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Introduction

The Gene Expression Omnnibus ( GEO ) is a public database for microarray data managed by the National Center for Biotechnology Information ( NCBI ). Some journals require you to submit your data to a public database prior to the publication of your results, and GEO is a popular choice. Submitting data to GEO is simple using their GEOArchive format and their Microsoft Excel templates for different types of microarrays.

To complete the submission process you must provide information about:

  • your experiment design
  • your samples
  • the microarrays you used
  • information about how the microarrays were processed
  • your normalized data set
  • and your raw data files.

Taken together, this information satisfies the requirements for MIAME-compliancy.

Step-by-step

  1. Create yourself a login at GEO.
    1. Navigate to the GEO site.
    2. Click on the ">>New account" link.
    3. Fill out the form, and click on "Save".
  2. Download the GEOArchive template.
    There are different GEOArchive templates for Affymetrix arrays, Agilent 1-color arrays, or Agilent 2-color arrays.
    1. Log in to GEO.
    2. Click on "New submission".
    3. Click on the link for your array type, Affymetrix or Agilent.
    4. Scroll down to find the link for your experiment type: Agilent one-color experiment, Agilent two-color experiment, or one of the Affymetrix options. Click the link for "Matrix table option" for your experiment type.
    5. Save the template (.xls file) that you downloaded into a new folder.
  3. Collect your raw data files.
    1. Download your raw data files from GNomEx if you have not already done so. These would be the .txt files from an Agilent microarray experiment, or the .CEL files from an Affymetrix microarray experiment.
    2. Move or copy these files to the folder where you saved the template file.
    3. You can rename these files if you like (GNomEx typically assigns them very long, cumbersome names).
  4. Find the platform id for your microarrays.
    The platform id number is GEO's identifier for your array type. These are ids that begin with GPL, and are specific to each array design.
    1. From the GEO home page click on Platforms.
    2. Click the "FIND PLATFORM" link.
  5. Fill in the metadata page in the GEOArchive template.
  6. Fill in the data matrix page in the GEOArchive template.
  7. Create a .zip file.
    On a Mac, use the Finder to locate your folder that contains the template and raw data files. Control-click on the folder, and choose "Compress".
    On Windows, right-click on the folder, and select "Send to > Compressed (zipped) folder".
  8. Submit the .zip file.
    1. Log in to the GEO site.
    2. Click on "New submission", and scroll down to see the "Array deposit options".
    3. Click on the "Submit" button next to the GEOArchive option.
    4. Select the "GEOArchive format, use the Browse button to locate your .zip file, and enter a release date.
    5. Hit the "Submit" button.

Results

The GEO data curators are very efficient, and will acknowledge your data submission typically within 1 day by email. The email will include your GEO dataset number (GSE number) which you can include in a manuscript, notes regarding any corrections or omissions, and instructions for viewing or changing your data set. GEO also provides a mechanism for generating a private link which you can send to reviewers of your manuscript, so they can view your data prior to publication.

As the release date of your data set approaches, GEO will send you a reminder by email to confirm that you want the data to be accessible by the public.