Assay Design

1.

From the Microarray Designer toolbar, select Start Design.

2.

[Optional] To view a detailed comparison between the iSelect and XT iSelect assays, select Compare Assays.

This option is available if you have access to XT iSelect.

3.

Select one of the following assay options:

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EX-24 iSelect / EX-24 iSelect +

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EX-48 iSelect / EX-48 iSelect +

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HTS iSelect / HT iSelect+

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XT iSelect / XT iSelect+

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Commercial+

Each assay option includes information on the minimum and maximum limits.

4.

Select one of the following design options:

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Custom—Create a fully custom design.

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Add on to Existing Design—Add content to an existing custom design.

5.

Enter a name for the design.

Invalid characters include: plus sign (+), ampersand (&), backslash (\), slash (/), colon (:)

6.

[Optional] Enter a description for the design.

7.

Select Next.

The Configure Design screen opens.

8.

Select a species from the Select your species drop-down list, and then select Add Species.

You can select up to four species for XT iSelect.

9.

Select Next.

The Upload Targets screen opens. Refer to Input Target Files for information on input target files, including templates and settings.

10.

From the Select File Type drop-down, select the file type you want to upload.

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[Optional] Select the Lowercase Weighting sequence file type option to weight the final score of lowercase nucleotides to reflect suboptimal probe placement for lowercase regions.

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[Optional] Select Update Annotations to display updated annotations (if available) for design targets in the resulting score file. This option only applies to existing design or score file types.

11.

Select Submit for Design.

When the design completes without errors, the software updates the session status and sends you an email notification. If the design fails, an error message appears with details of the issue. Refer to Output Files for more information on errors.

When the design completes, DesignStudio shows the design summary in the Review and Order Design screen.

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To download the created files for troubleshooting, select Download Files.

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To upload new target files for the design tool to validate, select Upload New Targets.

The design summary includes the following items:

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Number of assays submitted.

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Number of assays designed.

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Number of assays excluded.

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Options selected.

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Content breakdown by species.

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Normalization bins and total bead count for selected species.

When you are ready to order your products, contact Illumina Customer Care.

1.

From the Microarray Designer toolbar, select Start Design.

2.

Select Commercial+.

3.

Select Select Base Content.

The Select Commercial+ Base Content dialog opens.

4.

[Optional] In the Search field, enter the design name, ID, or species.

5.

Select the content in the order that you want to use as base content for your design, and then select Use as base content.

The selected content appears in the Commercial Base Content field on the Select Assay screen.