ArrayExpress update - from bulk to single-cell expression data

• Type: Article in International Scientific Journal
• Date: 2019

Authors

Athar, A (Author) Other; Fullgrabe, A (Author) Other; George, N (Author) Other; Iqbal, H (Author) Other; Huerta, L (Author) Other; Ali, A (Author) Other; Snow, C (Author) Other; Nuno A Fonseca (Author) FEUP; Petryszak, R (Author) Other; Papatheodorou, I (Author) Other; Sarkans, U (Author) Other; Brazma, A (Author) Other

Journal

Title: Nucleic Acids Research

Vol. 47

Pages: D711-D715

ISSN: 0305-1048

Publisher: Oxford University Press

Indexing

ISI Web of Knowledge - 59 Citations

Scopus - 59 Citations

Other information

Authenticus ID: P-00P-SS2

DOI: 10.1093/nar/gky964

Abstract (EN): 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.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 5