{"id":"doi:10.1093/nar/gky964","kind":"article","title":"ArrayExpress update – from bulk to single-cell expression data","authors":["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"],"author_count":12,"year":2018,"published":"2018-10-10","venue":"Nucleic Acids Research","cited_by":606,"doi":"10.1093/nar/gky964","arxiv_id":null,"nct_id":null,"source_url":"https://doi.org/10.1093/nar/gky964","archive_url":"https://space-kitty.com/papers/doi:10.1093/nar/gky964","updated":null,"pmid":"30357387","pmcid":null,"openalex_id":"W2898321887","pdf_url":"https://academic.oup.com/nar/article-pdf/47/D1/D711/27436407/gky964.pdf","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_license":"CC-BY (publisher license, via OpenAlex)","license":"cc-by","is_open_access":true,"retracted":false,"peer_reviewed":null,"categories":["Research Data Management Practices"],"details":null,"provenance":"openalex","attribution":"Abstract of \"ArrayExpress update – from bulk to single-cell expression data\" by Awais Athar, Anja Füllgrabe, Nancy George et al., https://doi.org/10.1093/nar/gky964, used under its Creative Commons Attribution license (CC-BY); markup removed, otherwise unmodified.","topics":[{"slug":"single-cell-spatial","name":"Single-Cell & Spatial Omics","domain_slug":"biotech"}],"cited_in_dossiers":[]}