource the BioStudies Database has been developed, which will eventually supersede ArrayExpress. Data submissions will continue unchanged; all existing ArrayExpress data will be incorporated into BioStudies and the existing accession numbers and application programming interfaces will be maintained.

_Abstract reproduced under CC-BY (publisher license, via OpenAlex)._

Topics: [Single-Cell & Spatial Omics](https://space-kitty.com/topics/single-cell-spatial)

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