What is a standard probe search?

In a standard probe search, you use the Search Standard Probes tool to retrieve and take action on your custom probe content. With this tool, you search for probes based on the annotation, accession, or sequence information that is associated with them.

Note: For the Gene Expression application type, you can also retrieve probes from the Agilent catalog as well as custom probes. For the microRNA application type, you can only retrieve probes from the Agilent catalog.

You can use the Search Standard Probes tool to set up a more generalized search in which you specify a single search term, and retrieve all probes that contain the term within any annotation or accession. For example, if you type kinase as the search term, and do not require an exact match, the search returns all probes that have this word in their annotation, including probes with annotation such as protein kinase C, delta, and hexokinase 3. This is a good search methodology to use when you first explore the content of the database, and want to see what types of probes exist in the system. You can retrieve a single probe with a minimal amount of information, and you can also retrieve a large number of probes using more liberal search criteria. However, if your search criteria are too general, the method may retrieve many more probes than you intended. To make this type of search more selective, you can require an exact match with the search term—For example, if your search term is Q005, probes with an accession or annotation value of Q0057 would not appear in your search results.

Another option with Search Standard Probes is to set up a search that specifically searches one type of annotation or accession. The specific criteria that are available vary by application type, but can include, for example, probe IDs, accession numbers, gene names, or cytobands. To return probes when it searches for a specific type of annotation or accession, eArray always requires exact matches, and when you set search parameters, you must specify values completely. You can also type or upload multiple search values, and eArray returns probes that match each of the values. This is a powerful search methodology that can retrieve a set of well-defined probes, or a single probe based upon a specific set of criteria. However, it can require a lot of effort to effectively define the parameters necessary to achieve the desired results, and it may be too stringent for your purposes.

Search Standard Probes also lets you limit returned probes to those associated with a particular species, probe group, or microarray, and/or that are located within a specific folder. In addition, for the Expression application type, you can search for specialized probes, including probes for large intervening non-coding RNAs (lincRNA), and mitochondrial RNA (mitoRNA).

You can use the probes that are returned by the Search Standard Probes tool to create a new probe group, which you can then use in a microarray design or set. You can also download the probes, or use the results to select probes for deletion. See Search Standard Probes.

Note: You must use other search tools to retrieve certain specialized types of probes, including SNP probes, HD Probes, and Exon probes. Search Standard Probes does, however, retrieve standard Expression probes from the Agilent Catalog that map to exons.