Agilent Launches Next Generation of Microarrays for ChIP-on-Chip Analysis, Providing Sixfold Increase in Density

PALO ALTO, Calif.,– Agilent Technologies Inc. (NYSE: A)announced the availability of oligo array-based ChIP-on-chip (chromatin immunoprecipitation on a chip) microarrays with a more than sixfold increase in density over previous offerings. The higher density microarrays complement the platform’s superior sensitivity and reproducibility, letting researchers conduct genomic tiling experiments.

These microarrays are available in two formats: one microarray per slide with 244,000 features or four microarrays per slide each with more than 44,000 features.

“Researchers recognize that having more features per array increases efficiency because they use fewer slides,” said Kevin Meldrum, Agilent director of Genomics Marketing. “They also acknowledge that more features do not necessarily mean more accurate measurements. Tiling experiments require optimized probe design to detect a binding event with ChIP-on-chip. Our arrays deliver the density, flexibility and sensitivity that these investigators demand.”

The ChIP-on-chip assay is used to detect proteins, including but not limited to transcription factors, binding to particular regions of DNA across the whole genome. Common applications include characterization of transcription, DNA replication and DNA repair events; mapping of chromatin modifications such as DNA methylation; determination of modalities and interactions between therapeutic compounds and target genes; and validation of gene expression data.

“This technique is being rapidly adopted worldwide,” said Rini Saxena, Agilent product manager. “ChIP-on-chip provides biological insights that have not been previously identified by solely using gene expression.”

Evidence of Rapid Adoption of ChIP-on-Chip Technique

“Our investigations are currently focused on the ETS gene family as a model system, and the issue of transcription factor specificity is central to the control of cell growth and differentiation as well as the misregulation of these processes during oncogenesis,” said Dr. Barbara Graves, chairman of the Department of Oncological Sciences at the Huntsman Cancer Institute. “Agilent’s ChIP-on-chip platform enables us to investigate binding events on a global scale.”

A paper from the Rudolph Jaenisch laboratory at the Whitehead Institute, in the April 19 issue of Nature, describes embryonic stem cell regulation. Using Agilent ChIP-on-chip, the researchers discovered regulatory proteins that repress certain genes which, in turn, maintain embryonic stem cell pluripotency during development.

A paper in the July 28 issue of Science, from the Rick Young laboratory at the Whitehead Institute, describes how researchers identified a novel application for ChIP-on-chip. They present evidence that most mitogen-activated protein kinases and protein kinase A subunits become physically associated with the genes they regulate in the yeast genome. The ability to detect this interaction of signaling kinases with target genes can be used to map more precisely and comprehensively the regulatory circuitry that eukaryotic cells use to respond to their environment.

“We think this discovery has far-reaching implications for biology and medicine,” said Dr. Young. “Kinases regulate all aspects of cellular growth and development and it is important to understand how they control our genes. Pharmaceutical companies have devoted considerable effort to developing drugs for specific kinases, as several have been implicated in human diseases such as cancer.”

As an example, Gleevec, manufactured by Novartis, was the first approved drug to directly turn off the signal of a protein known to cause a cancer.

Agilent’s 60-mer probes provide superior sensitivity to competing platforms, enabling researchers to accurately detect binding events without complex statistical analysis or data smoothing. Investigators can also access Agilent’s extensive tiling database of optimized probes across the genomes of human (~13 million probes), mouse (~13 million probes), rat (~10 million probes) and other model organisms through eArray, the Web-based design tool that facilitates rapid and convenient array customization.

Agilent’s ChIP-on-chip array portfolio includes human, mouse and zebrafish promoter arrays as well C. elegans, Drosophila, Arabidopsis and yeast whole-genome arrays.

“The 4-array format lets researchers run four samples on a single slide, significantly reducing the total cost of experiment,” Saxena added. “For example, researchers in the yeast community will be able to study four different conditions against four whole genomes by simply using one slide.”

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