Create an Exon microarray |
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Gene Expression Exon microarrays (Exon arrays) are an extension of Agilent's Gene Expression platform. Unlike standard Expression arrays, which contain one probe per gene biased toward the 3' end, Exon arrays contain probes that can be distributed along the entire gene, targeting exons. The use of these arrays makes it possible to perform both gene-level and exon-level analyses in the same experiment. Because the probes cover entire genes, the arrays are not compatible with standard oligo-dT-based labeling methods. Exon arrays are compatible with Agilent's LIQA WT Kits, which use random primers for whole transcript labeling.
An exon is a segment of nucleic acid that either remains in a mature RNA molecule after other segments (introns) have been removed from a precursor RNA, or that results from the splicing of two of more precursor RNAs. Agilent Exon probes are designed to bind specifically to exonic regions. The figure below illustrates the probe design process.
Figure – Design of Exon probes. To design probes for exons, Agilent combines transcripts from multiple sources and maps segments of each transcript onto the applicable genome. Probes are then designed to the exons. The majority of exons for the supported species are each represented by a single probe; however, some exons are represented by more than one probe.
To search for Agilent Exon probes, see Search for Exon probes.
To create an Exon microarray design, you must first create one or more Exon probe groups, and then include those probe group(s) in an Exon microarray design. An Exon microarray design may also contain standard Expression probe groups. Follow these general steps:
Create an Exon probe group from the results of the Exon probe search. Exon probe groups contain the probes from the results of an Exon probe search. They can also contain any other type of expression probe, including standard Agilent gene expression probes and probes that you upload.
Include the Exon probe group(s) and any other desired expression probe groups in a new microarray design. The easiest way to do this is to use the microarray design wizard named Create a Microarray Design from Existing Probe Groups. You select Exon as the microarray type when you begin the wizard, and then select the desired Exon probe group(s), as well as any other expression probe group(s), for the microarray design. At the end of the wizard, you save the design with one of several statuses. If you save the design with a status of Submitted, eArray submits the design to Agilent Manufacturing, which makes the design available for price quotes and online purchase.
You can also create an Exon microarray design without the use of this wizard. See Create a microarray design using existing probe groups.
Note:
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A probe group is an Exon probe group if it is created from the results
of an Exon probe search.
Exon probe groups are not limited to Exon probes—they can contain any type of Expression
probe.
•
Some standard gene expression probes map within exons. These probes
are returned by both standard Expression probe searches (i.e. Search
Your Probes and GO Search)
as well as Exon probe searches.
These probes can be included in Exon probe groups, or in standard
Expression probe groups.
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An Exon microarray design must contain at least one biological probe
group and one replicate
probe group.
•
Agilent supplies specific replicate probe groups for Exon microarrays.
These probe groups are included on Exon microarray designs by default,
and are different from the default replicate probe groups on standard
Expression microarrays. However, you can use any type of Expression
probe group as a replicate probe group on an Exon microarray.
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Agilent supplies specific control grids for Exon microarrays. These
required control grids are different from the control grids that are
available for standard Expression microarrays.
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Exon probe groups can also be used as replicate or filler probe groups,
but only on Exon microarray designs.
•
Some Exon probes are designed to short exons. These probes, which
are initially from 35 to 49 nucleotides in length, are padded on their
3' ends with dT nucleotides to make probes
with a total length of 50 nucleotides.
•
Standard Expression probe groups cannot contain Exon probes.