The layout of the NCBI databases were designed based on the central dogma:

DNA -> RNA -> Protein

The GEO databases are focused on the first step of the process: RNA expression.

RNA expression is measured in two primary ways: microarray assays and more recently Next Generation Sequencing (NGS). The GEO databases contain both types of data. 

The Gene Expression Omnibus (GEO) was created by the NCBI to store gene expression data from microarray experiments. Most of the content is still microarrays, but some NGS data is also present (with the raw reads in the SRA database). Additionally, it now contains other types of high-throughput genomics data, like CHiP-chip.

GEO exists as two separate databases:

• GEO DataSets: original submitter-supplied records and curated data sets
• GEO Profiles: Expression profiles of individual genes from curated GEO data sets

Additionally, provides an analysis tool, GEO2R, for data sets that have not been curated.

See the pages listed under Gene Expression for more information on these Databases.