Details

Autor(en) / Beteiligte

• 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

Titel

ArrayExpress update - from bulk to single-cell expression data

Ist Teil von

• Nucleic acids research, 2019-01, Vol.47 (D1), p.D711

Ort / Verlag

England

Erscheinungsjahr

2019

Link zum Volltext

Quelle

MEDLINE

Beschreibungen/Notizen

• 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.