Recommendations for Illumina submissions
This page contains deposit recommendations, instructions and templates specific to Illumina arrays (for Illumina sequence deposits, please go to Submitting High-throughput Sequence Data instructions). These recommendations simply describe what we believe is the easiest batch deposit method for the majority of Illumina researchers, but keep in mind that Illumina array data may be submitted to GEO using any of the deposit options described on the Submitting data page. If you need additional guidance for your submission, please e-mail us with a brief description of the type of data you are trying to submit, and one of our curators will quickly get back to you.
The GEOarchive spreadsheet-based submission method is recommended for Illumina array deposits.
With this submission option, you provide the following components:
- A Metadata worksheet containing descriptive information and protocols for the overall experiment and individual Samples.
- A Matrix worksheet containing the final processed/normalized data used to draw the conclusions from your study (e.g., cubic spline). If the processed data row count exceeds Excel's limit, please supply your Matrix as a tab-delimited, plain-text file (.txt).
- IDAT files containing the raw data. You are also welcome to submit a text file containing non-normalized data.
Finding the Platform
On the metadata worksheet you are asked to specify what array (Platform) you used. Most commercial Illumina arrays are already represented in GEO, to find the accession number (GPLxxx) use the FIND PLATFORM tool. Please use Illumina's GEO Data Submission Report Plug-in for Gene Expression (download) to format the normalized and raw data generated by BeadStudio. For issues related to the plug-in, please contact Illumina's technical support department at [email protected].
Illumina GEOarchive templates and examples
The following Excel files illustrate the structure of different types of GEOarchive Illumina data submissions. Each Excel file consists of several worksheets, including a metadata template, and metadata and matrix examples. Click the tabs at the bottom of the spreadsheet window to switch between worksheets. Guidelines for the content of each field is provided on the worksheets.
Bundle all components (Excel metadata file, unnormalized and processed matrix tables) together into a .zip, .rar, or .tar archive using a program like WinZip, and transfer to GEO using the Submit to GEO page. Incomplete submissions will result in processing delays.