Ways to create custom microarray designs/sets

To create microarray designs and sets, you must be an eArray registered user.

A microarray design consists of one or more probe groups that have been organized onto the slide in a specified layout. The design includes information on the organization and location of probes on the slide, as well as the quantity of probes, types of probes and other design details. When you want your slide to include more probes than a particular design format can accommodate, you can group your designs to create a microarray set, which accommodates your full complement of probes over multiple slides. In eArray, you do not have to decide ahead of time whether to create a design or to create a set—you can select the probes that you want, and try out many potential configurations. Microarray sets do have a few limitations:

One microarray design can be part of only one microarray set.
Microarray designs from a microarray set cannot be used as templates for creating new microarray designs.
You cannot use a microarray set as a template to create a new microarray set.

When you create a custom microarray design or set, you create the exact specifications that Agilent Manufacturing can use to produce microarray slide(s) for your experiments. To create microarray designs and sets, you must be an eArray registered user. eArray can guide you step-by-step through the microarray creation process. See Use a wizard to create a microarray design/set. Also, aAs you design your microarray, read Agilent's custom microarray design guidance document for your specific application type.

In eArray, you can create a new microarray design in several ways:

Use existing probe groups – This is the best methodology to use when you create a new design that has few or no probes in common with an existing design, and it is also a method for creating microarray sets. You select to create a set, rather than a design, within the microarray design process. This method is available for all application types. It is also the only method that you can use to create a CGH+SNP microarray design or an Exon microarray design. You can also use a Design Wizard to guide you step by step through the process. See Create design from existing probe groups (Wizard).

When you use this method to create a microarray design or set, you search for and select one or more probe groups to include. You can use Agilent Catalog probe groups, or your own probe groups that you create with eArray's extensive tool set for working with probes and probe groups.
Use an existing microarray design as a template – This method is useful when a completed design (which has a status of Complete, and is thus uneditable) needs to go through revision. You can use this method in any application type, and it reduces the amount of time it takes to complete the array creation process. However, this approach can become tedious if many features on the microarray need to be changed. Note: You cannot use a microarray set as a template with this method. Also, you cannot create a microarray set from a copied design, even if you add additional probes and exceed the capacity of the selected design format.

To begin the process, you search for an appropriate existing microarray design, either in the Agilent Catalog, or in the folders of your own workgroup. Once you find the desired microarray design, you make a copy of it, then modify the copy to your specifications.
Use uploaded probes – This method, which uses one of eArray's Design Wizards, creates a microarray design from an uploaded file of probe sequences. The wizard leads you through each step required to create the array, from probe upload, to design creation, to design submission. This wizard is available for all application types, except microRNA.

For the CGH, ChIP, and Expression application types, you can use the Express Array feature to upload a file of probes directly to Agilent Manufacturing, and bypass several steps of the design process.
Use HD CGH/Chip database probes – This method uses a Design Wizard to create a CGH or ChIP microarray design from probes identified in an HD Probe Search. HD Searches are searches of the Agilent HD-CGH or HD-ChIP databases. These special databases contain probes that cover the genomes of several species at extremely high densities.
Use target transcripts to create new probes – In this method, which is exclusively for the Expression application type, you use an eArray Design Wizard to upload the sequences of the target transcripts that you want to detect on your microarray. eArray then designs the probe sequences for you and walks you through the process of creating a design.
Create new probe groups – eArray offers a variety methods for creating new probe groups, which can then be used with a Wizard (see Create design from existing probe groups (Wizard)) to build a microarray design.

During the array design process, consider using Array Calculator to calculate microarray statistics and to help you choose the best design format.

Note:
• If you would like Agilent to upload a specific GEML format file, contact eArray Technical Support. You will need to supply the AMADID number and the account to which the microarray design should be uploaded.

• A separate set of topics describes how to create bait libraries in the SureSelect Target Enrichment and SureSelect RNA Enrichment application types. See SureSelect Target Enrichment libraries and RNA enrichment libraries.

• Once you create a microarray design, you cannot subsequently convert it into a microarray set, even if you add additional probes and exceed the capacity of the selected design format. Similarly, once you create a microarray set, you cannot convert it into an individual microarray design.