The functionality described in this topic is only available when you mark Show Advanced Options.

SureSelect RNA advanced wizard:

Add/Review Content

The Add/Review Content step consists of a series of selections that allow you to add content (i.e., probes organized into probegroups) to your design, define certain parameters, and review the content of the design. The advanced wizard lets you repeat the Add/Review Content step multiple times to continue adding more content to the design.

Each time you begin this step, you must first select a method for adding content. The SureSelect RNA advanced wizard offers multiple methods for adding content, which are described in detail below.

Select Add Content Method

Select the method you want to use for adding probes to your design:

·        Design probes by transcript tiling - With transcript tiling, you define the target RNA regions by entering your transcripts or genes of interest. When the inputted target is an identifier for a gene symbol, SureDesign locates all of the RNA transcripts for that gene that are present in the selected transcriptome. It then uses those transcript sequences to perform transcript tiling, in which SureDesign finds probes by tiling across the transcript sequences at the indicated density. After you define the targets and set the parameters, you submit the design to Agilent as a probe selection job. You are notified via e-mail when your job is complete. See Add/Review Content > Transcript Tiling for instructions. (To add a new custom transcriptome to your workgroup, click Upload Custom Transcriptomes and see instructions in To add a new custom transcriptome.)

·        Design probes by genomic tiling - The genomic tiling method allows you to define the target regions by entering gene identifiers or genomic coordinates. SureDesign then finds probes by tiling across the selected DNA regions at the indicated density. After you define the targets and set the parameters, you submit the design to Agilent as a probe selection job. You are notified via e-mail when your job is complete. See Add/Review Content > Genomic Tiling for instructions.

·        Upload probes - This method allows you to upload probes that you designed with your own algorithms. See Add/Review Content > Upload Probes for instructions.

·        Select probes from an existing Design or Probegroup - This method allows you to add probes by selecting an existing probegroup or design (custom SureSelect RNA designs and probegroups only) and then selecting probes from that design/probegroup to include in the new design. If you choose this method, you must specify how you want to select the subset of specific probes from the existing design or probegroup. The three options to select the subset of specific probes are:

·        Select all probes - to select all the probes in the selected design or probegroup

·        Select probes for specific genes or transcripts - to select probes from the selected design or probegroup that cover specific genes or regions

·        Select probes by probe ID - to select specific probes from a selected design or probegroup by probe ID

OR

·        Finalize this Design - This option only appears if you have already added at least one probegroup to the design. When you are finished adding probes to the design, and are satisfied with the probegroups in the Probegroup Summary, select this option to exit the Add/Review Content step and proceed to finalizing the design.

Once you have made a selection, click Next to continue.

Probegroup Summary

This table only appears if you have already added at least one probegroup to the design.

The Probegroup Summary table displays the probegroups that are currently included in the design. You can adjust the replication number of each probegroup or remove probegroups from the design.

The columns of the Probegroup Summary are described in the table below.