Search Standard Probes

Search Type

Instructions/Details

ALL

In this type of search, you specify a single search term. eArray retrieves probes that have any annotation or accession value that matches the search term.

1. In Search Term(s), type the desired search term.

2. Do one of the following:

   • To return probes that have an annotation or accession value that exactly matches the search term, including case, mark Exact Search.

   • To return probes that have an annotation or accession value that contains the search term, without regard to case, clear Exact Search.

Probe ID

In Search Term(s), type probe ID(s). Separate multiple IDs with pipe "|" characters. Alternatively, to upload a file that contains the desired probe ID data, click Upload, then select the desired file. See Upload data for probe searches.

Gene Symbol

(Available for all application types except microRNA) In Search Term(s), type valid gene symbol(s). Separate multiple gene symbols with pipe "|" characters. Alternatively, to upload a file that contains the desired gene symbol data, click Upload, then select the appropriate file. See Upload data for probe searches.

Accessions

(Available for all application types except microRNA) In Search Term(s), type valid accession number(s), without sources. Separate multiple accessions with pipe "|" characters. Alternatively, to upload a file that contains the desired accession data, click Upload, then select the desired file. See Upload data for probe searches.

• Note: To search for microRNA probes based on miMAT accessions, select the miMAT search type.

Cytoband

(Available for all application types except microRNA) In Search Term(s), type cytoband identifier(s) in the box. Separate multiple cytobands with pipe "|" characters. Alternatively, to upload a file that contains the desired cytoband data, click Upload, then select the appropriate file. See Upload data for probe searches and Genomic interval formats.

miMAT#

(microRNA application type only) In Search Term(s), type a miMAT accession in the box, or multiple miMAT accessions separated by pipe "|" characters. The search returns probes that are associated with the miMAT accession(s).

Alternatively, to upload a file that contains the desired miMAT accession data, click Upload, then select the appropriate file. See Upload data for probe searches.

microRNA Name

(microRNA application type only) In Search Term(s), type the name(s) of a mature microRNAs. Separate multiple names with pipe "|" characters. Alternatively, to upload a file that contains the desired microRNA names, click Upload, then select the desired file. See Upload data for probe searches.

• Note: 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.

Chromosomal Location

(Available for the Expression and microRNA application types) In Search Term(s), type a chromosomal location, or multiple locations separated by pipe "|" characters. The search returns any probes that are designed to  the exact genomic coordinates that you specify.

Alternatively, to upload a file that contains the desired chromosomal locations, click Upload, then select the appropriate file. See Upload data for probe searches.

Probe Sequence

In Search Term(s), type a valid probe sequence in the box, or multiple sequences separated by pipe "|" characters. The search returns probes whose sequences are exact matches.

To upload search sequences from a file, click Upload. See Upload data for probe searches.

Criterion

Instructions/Details

Folder

(Required) Select a folder from the list. The search retrieves probes only from the chosen folder. To include the folder's subfolders in your search, mark Include Subfolders.

• Note: Agilent Catalog probes are available for microRNA and Expression applications. You can search for your own (non-Agilent) probes for all microarray applications except microRNA.

Species

(Required) Select the desired species from the list.

• Note: For microRNA designs, you can create a multi-species array. For details on how eArray handles microRNAs from multiple species, see Creating multi-species arrays.

Used in Probe Groups

If you set this criterion, the search returns probes only from the specified probe group(s). Note that Search Standard Probes cannot search High Density (HD) probe groups. To specify probe groups, click Select and Add. See Select probe groups for probe searches.

Used in Array Designs

If you set this criterion, the search returns probes only from the specified microarray design(s). Note that Search Standard Probes cannot search High Density (HD) probe groups within microarray designs. To specify microarray designs, click Select and Add. A microarray selection window appears. This selection window functions similarly to the one for probe groups described in Select probe groups for probe searches.

miRBase Version

(microRNA application type only) (Required) From the list, select the desired microRNA database version to search. To search all available versions, select All. miRBase is a comprehensive database that contains all published microRNAs, including their sequences, genomic locations, and related annotation. For more information, go to microrna.sanger.ac.uk.

• Note:
  • It can be especially useful to search a previous version of miRBase if you have legacy data, for example from the Agilent V1 miRNA array, for a miRNA that has changed in subsequent versions of miRBase.
  
  • Probes are annotated to microRNAs from previous versions of miRBase only when the microRNA sequences change (and then only if that change requires new probes), or if the microRNA has been removed from subsequent versions of miRBase.
  
  • Probes that are annotated to previous versions of miRBase have the database version appended to the microRNA name. For example: miR-hsa-###_v9.1.

Include * Sequence

(microRNA application type only) Star "*" sequences are an alternate class of miRNAs derived from the same precursor miRNAs as corresponding "non-star" miRNAs. A star sequence is generally the less predominant mature miRNA species. For example, both miR-56 (the predominant species) and miR-56* (the less-predominant "star" sequence) are both thought to be derived from the same predicted precursor.

Mark this option to return probes for both star and non-star miRNAs.