ArrayExpress update – from bulk to single-cell expression data

By Awais Athar, Anja Füllgrabe, Nancy George, Haider Iqbal, L. Huerta, Ahmed Ali, Catherine Snow, Nuno A. Fonseca, R. Petryszak, I. Papatheodorou and 2 more. 2018

508 citations recorded by the source corpus.

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.

Subfields: Cancer Research, Molecular Biology

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Citations in the corpus

TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment (2020, methodology): “TISCH builds a scRNA-seq atlas of 76 high-quality tumor datasets across 27 cancer types, which were mainly collected from Gene Expression Om-nibus (GEO; 16) and ArrayExpress (17).”
Expression Atlas update: from tissues to single cells (2019, background): “It was originally developed in 2009 (1) as a resource to uniformly analyse, annotate and display the results of microarray and RNA-Seq experiments from the ArrayExpress archive (2).”