geo-database

Topics in the source

• GEO Database
• Overview
• When to Use This Skill
• Core Capabilities
• 1. Understanding GEO Data Organization
• 2. Searching GEO Data
• 3. Retrieving GEO Data with GEOparse (Recommended)
• 4. Using NCBI E-utilities for GEO Access

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. 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. 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 Largest organizational unit in GEO Current count: 264,928+ series Sample (GSM): A single experimental sample or biological replicate Example: GSM987654 Contains individual sample data, protocols, and metadata Linked to platforms and series Current count: 8,068,632+ samples Platform (GPL): The microarray or sequencing platform used Example: GPL570 (Affymetrix Human Genome U133 Plus 2.0 Array) Describes the technology and probe/feature annotations Shared across multiple experiments Current count:

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