ChIP-on-Chip

Roche NimbleGen provides the most sensitive ChIP-chip (chromatin immunoprecipitation on chip) microarrays and services on the market. These arrays enable rapid identification of precise binding sites of specific DNA-binding proteins—such as transcription factors, histones, and polymerases—within a target genome, as well as uncover chromatin remodeling in any region of a genome. NimbleGen ChIP-chip microarrays and services have become the platform of choice supported by an ever-growing list of peer-reviewed publications.

Advantages

Comprehensive Set of Array Designs Cover All Your Needs

Roche NimbleGen offers whole genome, promoter, and custom array designs, allowing you to choose the design that meets your research requirements. Our whole-genome ChIP-chip designs interrogate the non-repetitive regions of human, mouse, Arabidopsis, rat, dog, chicken, worm, fly, yeast, and E. coli genomes at intervals of 100bp or less for unbiased discovery of promoter/enhancer elements, transcription factor binding, histone modification/replacement, and DNase-I hypersensitivity. NimbleGen human and mouse promoter array designs, based on the latest public genome builds, tile across the promoters of known gene transcripts. You can also order an array design utilized by the ENCODE consortium or tailor an array specific to your experimental design.

High-Resolution Tiling = High-Resolution Detection of Binding Sites

NimbleGen high-density microarrays are available in three formats: 2.1M (2.1 million probes on a single glass slide), 385K (385,000 probes on a single glass slide) and 4x72K (test up to 4 samples per 72,000 probe array on a single glass slide). This high density provides for high-resolution tiling of your research genome and precise mapping of protein binding sites. With 2.1M arrays, the entire non-repetitive human and mouse genomes can be surveyed at 100bp intervals, each with a set of 10 arrays. Now with 4x72K arrays, you can increase sample throughput and lower cost per sample for targeted ChIP-chip analysis.

High Sensitivity and Specificity Provide Unparalleled Results

Roche NimbleGen's proprietary, light-mediated synthesis process produces high-density microarrays of long oligonucleotide probes (50-75mer). These long oligo arrays, when used in combination with high-stringency hybridization protocols, produce results of unparalleled sensitivity and specificity. In addition, because Roche NimbleGen performs ChIP-chip experiments in a two-color protocol, where control and test samples are co-hybridized to the same array, inter-array variation is eliminated. As a result, NimbleGen ChIP-chip service can readily detect enrichment as low as two-fold of the target binding site in a ChIP sample, which can be extremely challenging for other array platforms to match.

Figure A. Identification of RNA Polymerase II Binding Sites in MCF7 cells using a HG18 RefSeq Promoter array. NimbleGen's graphical output enables you to visualize protein/DNA interactions.

Easy-to-use Graphical View of Data Aids Discovery

Roche NimbleGen SignalMap software enables you to visually interpret your data and perform peak finding. SignalMap’s graphic representation of your data aids the discovery of promoter/enhancer elements, transcription factor binding, and histone modification/replacement, and DNase-I hypersensitivity. A free, 30-day demo version of SignalMap software is available for download.

Most Up-to-date Genome Builds Ensure Most Accurate Results

NimbleGen ChIP-chip designs are based on the latest genome assemblies and sequence annotations to ensure comprehensive and accurate representation of the genome. In addition, you can continue to access array designs based on past genome data builds, which can be particularly useful for comparisons to prior studies.

Array Formats

	2.1M	385K	4x72K*
Arrays per Slide	1	1	4
Total Number of Probes	2,100,000	385,000	4 x 72,000
Feature Size	13µm x 13µm	16µm x 16µm	16µm x 16µm

For more information, please click the link below: http://www.nimblegen.com/products/