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-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.

Figure 1.

(A) Experiment submissions to ArrayExpress via Annotare during the last 3 years by experiment type. Data from September 2017 to August 2018 include 34 submissions using the newly introduced plant templates (27 plant sequencing, 5 plant one-colour microarray and 2 plant two-colour microarray experiments). (B) Number of experiments in ArrayExpress (public or private) with experiment type ‘RNA-seq of coding RNA from single cells’ by submission year.

Figure 2.

Annotare submission set-up and template selection. First, the user chooses the template type e.g. ‘Plant - high-throughput sequencing’. Then, the study design can be selected from a list of suggestions. Based on these choices, the relevant sample attributes and experimental variables are preselected.

Figure 3.

The updated Annotare interface featuring an uncoupled file upload panel, simplified navigation, improved validation error reporting and a new protocol entry panel.