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

Area of Science:

• Genomics
• Bioinformatics
• Functional Genomics Data Archiving

Background:

• ArrayExpress archives functional genomics data from diverse technologies.
• There's a growing trend towards sequencing-based experiments, particularly RNA sequencing (RNA-seq).
• Single-cell RNA sequencing (scRNA-seq) is increasingly prevalent over bulk sample analysis.

Purpose of the Study:

• To adapt the ArrayExpress archive to accommodate the increasing volume and types of functional genomics data.
• To enhance data submission and interpretation tools for researchers.
• To outline the transition of ArrayExpress to a new, more comprehensive archival resource.

Main Methods:

• Updating the Annotare submission tool to collect comprehensive metadata for RNA-seq and scRNA-seq.
• Reprocessing selected datasets for the Expression Atlas and Single Cell Expression Atlas for enhanced data interpretation and quality control.
• Developing the BioStudies Database as a successor to ArrayExpress for multi-omics data.

Main Results:

• The submission tool Annotare has been updated to handle new data types and metadata requirements.
• The Expression Atlas and Single Cell Expression Atlas provide value-added data interpretation.
• The BioStudies Database is established to supersede ArrayExpress, integrating all existing data.

Conclusions:

• ArrayExpress is evolving to meet the demands of modern functional genomics research, especially RNA-seq and scRNA-seq.
• The transition to BioStudies Database ensures the long-term accessibility and usability of functional genomics data.
• Continued support for existing data and access methods is maintained during the transition.