Create a microarray design/set with Agilent probes

Agilent probes are ready-made, easily-accessed probes that have gone through a validation process that assures that they will work on the Agilent platform. Because of this, Agilent recommends that you use Agilent probes if suitable ones are available for your particular research application. To retrieve Agilent probes, you can use several different probe search tools, shown in the table below.

Source of Agilent Probes	Available in these application types	Comments
Probe search of AgilentCatalog folder	Expression & microRNA	Probes can be used in microarray designs and microarray sets. For the Expression application type, available probes also include probes for lincRNA and mitochondrial RNA.
High Density (HD) probe search	CGH & ChIP	Probes can be used in microarray designs and microarray sets
Agilent SNP probe search	CGH	Probes specifically for use in CGH+SNP microarray designs. Microarray sets are not supported.
Agilent Exon probe search	Expression	Probes specifically for use in Exon microarray designs.

Perform a search for probes. For the Folder search criterion, if it appears, select AgilentCatalog and mark Include subfolders. You can also do a High Density (HD) Search, SNP probe search, or an Exon probe search.
Use the search results to create a new probe group. You can do multiple searches and create multiple probe groups. You can also edit the probe groups.
Use the probe groups that you created to create a new microarray design/set. You can include Agilent catalog probe groups, as well. To find them, do a search for probe groups with AgilentCatalog as the Folder search criterion, and Include subfolders marked. You can also use the Browse Probe Group function.
Place the design/set in review, if desired, then wait for other users to make comments and changes.
After enough review has occurred, complete the design/set, and submit it to Agilent Manufacturing. You can then request a quote. Agilent does not fabricate the actual microarray slides until you subsequently order them through your Agilent representative, or buy them from the Agilent Online Store through eArray.
Subscribe to update notification, if desired, to have Agilent send you an e-mail if the content of your design/set or its associated annotations change.
If you like, you can share your microarray design with your colleagues around the world on OpenGenomics.com, Agilent's Web site dedicated to genomics-related news, presentations, research, resources, and products. The site includes a repository of microarray designs and SureSelect Target Enrichment libraries created in eArray. See Publish content on OpenGenomics.
Notes:
· A separate topic describes how to create a bait library for the SureSelect Target Enrichment and SureSelect RNA Enrichment application types.
· You can tell if a probe is an Agilent probe from its probe ID. Agilent probes have probe IDs with the structure A_NN_PNNNNN, where N is any numeric value, for example: A_23_P23650.
· As you design your microarray design or set, read Agilent's custom microarray design guidance document for your specific application type. eArray also contains many Design Wizards that lead you through the microarray creation process.