ArrayExpress update – from bulk to single-cell expression data

TLDR

ArrayExpress is a functional genomics data archive that has seen a surge in RNA‑seq and single‑cell RNA‑seq submissions, surpassing microarray experiments in the past year. The authors aim to adapt to these trends by revamping the Annotare submission tool to capture comprehensive metadata and by creating the BioStudies Database to eventually replace ArrayExpress. They re‑process selected datasets into the Expression Atlas and Single Cell Expression Atlas, while continuing unchanged submissions and migrating all existing ArrayExpress data into BioStudies with preserved accession numbers and APIs.

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.