Set up a Genomic Tiling job

Genomic Tiling creates probes for the CGH, ChIP, and SureSelect Capture Array applications types that span specified regions of a genome at even intervals. A genome build of your species of interest must exist in the eArray database. To see the list of supported species, look under Target File Details, in Species, when you set up a Genomic Tiling job. To specify the desired genomic intervals to tile, you either type them directly in eArray, or upload a file of chromosomal locations or cytobands. See Genomic interval formats. You can also use the Interval Finder tool to retrieve a list of genomic intervals that are associated with specific annotations.

Before you set up a Genomic Tiling job

You must be an eArray registered user with a valid login name and password.
A current genome build of your species of interest must be available within eArray. To see the list of supported species, look Under Target File Details on the Genomic Tiling page, in Species.
(Optional) Prepare a text file that contains the chromosomal locations or cytobands that you want to tile, one interval per line. See Genomic interval formats. You can use Interval Finder to retrieve a list of genomic intervals associated with specific gene annotations or accessions.

Note: Genomic Tiling is not available to guest users, or within a collaboration.

To set up a Genomic Tiling job

Click the Workspace tab. Genomic tiling is not available within a collaboration.
Set the application type to CGH, ChIP, or SureSelect Capture Array.
Click Probe > Genomic Tiling.

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

Parameter	Instructions/Details
Probe Details
Design Job Name	Type a name to identify this Genomic Tiling job
Probe Length	Type the desired length (from 45 to 60 bp) for the generated probes. If you intend to select Tm trimming of probes, keep the length set to its default value of 60 bp. For the SureSelect Capture Array application type, the probe length is set to 60 bp, and cannot be changed.
Probe Spacing and Number	Select one of the following options, then type an appropriate number in the associated box. Average Probe Spacing – Defines the average distance (in bp) between the center points 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 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. Guidance from Agilent on probe density for CGH microarrays
Target File Details
Species	Select the desired species. The currently available genome build for the species appears in Genome Build.
Genomic Intervals	Type cytobands or chromosomal locations separated by pipe "\|" characters. See Genomic interval formats. You can also upload a file of genomic intervals: Click Upload. A file upload window appears. Click Browse. A dialog box appears. Select the file that contains the desired genomic intervals, then click Open. The location of the file appears in File Name. Click Upload File. The genomic intervals from the file appear in Genomic Intervals. Multiple intervals are separated by pipe "\|" characters. Note: You can use Interval Finder to retrieve a list of genomic intervals associated with specific gene annotations or accessions.
Skip Repeat Masked Regions	Mark this option to ignore repeat regions within the selected genomic intervals during the tiling process.
Allow Probes to be Trimmed	(Available for CGH and ChIP application types, if you set Probe Length to a value of 46 bp or more.) Mark this option to allow probes to be trimmed shorter than the size in Probe Length. This can yield tighter compliance with the desired Tm. eArray will not trim probes to shorter than 45 bases.
Preferred Probe Tm	(Available for CGH and ChIP application types) Type the preferred probe Tm (in °C). The probe tiling algorithm trims probes so that they have a Tm close to the requested one. Set the Preferred Probe Tm approximately 20°C higher than your intended hybridization temperature. The Tm is the temperature at which equal populations of a probe and its target sequence would exist as a 50:50 mixture of duplex and single-stranded forms.
Avoid Restriction Sites	(Available for the CGH application type) Mark this option if you use the Agilent CGH enzymatic labeling protocol. This option avoids Rsa I and Alu I restriction enzyme recognition sites within the selected genomic intervals during the Genomic Tiling process. The CGH enzymatic labeling protocol uses these two enzymes. Because the target DNA is always cut at these sequences, probes that contain these sequences may not be able to hybridize effectively with the labeled DNA.
Extend Interval Boundaries	(Available for the SureSelect Capture Array application type) Mark this option to allow eArray to tile probes into the regions that flank your target intervals. In 5' base pairs and 3' base pairs, type the additional number of base pairs to be added to the 5' and 3' ends of the target region.

Click Submit.

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

Your job appears in the Search Results pane at the bottom of the Genomic Tiling page, with its status listed in the Status column. A status of ERROR indicates that eArray was not able to complete the job, and that you must submit the job again. The pane is not dynamically updated — click Refresh to update the pane to its most current version.

It can take up to one day or more for eArray to finish your job, depending on the number of jobs ahead of yours in the queue, and the size of your uploaded file. When eArray finishes your job, you receive an e-mail, and the status of the job changes to Completed. You can view or download the results, and you can also create a new probe group from the results.