GEO Database

Overview

The Gene Expression Omnibus (GEO) is NCBI's public repository for high-throughput gene expression and functional genomics data. GEO contains over 264,000 studies with more than 8 million samples from both array-based and sequence-based experiments.

When to Use This Skill

This skill should be used when searching for gene expression datasets, retrieving experimental data, downloading raw and processed files, querying expression profiles, or integrating GEO data into computational analysis workflows.

Core Capabilities

1. Understanding GEO Data Organization

GEO organizes data hierarchically using different accession types:

Series (GSE): A complete experiment with a set of related samples

• Example: GSE123456
• Contains experimental design, samples, and overall study information