Provide feature order

eArray's standard probe layout method is to assign probes randomly to feature positions. eArray also supports non-randomized layouts. Although not recommended by Agilent, these non-randomized "ordered" layouts allow you to specify the location of probes on the array. eArray supports ordered layouts for CGH, ChIP, and Expression microarray designs, but not microarray sets.

To create an array with a non-randomized probe layout, you first select Customer specified as the Feature Layout option when you create the design. After you finalize the design, and save it with a status of Complete, you download the unordered list of probes for your design from eArray. You rearrange the order of the probes in the file, as desired, and upload the rearranged file. eArray reads the file and arranges the probes by rows. In each row, it lays out probes from left to right.

Note:
• When you create a microarray design with a Design Wizard, only Randomized feature order is available.

• Customer specified feature layout is not available for the microRNA and SureSelect Capture Array application types.

Create, edit and complete a microarray design. Be sure to select Customer specified as the Feature Layout design parameter.
Search or Browse for your design.
In the Actions column of the search results, next to the desired microarray design, click Provide Feature Order.

The Probe Ordering for Microarray Design page opens in a new window. If you no longer want to specify the order of features in the design, select Randomized, then in the dialog box that appears, click OK.
Click Download list for ordering.

A dialog box appears.
Click Save.

A Save As dialog box appears.
Select a location for the file, then click Save.

eArray downloads the probe list in .zip format.
Extract the probe file from the .zip archive and edit it, placing the probes in the desired order. You can edit the extracted TDT format file with a spreadsheet program. Do not add or delete probes from the list. Leave the column headings intact, and save the edited file as *.tdt file.
On the Probe Ordering for Microarray Design page, in Upload ordered list, click Browse.

A dialog box appears.
Select the TDT file that contains the list of reordered probes, then click Open.

The location of the file appears in Upload ordered list.
Click Upload.

eArray uploads your edited probe list. A message appears.
Click Close.

After you upload the probe file successfully, you can submit the design to Agilent Manufacturing. After you submit the design, you can request a quote for it or buy the microarray from the Agilent Online Store through eArray.

Note:
• If you are adding linkers, these linkers do not appear in the probe sequences in the downloaded probe list. The linkers will, however, appear in the final print file that eArray sends to Agilent Manufacturing when you submit your design.

• If you choose to change the control type of probe group(s) in the design, this has no effect on the order of probes. eArray still uses your uploaded ordered probe list.

• Upload the ordered probe list only once.