Nimblegen Announces Limited Access Program for Nimblechip™ HD2 CHIP Arrays

NimbleGen Systems, Inc. has announced that a number of limited access partners have been selected to work with the company’s second-generation NimbleChip™ HD2 microarrays, each containing 2 million probes.

These partners will have the opportunity to work with the higher density arrays by applying the technology to NimbleGen’s 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 highdefinition 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 synthesize 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."

"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 hybridization by 5 to 10 times, while still collecting high-quality data."

NimbleGen recently released 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 utilized by the ENCODE consortium or tailor a chip specific to their experimental design.

NimbleGen’s 400,000 probe ENCODE ChIP-chip array is used by the majority of laboratories working on ChIP in the NHGRI’s ENCODE consortium.

NimbleGen’s ChIP products have also been developed and validated for re-use, which scientists have found reduces operating costs without sacrificing data quality, sensitivity or reproducibility.

The following ChIP-chip products are commercially available to order from NimbleGen:

Human ChIP-chip products

Human whole-genome: 38-chip set tiles every 100bp across non-repetitive regions on the forward strand of the entire genome (based on NCBI Build 36 and UCSC hg18).

Human promoter (based on NCBI Build 36 and UCSC hg18):

o A single chip tiles across known, standard (or “model”) promoter regions as defined in RefSeq.

o A single chip tiles across “experimental” promoter regions as defined in RefSeq.

o A two-chip set tiles across all known promoter regions as defined in NCBI and UCSC.

ENCODE: A single chip uniformly tiles across ENCODE-designated regions, or approximately one percent of the human genome (based on NCBI Builds 34 and 35 and UCSC hg16 and hg17).

Mouse ChIP-chip products

Mus musculus whole-genome: 38-chip set tiles every 100bp across non-repetitive regions on the forward strand of the entire genome (based on NCBI Build 36 and UCSC mm8).

Mus musculus promoter (based on NCBI Build 36 and UCSC mm8):

o A single chip tiles across known, standard (or “model”) promoter regions as defined in RefSeq.

o A single chip tiles across “experimental” promoter regions as defined in RefSeq.

o A two-chip set tiles across all known promoter regions as defined in NCBI and UCSC.

Arabidopsis ChIP-chip products

Arabidopsis thaliana whole-genome: Three-chip set tiles every 90bp across non-repetitive regions of the entire genome (based on TIGR Release 5).

Arabidopsis thaliana promoter: A single chip tiles 2000bp upstream of all annotated promoters (based on TIGR Release 4).

Rat ChIP-chip products

Rattus norvegicus whole-genome: A single chip tiles every 100bp across non-repetitive regions on the forward strand of the entire genome (based on UCSC rn3).

Dog ChIP-chip products

Canis familiaris whole-genome: A single chip tiles every 100bp across non-repetitive regions on the forward strand of the entire genome (based on UCSC canFam2).

Chicken ChIP-chip products

Gallus gallus whole-genome: A single chip tiles every 100bp across non-repetitive regions on the forward strand of the entire genome (based on UCSC galGal3).

Worm ChIP-chip products

C. elegans whole-genome: A single chip tiles every 86bp across non-repetitive regions on the forward strand of the entire genome (based on UCSC ce2).

Fly ChIP-chip products

Drosophila melanogaster whole-genome: A single chip tiles every 97bp across non-repetitive regions on the forward strand of the entire genome (based on UCSC dm2).

Yeast ChIP-chip products

S. cerevisiae whole-genome: A single chip tiles every 32bp across non-repetitive regions on the forward strand of the entire genome (based on UCSC rn3).

E. coli ChIP-chip products

E. coli K12 whole-genome: A single chip tiles every 24bp across non-repetitive regions on both strands of the entire genome (based on UCSC rn3).