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:

1. A Metadata spreadsheet containing descriptive information and protocols for the overall experiment and individual Samples (see templates below).
2. Raw data files (unedited). Usually, these will be the Agilent Feature Extraction result text files.
3. Processed/normalized data used to draw the conclusions from your study. Two-color experiments typically have log(test/control) ratios, one-color experiments have normalized signal intensities. Processed data should be provided as a single value matrix in a spreadsheet or tab-delimited text file. This is suitable for example, if the data were processed using a third party software such as GeneSpring.
   Note: If your processed/normalized data are included in the Agilent Feature Extraction files, you do not have to submit a matrix table. In this case, use the "Agilent Feature Extraction files" template.

Finding the Platform

On the metadata spreadsheet you are asked to specify what array (Platform) you used. There are 2 versions of each Agilent platform deposited in GEO. One version has the Agilent Feature Numbers in the ID column, the other version has the Agilent Probe Names (e.g., A_23_P158231). For example:
	Agilent-012391 Whole Human Genome Oligo Microarray:	Feature Number version Probe Name version
To check whether your Platform is already represented in GEO, use the FIND PLATFORM tool and select the Platform accession number (GPLxxxx) which best aligns with your processed data. The Matrix table ID_REF column should include unique identifiers, therefore please do not select the Probe Name version if your processed data includes replicate Probe Names. If the Platform you used is not represented in GEO, please provide the Platform annotations as in our 'Generic single channel submission with Platform' or 'Generic dual channel submission with Platform' templates.

Agilent GEOarchive templates and examples

The following Excel files illustrate the structure of different types of GEOarchive Agilent data submissions. Each Excel file consists of several spreadsheets, including a metadata template, and metadata and matrix examples. Click the tabs at the bottom of the spreadsheet window to switch between spreadsheets. Guidelines for the content of each field is provided on the spreadsheets.

two-color experiment	Matrix table option Feature Extraction files option
one-color experiment	Matrix table option Feature Extraction files option

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 by selecting the 'GEOarchive' option on the Direct Deposit page. Incomplete submissions will result in processing delays.