ArrayExpress update – from bulk to single-cell expression data

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...

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Veröffentlicht in:Nucleic acids research Jg. 47; H. D1; S. D711 - D715
Hauptverfasser: 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
Format: Journal Article
Sprache:Englisch
Veröffentlicht: England Oxford University Press 08.01.2019
Schlagworte:
Database Issue
Databases, Genetic
Oligonucleotide Array Sequence Analysis - methods
RNA-Seq - methods
Single-Cell Analysis - methods
Software
ISSN:0305-1048, 1362-4962, 1362-4962
Online-Zugang:Volltext
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Zusammenfassung: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.
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The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint First Authors.
ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gky964