A number of limited access partners have been selected to work with the company's second-generation NimbleChip HD2 microarrays, each containing more than 2 million probes.
NimbleGen Systems have announced that a number of limited access partners have been selected to work with the company's second-generation NimbleChip HD2 microarrays, each containing more than 2 million probes.
These partners will have the first opportunity to work with the new higher density arrays by applying the technology to NimbleGen's market-leading chromatin immunoprecipitation (ChIP) products and services.
NimbleGen HD2 limited access partner Dr Michael Snyder, director of the Yale Center for Genomics and Proteomics, said he will use the arrays for mapping transcription factor binding sites and probing human variation.
"The move to 2.1 million feature arrays should result in considerable cost savings and allow us to perform experiments currently unattainable," Snyder said.
"I look forward to using them." NimbleGen's advance in feature density leverages Texas Instrument's (TI) ongoing development of their Digital Micromirror Device (DMD), which has made possible HDTV and high-definition digital cinematography.
Availability of higher density DMDs provides NimbleGen with a straightforward path for offering arrays with much higher data content to its customers.
NimbleGen currently uses an earlier version DMD in their Maskless Array Synthesis (MAS) instruments to synthesise close to 400,000 distinct oligonucleotide probes on its standard arrays.
NimbleGen chose its ChIP-chip product as the initial application for the NimbleChip HD2 rollout because of strong demand from their customers.
"NimbleGen was the first to offer high-density oligo arrays for ChIP-chip, and we're now pushing the field forward again," said Dr Stan Rose, President and CEO of NimbleGen.
"With the introduction of NimbleChip HD2 arrays for ChIP-chip, we will be setting a new standard for both data quality and value in genome-wide analysis of proteins that bind to DNA." ChIP is a standard method for investigating protein - DNA interactions inside the cell.
Many biological processes, such as transcription and DNA replication, depend on complex but coordinated interactions between proteins and DNA.
To understand the mechanisms of such processes and gain insights into the principle of biological phenomena (such as development, disease processes and evolution), researchers study how various proteins associate with their specific DNA target sequences in cells.
"From expression analysis, one can learn what kind of genes are expressed in a given cell, but to find out the mechanisms responsible for these genes' specific expression pattern, one needs to study the transcription factors that control their transcription," said Dr Bing Ren, head of the Laboratory for Gene Regulation at the Ludwig Institute for Cancer Research, UCSD, and HD2 limited access partner.
"NimbleGen's increased probe density with HD2 reduces a whole-genome scan from 38 arrays to about 7," he continued.
"I'm looking forward to the expanded capabilities this offers - that is, the ability to run more whole-genome scans because of the cost savings or to tile through the genome at even higher resolution." Dr Peggy Farnham, associate director of the UC Davis Genome Center and HD2 limited access partner, agreed.
"My lab has been working with the NimbleGen ChIP-chip platform for the past several years".
"We are excited by the prospect of increasing the amount of information obtained per hybridisation by 5 to 10 times, while still collecting high-quality data." NimbleGen recently released new human and mouse promoter array designs, which tile across the promoters of known gene transcripts, based on the latest genome build at the UCSC Genome Browser Database, hg18 and mm8, respectively.
Whole-genome ChIP-chip microarray designs are also available, interrogating the non-repetitive regions of human, mouse, Arabidopsis thaliana, rat, dog, chicken, worm, fly, yeast and E.
coli genomes at an average of 100 bp or less intervals for unbiased discovery.
Researchers may also order an array design utilised by the ENCODE consortium or tailor a chip specific to their experimental design.
