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Agilent Launches Online Microarray Design Tool with Probe Design Capability

Date Posted: Monday, September 18, 2006

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Agilent Technologies Inc. has announced that its secure online custom microarray design tool now includes probe design capability.

The eArray v4.5 is designed to enable scientists to harness the flexibility, sensitivity and increased density of Agilent 60-mer SurePrint microarrays for their specific experiments.

In July, Agilent began shipping its next generation SurePrint DNA microarrays containing 244,000 features on a standard 1" x 3" slide, optimized for applications such as gene expression, array-based comparative genomic hybridization (aCGH), chromatin immunoprecipitation on a chip (ChIP-on-chip), splice variant analysis, DNA methylation and microRNA studies.

"The ability to perform gene expression probe design on-line will save customers substantial amounts of time and money," said Scott Harrison, Agilent custom microarray marketing manager.

"Researchers can now use eArray v4.5 to quickly design probes to their target sequences at no cost, and they have the option of having Agilent design the probes."

"Our customers are closer than ever to an unfettered ability to design and manufacture any probe set for any application and any genome."

Agilent claims that, eArray v4.5 users can query databases containing 21 million tiled CGH and ChIP-on-chip probes, allowing them to create high-resolution arrays that specifically target genomic regions of interest.

Probe libraries from Agilent's entire portfolio of catalog microarrays are available to browse, download, save and repurpose for customer designs.

eArray v4.5 is the web-based application that is designed to enable researchers to design their own microarrays to many formats and then submit print requests directly to manufacturing facilities at their own convenience.

The eArray v4.5 contains genome-wide mouse and human ChIP probe databases, each containing 13 million probes, and mouse and human probe data sets of 8 million probes each for CGH applications.

The design tool provides enhanced search functions to access these datasets for use in high-density aCGH and ChIP-on-chip experiments.

In addition, the eArray v4.5 provides utilities that enable customers to upload their own gene expression, aCGH and ChIP-on-chip probe content, as part of the microarray-creation process.

In addition to the above model organisms and functionality, Agilent continues to expand the genomic datasets available through eArray. The recent additions are:

- Rhesus Macaque - A second-generation rhesus macaque microarray developed by the Michael Katze Laboratory and the Primate Genomics Division of the Washington National Primate Center, University of Washington, is now available.

Based on Baylor Rhesus Genome Project sequences, this microarray contains 22,559 60-mer oligo sequences corresponding to 17,173 distinct rhesus macaque genes, 468 human genes, 96 viral genes (representing 27 different viruses) and 350 human microRNAs.

Agilent contributed probe design services and in-situ synthesis of calibration microarrays used in the manufacture and testing of the new rhesus array.

Professor Katze, head of the Primate Genomics Division, developed the first commercial rhesus macaque-specific oligonucleotide microarray in fall 2004, collaborating with Agilent.

The rhesus macaque is a primate model used to study human disease and development, particularly HIV and AIDS.

Because there were no commercial rhesus macaque microarrays until last year, rhesus macaque researchers were restricted to either examining one gene at a time or using human microarrays.

Katze lab bioinformaticist Jim Wallace, who led the new rhesus microarray project, said, "We received excellent support from Scott Harrison and the eArray Group at Agilent from initial concept through manufacture and testing of the new array."

- Bovine. "Bos Taurus" is an agriculturally and economically important livestock species, and is also a useful large-animal model for metabolic and reproductive studies.

The bovine microarray, developed by ViaLactia Bioscience in collaboration with Agilent, contains 21.475 unique 60-mer probes, representing approximately 19,500 distinct bovine genes.

The probes were developed by clustering 450,000 mRNA and EST sequences available from public sources and ViaLactia's proprietary databases, and were complemented by putative transcript sequences identified by NCBI from the second draft of the bovine genome (Btau 2.1).

Bovine miRNAs are represented by 219 array probes. The majority of probe target sequences are extensively curated by expert biologists and contain dense functional annotation derived from their human orthologues.

This microarray is a third-generation design and a continuation of bovine microarray development commenced by ViaLactia and Agilent in February 2001.

500 arrays have been used and verified by three independent laboratories for gene-expression profiling and CGH applications.

- Dog. "Canis familiaris" (domestic dog) is an important biomedical organism for research in cardiology, cancer, diabetes, behavioral disorders, toxicology and numerous other human conditions with suspected genetic origins.

Centuries of selected inbreeding and resulting narrow gene pools of individual breeds have linked specific breeds with unique susceptibility to certain diseases, making them particularly useful for studying the genetic bases for these diseases in both dogs and humans.

Each 44,290-feature microarray contains 42,034 probes representing predicted Canis familiaris genes.

The sequence and annotation information is based on the canine genome from public data sources of RefSeq (Release 6), Unigene (build #12) Ensembl (Release 32), and TIGR (Release 6, January 2005).

Agilent developed the content of this microarray with researchers at Johns Hopkins Medical Institute. 

There is no cost for Agilent customers to use eArray. eArray can be accessed at earray.chem.agilent.com/earray.

Further Information: http://www.agilent.com

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