GEO and MIAME (Minimum Information About a Microarray Experiment)

The MIAME guidelines outline the minimum information that should be included when describing a microarray experiment. Many journals and funding agencies require microarray data to comply with MIAME. GEO deposit procedures enable and encourage submitters to supply MIAME compliant data.

More information and background regarding GEO and MIAME are discussed in this Nature Biotechnology correspondence.

MIAME compliance is not related to the submission format or route, but rather to the content provided

The six most critical elements contributing towards MIAME are:

The raw data for each hybridization (e.g., CEL or GPR files)
The final processed (normalized) data for the set of hybridizations in the experiment (study) (e.g., the gene expression data matrix used to draw the conclusions from the study)
The essential sample annotation including experimental factors and their values (e.g., compound and dose in a dose response experiment)
The experimental design including sample data relationships (e.g., which raw data file relates to which sample, which hybridizations are technical, which are biological replicates)
Sufficient annotation of the array (e.g., gene identifiers, genomic coordinates, probe oligonucleotide sequences or reference commercial array catalog number)
The essential laboratory and data processing protocols (e.g., what normalization method has been used to obtain the final processed data)

All GEO submission procedures are designed to closely follow the MIAME checklist.

There are currently three ways to submit data to GEO:

If you have any comments or concerns regarding these issues please email us at geo@ncbi.nlm.nih.gov.