Set up a Simple Tiling job

Simple Tiling creates Expression type probes that span target sequences at even intervals. To define the target sequences, you upload a FASTA format file that contains the target sequence data. Create a compressed *.zip format version of this file for upload purposes.

Click the Workspace tab. Simple Tiling is not available within a collaboration.
Set the application type to Expression.
Click Probe > Simple Tiling.

The Simple Tiling page appears.
Set the following parameters. All are required.

Parameter	Instructions/Details
Probe Details
Design Job Name	Type a name for this Simple Tiling job.
Probe Length	Type the desired length (from 45 to 60 bp) for the generated probes. Agilent has found that a probe length of 60 bp provides the optimal balance between sensitivity and specificity for most applications on the Agilent in situ microarray platform.
Probe Spacing and Number	Select one of the following options, and type an appropriate number in the appropriate box. Average Probe Spacing – Defines the average distance (in bp) between the centers of the probes. Because of repeat regions, the actual spacing between probes may deviate from the ideal average probe spacing. Number of Probes per Sequence – Defines the average number of probes designed for each target sequence. eArray uses this value to calculate average probe spacing on a per-sequence basis. The actual number of probes designed for each sequence may deviate from the specified value, because of repeat regions and rounding, but this deviation should not be large unless sequence length limits the design process. Total Number of Probes – Defines the total number of probes generated, to be spaced evenly over all of the target sequences. eArray first calculates the number of probes to be generated for each sequence, and then uses these numbers to calculate average probe spacing.
Target File Details
Species	Select the desired species. This is the species represented by your target sequence data.
Upload in FASTA Format	Click Browse. A dialog box appears. Select the desired .zip FASTA format target sequence file, then click Open.* The location of the file appears in Upload in FASTA Format.

Click Submit.

eArray submits your Simple Tiling job to Agilent for processing. A message tells you that you will receive an e-mail when the job is complete.
Click Exit.

The Simple Tiling page reappears. Your Simple Tiling job appears in the Search Results pane at the bottom of the page, where you can monitor its status.

It can take up to one day or more for your Simple Tiling job to finish, depending on the number of jobs ahead of yours in the queue, and the size of your uploaded file. When eArray completes your Simple Tiling job, you receive an e-mail, and the job's status changes to Completed. You can then view or download the results, and you can also create a new probe group from them.
Note: eArray also has tiling tools for other application types. See Set up a Genomic Tiling job, Bait Tiling (SureSelect Target Enrichment), and Bait Tiling (SureSelect RNA Enrichment). In addition, you can do an HD Search to retrieve probes from the Agilent HD Probe Database, which contains HD-CGH and HD-ChIP probes that cover the genomes of several species at very high densities.