Roche NimbleGen has expanded its growing line of tools for analyzing the epigenome and genome-wide transcriptional regulation mechanisms by launching HD2 (2.1 million probes) arrays and services for chromatin immunoprecipitation (ChIP-chip). NimbleGen ChIP-chip HD2 arrays now provide more than a 5-fold increase in probe density per array, which allows for increasing the coverage of key biological features, such as promoters and CpG islands, and decreasing the number of arrays needed to perform whole-genome analysis at high resolution.

ChIP-chip is a powerful technique that allows for the high-resolution mapping of chromatin structure including histone modifications, transcription factor and nucleic acid polymerase binding, nucleosome location, and DNase I hypersensitivity. These various applications enable researchers to determine what regions of the genome are transcriptionally active, which regions are repressed, and what mechanisms regulate these processes. Unraveling the fundamental epigenomic and genomic regulatory pathways underlying normal cell growth and tissue differentiation, as well as changes in regulatory control associated with disease, is crucial for the development of drugs that target these pathways.

Roche NimbleGen is recognized as the leading platform for ChIP-chip studies and the main array platform used by researchers participating in the ENCODE consortium, a project aimed at characterizing the functional elements of the human genome. The NimbleGen platform is also widely accepted as the method of choice for ChIP-chip experiments with the number of peer-reviewed publications totaling over 80, far exceeding that of all other ChIP-chip products on the market.

Dr. Bing Ren, a prominent epigenomics and genomics researcher from the Ludwig Institute, University of California, San Diego School of Medicine, said “NimbleGen ChIP-chip high-definition 2.1 million probe arrays are a flexible and robust platform for investigating the transcription factor binding sites and chromatin modification patterns in the genome of a variety of model organisms and have been extremely valuable for our research of the transcriptional regulatory elements in the Drosophila, mouse and human genomes.” Peggy Farnham, Ph.D., Professor of Pharmacology and Associate Director of Genomics, University of California-Davis, appreciates the superior performance of NimbleGen ChIP-chip arrays, adding, “We have been very pleased with the high sensitivity and reproducibility of NimbleGen arrays. The high sensitivity has been especially critical for our studies of site-specific factors that are present at modest levels in human cells and tissues.”

Building upon its strong position within the research community, Roche NimbleGen has introduced the most comprehensive epigenomics array on the market. The Human Deluxe Promoter array allows researchers to interrogate all known and alternative start site promoters at 10kb promoter coverage, all annotated CpG islands (ca.28,000), and ca.500 miRNA promoters on a single glass slide. Also available are whole-genome tiling sets for human, mouse, rat, D. melanogaster, and C. elegans. The human whole-genome sets are available as either 10-array sets (100bp spacing) or 4-array sets (205bp spacing). Customers can access NimbleGen ChIP-chip HD2 arrays by ordering arrays, instrumentation, and software and performing the research in their laboratory or core facility or by simply submitting immunoprecipitated and input samples to the Roche NimbleGen service facility for full service analysis. Researchers may also target only their genomic regions of interest at any desired tiling resolution by creating a custom design with the expert support of Roche NimbleGen scientists.

Roche NimbleGen is a leading innovator, manufacturer, and supplier of a proprietary suite of DNA microarrays, consumables, instruments, and services. Roche NimbleGen uniquely produces high-density arrays of long oligo probes that provide greater information content and higher data quality necessary for studying the full diversity of genomic and epigenomic variation. The improved performance is made possible by Roche NimbleGen proprietary Maskless Array Synthesis (MAS) technology, which uses digital light processing and rapid, high-yield photochemistry to synthesize long oligo, high-density DNA microarrays with extreme flexibility. For more information about Roche NimbleGen, please visit the company’s website at www.nimblegen.com