Recommendations for Agilent submissions
This page contains deposit recommendations, instructions and templates specific to Agilent arrays. These recommendations simply describe what we believe is the easiest batch deposit method for the majority of Agilent researchers, but keep in mind that Agilent 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 Agilent 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 (see templates below).
- Raw data files (unedited). Usually, these will be Agilent Feature Extraction result text files. GPR files are also acceptable if they include the Agilent Probe Names (e.g., A_23_P158231).
- Processed/normalized data used to draw the conclusions from your study. Two-color experiments (e.g., Cy3/Cy5) will typically have log (test/control) ratios; one-color experiments will have normalized signal intensities. Processed data should be provided as a value matrix containing data for all Samples. Data can be provided in an Excel worksheet or a tab-delimited text file. The table should include the Agilent Probe Names (e.g., A_23_P158231).
Finding the Platform Back to top
On the metadata worksheet you are asked to specify what array (Platform) you used. If you are using a commercial array, include the 6-digit Agilent Design ID (Agilent-nnnnnn) or the GEO Platform accession number. If you are using a custom array not represented in GEO, download the file in "GEO" format from the Agilent eArray or SureDesign website (contact Agilent for instructions) and include it with your submission.
The GEO accession number of an Agilent platform can be retrieved using the FIND PLATFORM tool. It is recommended that you use keyword "Agilent-nnnnnn" in the Free text box where nnnnnn represents the 6-digit Agilent Design ID (e.g., Agilent-014850).
Agilent GEOarchive templates and examples Back to top
The following Excel files illustrate the structure of different types of GEOarchive Agilent 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 are provided on the worksheets.
Bundle all components (Excel metadata file, raw files, and processed files or matrix table) 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.