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

ChIP 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 ChIP advanced wizard offers four different 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:

·        Select probes from Agilent High Definition Database - When you select this method, SureDesign uses a distinct probe database that contains high-density (HD) probes to search for probes that cover your target regions of interest. HD probes cover the genomes of several species at extremely high densities. 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. The probes are annotated and scored, which allows SureDesign to select optimal, Tm-balanced probes. See Add/Review Content > Select probes from Agilent HD database 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 or Catalog) 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/probegroup. The three options are:

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

Select probes by Probe ID - to select probes from the selected design or probegroup that cover specific Probe IDs

See Add/Review Content > Select Probe Source 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.

·        Design new probes by tiling genes or regions - This method walks you through the steps to create a ChIP or CH3 design by defining the target regions of interest, setting a probe selection parameters, and then submitting the design to Agilent as a probe selection job. You are notified via e-mail when your job is complete. See Add/Review Content > Tile Genes or Regions for instructions.

OR

·        Finalize this Design - This option only appears if you have already added at least one probegroup to the design, or have a probegroup in processing status. 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.

 NOTE  When you select Finalize this Design and click Next, SureDesign performs a check of the design and opens a warning message if it identifies any issues with the design. Agilent recommends addressing these issues before finalizing a design.

Probegroup Summary

This table only appears if the design contains at least one probegroup, or has a probegroup in processing status.

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. For probegroups added from the High Definition Database or from tiling, you can modify the probes in the probegroup by redoing the probe selection process.

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