ArrayExpress update – from bulk to single-cell expression data. Issue Volume 47:Issue D1(2019) (24th October 2018)

• Record Type: Journal Article
• Authors: Athar, Awais; Füllgrabe, Anja; George, Nancy; Iqbal, Haider; Huerta, Laura; Ali, Ahmed; Snow, Catherine; Fonseca, Nuno A; Petryszak, Robert; Papatheodorou, Irene; Sarkans, Ugis; Brazma, Alvis
• Is Part Of: Nucleic acids research. Volume 47:Issue D1(2019)
• Page Start: D711
• Page End: D715
• Publication Date: 2018-10-24
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gky964
• Languages: English
• ISSNs: 0305-1048

Abstract

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.