GSEs

GSEs are acronyms used in multiple fields, but in genomics the most common meaning is GEO Series, a record in the Gene Expression Omnibus (GEO) database maintained by the National Center for Biotechnology Information. A GEO Series represents a single study or experiment and groups all related samples, known as GEO Samples (GSMs), collected under that study. Each GSE links to one or more GEO Platforms (GPLs) that describe the technology used for measurement (for example, microarrays or RNA-seq). The GSE entry also contains metadata describing the organism, experimental design, treatments or conditions, and a concise summary of the study.

Data within a GSE may include raw data files and/or processed data files, depending on what was deposited by the researchers. The GEO infrastructure allows users to retrieve individual GSMs or entire GSEs and to connect series across platforms for cross-study comparisons. Researchers often use GEO records for meta-analyses, replication studies, or to reanalyze data with updated normalization pipelines. Access is web-based, with programmatic access available through NCBI’s E-Utilities and through the GEOquery package in R, among other tools.

While GSEs are widely used for data discovery and integration, they pose challenges. Incomplete or inconsistent metadata, varying data formats, and differences in experimental design can complicate cross-study analyses. Consequently, careful data curation, normalization, and validation are essential when combining GSE-derived data from multiple studies.