Chromatin Immunoprecipitation-on-chip (ChIP-chip)
Chromatin immunoprecipitation-on-chip (ChIP-chip) is a powerful tool to map target protein DNA binding sites across entire genomes or within biologically important regions such as promoters. This method is used to map chromatin structure and DNA binding sites of transcription factors and polymerases. Roche NimbleGen offers several types of ChIP-chip arrays for a variety of organisms to meet your specific research needs:
- Whole-Genome Designs cover all unique genomic regions in single arrays or multi-array sets and offer unbiased, comprehensive genome coverage for the most complete data sets possible.
- Promoter Designs cover important regulatory regions. Deluxe Promoter arrays offer extensive, single-slide coverage of those regions including gene and miRNA promoters, and CpG islands, while promoter arrays cover only gene promoters.
- Targeted Designs focus on ENCODE regions (up to 30 Mb), promoters of non-coding RNAs or the HOX clusters.
- Custom Designs allow researchers to specify their regions of interest for a fine-tiling approach or design their own targeted probes for a tailored array solution.
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, High-Throughput ChIP-chip Analysis
NimbleGen ChIP-chip microarrays are available in four formats: 2.1M (2.1 million probes on a single glass slide), 3x720K (3 identical arrays per glass slide with 720,000 probes per array), 385K (385,000 probes on a single glass slide), and 4x72K (4 identical arrays per glass slide with 72,000 probes per array). 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 3x720K and 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
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.
Workflows
ChIP-chip Delivery Workflow
- Purchase a NimbleGen catalog array or custom designed array of your choice.
- Prepare your ChIP-chip samples in your laboratory.
- Label the immunoprecipitated (IP) and Input DNA samples with Cy5 and Cy3 respectively, using the NimbleGen Dual-Color DNA Labeling Kit.
- Pool and hybridize the samples to the array using a NimbleGen Hybridization Kit and NimbleGen Hybridization System 4 or 12.
- Wash the arrays using the NimbleGen Wash Buffer Kit and the NimbleGen Microarray Dryer.
- Scan the array using the 2-μm, high-resolution NimbleGen MS 200 Microarray Scanner.
- Analyze the data using NimbleScan software and visualize your ChIP-chip results using SignalMap software.
ChIP-chip Service Workflow
- Purchase NimbleGen catalog arrays or custom designed arrays of your choice.
- Prepare your ChIP-chip samples in your laboratory and then ship them to Roche NimbleGen.
- Roche NimbleGen will manufacture and process the arrays from labeling through data analysis.
- Roche NimbleGen will send you raw and analzyed data, genome annotation, and promoter reports.
- Visualize your results using SignalMap software.
Availability
Delivery and Service Workflows are not available for every ChIP-chip array design. Please consult the Availability section on this page for a complete list.
Availability
The 2.1M, 3x720K, 385K, and 4x72K array formats and the Delivery and Service workflows are not available for every ChIP-chip array design. Use the table below to identify the availability of different formats and workflows across our ChIP-chip design offerings.
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- Delivery OR Service Workflow |
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- Delivery Workflow Only |
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- Service Workflow Only |
| N/A | - Not Available |
