Microarray data submit Guide GEO

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A GEOarchive submission consists of 4 parts (Listed below). Once you have all the required documentation, you can submit the data here - NCBI Data Submission Login Page

Please be aware that excel can sometimes inadvertently introduce errors, especially in gene names. Details - Zeeberg et al

Contents

Metadata

'Metadata' refers to descriptive information and protocols for the overall experiment and individual Samples. This information is supplied in an excel format. The templates available from the GEO's website are listed at the end of the page.

Matrix Table

The matrix table is a spreadsheet containing the final, normalized values that are comparable across rows and Samples, and processed as described in any accompanying manuscript.

Note: Affymetrix submitters can submit CHP files instead of a matrix table - but if your manuscript discusses data processed by RMA or another algorithm, submit a matrix of those values rather than CHP files.

Raw Data

In addition to the normalized data provided in the Matrix table, submitters are required to provide raw data, usually in the form of supplementary raw data files.

  • For Affymetrix submissions, the raw data files are the CEL files.
  • For Agilent and other single and dual color submissions analyzed using feature extraction, the raw files are the ".txt" files that feature extraction spits out.
  • For Agilent and other single and dual color submissions analyzed using Genepix, the raw files are the ".gpr" files that feature extraction spits out.

Platform

If your experiments are performed using a commercial array (e.g., Affymetrix GeneChip) or other array already deposited in GEO, please use the FIND PLATFORM tool to find the GEO accession number (GPLxxxx) for inclusion in the 'platform' column in the SAMPLES section of the metadata spreadsheet.

Otherwise, please include a PLATFORM section in your metadata spreadsheet and include Platform annotation columns in your matrix table. See the templates and examples listed below.

Templates

Additional Guidelines for the Excel - Individual item is explained.

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