What is an array design?
For a microarray experiment, an array design is the unique set of probes found on the microarray chip. In ArrayExpress, an ADF (Array Design Format) file captures information about a microarray chip. The ADF is a spreadsheet-like tab-delimited text file with some meta-data header rows, followed by a multi-column table of probe information (here is an example). Data from a microarray experiment cannot be interpreted properly if the array design used is unclear, especially when the microarray is custom-made for a particular research project.
Do I need to submit an array design for my experiment?
Many of the array designs, especially commercially available ones, are already accessioned in ArrayExpress as ADF files (one ADF for one microarray chip), in which case you do not need to submit any ADF to us. All you need to do is to specify the ADF by accession when asked by Annotare submission tool "What array did you use?".
To find out whether your array design is already in ArrayExpress and get its accession, search by keywords (e.g. manufacturer name, species name) on the ArrayExpress array design search page. If the search does not return any results, include array designs we imported from NCBI Gene Expression Omnibus (GEO) to broaden your search. Or if you know the NCBI GEO platform accession, you can be convert it to the ArrayExpress equivalent by replacing "GPL" with "A-GEOD", e.g. "GPL1234" will be "A-GEOD-1234". See this Array design search help page for further details.
How do I submit commercially available array designs?
If you use a commercially available (not custom-made) microarray which is not accessioned in ArrayExpress, please do the following:
- Download this meta-data header template file;
- Fill in the template with as much background information about the array design as possible (here is a guide), especially the mandatory fields. Save it as a tab-delimited text (*.txt) file when done;
- Send us the filled template (*.txt file) and any annotation/support files for the array design (e.g. NimbleGen NDF file, GAL file for spotted arrays) by FTP because the support files contain information about the probes;
- Write to us at firstname.lastname@example.org, mentioning the files which have been uploaded.
An ArrayExpress curator will create the full ADF on your behalf by combining the meta-data header and some information converted from the annotation/support files. As the format of annotation files differs quite a lot from one manufacturer to another, please note that creation of ADFs often requires manual processing by the curator and can take up to five working days.
How do I submit custom array designs?
If you have a custom microarray which is not accessioned in ArrayExpress, please download an array design format (ADF) template, fill it in, and submit it following these ADF submission guidelines. Find more information in this step by step guide on how to fill in the template.