Working with probes in eArray

If you are using eArray for microarray design, the program offers many tools that let you search for probes, create or upload new probes, and analyze and manage probes.

eArray probe tools

The table below describes the eArray probe tools. Click the links for more information.

Probe organization in eArray

In eArray, probes are partitioned by application type. When you select a specific application type, such as Expression, only probes that are designed for that application type are available. Probe searches only return Expression type probes, and only the probe creation tools appropriate for Expression type arrays are available (i.e. GE Probe Design and Simple Tiling).

For all microarray application types except microRNA, probes are independently searchable entities that you can individually include in microarray designs. You associate probes with each other into one or more probe groups. You then select one or more probe groups for your microarray design.

For the microRNA application type, probes are grouped by the specific microRNA to which they bind. Up to four related probes are grouped under the name of each mature microRNA target. In general, for microRNA arrays, each mature microRNA is represented by 1-4 probes, which vary in length. These probes act in concert to measure the microRNA of interest, and the data are combined downstream in Agilent’s Feature Extraction software.

Guidance from Agilent

The best way to generate probes depends on the application type you are investigating. Probes are mostly application specific, and different application types require different criteria for the design and selection of probes. Because of this, eArray partitions probes separately for different application types — for example, when you create a CGH array, only CGH probes are available for inclusion on the array. Because of the computational time needed to design probes for CGH and ChIP applications, Agilent suggests that you use the pre-designed probe sets in the High Density (HD) databases in eArray. For gene expression applications, successful probe design requires good quality data, but you can use the probe design tools in eArray to generate good quality probes.

Whether to design your own probes or to use Agilent catalog probes is an issue of personal choice. However, if your target sequence is well-represented by Agilent catalog probes, you can save time and effort if you use those probes. To see the probes that are available, search the Agilent catalog using GenBank identifiers, gene symbols, or other supported IDs. See Search Your Probes.

The GE probe design tools available to you in eArray are the same tools that Agilent uses to create expression type probes for the Agilent catalog. However, Agilent also employs a rigorous target assembly process to define the targets for catalog probes.

For probes that are already designed, the best search method depends upon your level of familiarity with the target sequences. For example, for gene expression applications, if you do not know specific transcript or gene identifiers, you can use GO Search to return probes for genes based upon their biological process or molecular function.

You can use Search Your Probes to take a similar, but less structured approach. By typing one or more keywords in the search criteria, you can search probe annotation, which often describes a target gene's function. A search can return all probes whose annotation contains the word or phrase you typed. If you know the specific targets for which you want probes, you can also use Search Standard Probes to advantage. You can upload lists of GenBank IDs or gene symbols, and return all probes that match the criteria. This allows you to be very specific about your search criteria.

For CGH and ChIP applications, you can search the HD CGH and ChIP databases to return probes within specified genomic regions, at a very high density. You can then use these probes to create a microarray that has higher resolution than is seen for catalog array offerings for these applications. To do an HD search, you define the genomic regions for which you want probes, and the density or number of probes that you want. For more information, see What is a High Density (HD) Search.

Tool	Purpose
Searching probes in eArray
Search Standard Probes	Search eArray's main probe database for probes with specific annotations. In some cases you can enter multiple search terms, or upload files of them.
GO probe search	Search Expression probes in eArray based on Gene Ontology (GO) terms.
High Density (HD) probe search	Search eArray for HD probes for CGH and ChIP microarrays. The probes cover the genomes of several species at extremely high densities. You can use the Interval Finder tool to define the genomic coordinates for your HD search, based on annotations that you specify.
SNP probe search	Search for Agilent SNP probes for use in an Agilent CGH+SNP microarray. These microarrays contain both CGH and SNP probes, and let you find copy-neutral variations such as uniparental disomy (UPD) and copy-neutral loss (or lack) of heterozygosity (cnLOH). SNP probe searches are available in the CGH application type.
Exon probe search	Search for Agilent Exon probes for use in an Exon microarray. These probes interrogate specific exons for a given species of interest. Exon microarrays can be used to perform both gene-level and exon-level analyses in the same experiment. Exon probe searches are available in the Expression application type.
Creating and uploading probes
Upload probes	Upload a file of probe sequences and annotations to eArray. This tool is available for all microarray application types except microRNA.
Gene Expression (GE) probe design	Create Expression type probes based on an uploaded file of desired probe target sequences or GenBank accessions..
Genomic Tiling	Create CGH, ChIP, or SureSelect Capture Array type probes that span specific regions of Agilent genomic sequence data available in eArray.
Simple Tiling	Create Expression type probes that span uploaded sequences at even intervals.
Express Array	Upload a file of probes directly to Agilent Manufacturing. This tool is available for Expression, CGH, and ChIP application types.
Analyzing and managing probes
GE Probe Check	Analyze Expression type probes to see if they will work on the Agilent platform, with Agilent protocols. Analyze probes for potential targets and possible cross-hybridization problems.
Probe Score	Calculate Probe Performance Scores for non-Agilent CGH or ChIP probes in a probe group that you own. The higher the score, the greater the likelihood that a probe will produce a good log ratio response when it is used in a CGH or ChIP microarray on the Agilent platform.
Array Calculator	Calculate the number of microarrays of a specified format that are needed to accommodate a given collection of probes.
Create probe groups	Organize probes into logical groups.
Monitor probe annotation changes	Subscribe to be notified when probe annotations change.
Re-annotate probes	Obtain updated annotations for your own CGH or Expression probes at any time. eArray aligns the sequences of your probes to the applicable genome, and then associates the most recent annotation available from public databases.
Download probes	Select probes, and save them to your computer.

Overview of working with probes

eArray probe tools

Probe organization in eArray

Guidance from Agilent