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Athar A, Füllgrabe A, George N, et al. ArrayExpress update - from bulk to single-cell expression data. Nucleic Acids Res. 2019;47:D711-D715doi: 10.1093/nar/gky964.
Athar, A., Füllgrabe, A., George, N., Iqbal, H., Huerta, L., Ali, A., Snow, C., Fonseca, N. A., Petryszak, R., Papatheodorou, I., Sarkans, U., & Brazma, A. (2019). ArrayExpress update - from bulk to single-cell expression data. Nucleic acids research, 47D711-D715. https://doi.org/10.1093/nar/gky964
Athar, Awais, et al. "ArrayExpress update - from bulk to single-cell expression data." Nucleic acids research vol. 47 (2019): D711-D715. doi: https://doi.org/10.1093/nar/gky964
Athar A, Füllgrabe A, George N, Iqbal H, Huerta L, Ali A, Snow C, Fonseca NA, Petryszak R, Papatheodorou I, Sarkans U, Brazma A. ArrayExpress update - from bulk to single-cell expression data. Nucleic Acids Res. 2019 Jan 08;47:D711-D715. doi: 10.1093/nar/gky964. PMID: 30357387; PMCID: PMC6323929.
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Nucleic Acids Res. 2019 Jan 08;47:D711-D715. doi: 10.1093/nar/gky964.

ArrayExpress update - from bulk to single-cell expression data.

Nucleic acids research

Awais Athar, Anja Füllgrabe, Nancy George, Haider Iqbal, Laura Huerta, Ahmed Ali, Catherine Snow, Nuno A Fonseca, Robert Petryszak, Irene Papatheodorou, Ugis Sarkans, Alvis Brazma

Affiliations

  1. European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  2. CIBIO/InBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Rua Padre Armando Quintas, 4485-601 Vairão, Portugal.

PMID: 30357387 PMCID: PMC6323929 DOI: 10.1093/nar/gky964

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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