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.

ChIP-chip Delivery Workflow

1. Purchase a NimbleGen catalog array or custom designed array of your choice.
2. Prepare your ChIP-chip samples in your laboratory.
3. Label the immunoprecipitated (IP) and Input DNA samples with Cy5 and Cy3 respectively, using a NimbleGen Dual-Color DNA Labeling Kit.
4. Pool and hybridize the samples to the array using a NimbleGen Hybridization Kit and the NimbleGen Hybridization System 4.
5. Wash the arrays using the NimbleGen Wash Buffer Kit.
6. Scan the array using the 2-μm, high-resolution NimbleGen MS 200 Microarray Scanner.
7. Analyze the data using DEVA software and visualize your ChIP-chip results using SignalMap software.

ChIP-chip Service Workflow

1. Purchase NimbleGen catalog arrays or custom designed arrays of your choice.
2. Prepare your ChIP-chip samples in your laboratory and then ship them to Roche NimbleGen.
3. Roche NimbleGen will manufacture and process the arrays from labeling through data analysis.
4. Roche NimbleGen will send you raw and analzyed data, genome annotation, and promoter reports.
5. Visualize your results using SignalMap software.

Roche NimbleGen Software

Roche NimbleGen offers comprehensive data processing and analysis software tools for ChIP-chip analysis. Software available from NimbleGen includes:

• DEVA automates the feature extraction, primary data analysis, and visualization process for Roche NimbleGen ChIP-chip arrays. Using Roche NimbleGen design files and scanned array images, DEVA software will automatically detect new scanned array images, process them, and run the analyses.
• SignalMap allows you to visually interpret the scaled log2-ratio and peak data generated by NimbleScan. Graphical 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.

Brochures & Sales Flyers

• NEW! Roche NimbleGen Research Solutions: Microarrays and target enrichment for genetic disease discovery
  Brochure (PDF Format 7.1MB)
• NimbleGen ChIP-chip & DNA Methylation Microarrays
  Brochure (PDF Format 6MB)
• NimbleGen ChIP-chip 4x72K Array Delivery
  Sales Flyer (PDF Format 256KB)
• NimbleGen ChIP-chip 2.1M Whole-Genome Tiling and Deluxe Promoter Array Delivery
  Sales Flyer (PDF Format 419KB)

User Guides

• NEW! NimbleGen Arrays User’s Guide: Epigenetics Arrays – ChIP-chip and DNA Methylation (Version 1.0)
  User’s Guide (PDF Format 2.2MB)
• Guide to Identifying Motifs from Your ChIP-chip Data
  CEAS User’s Guide (PDF Format 108KB)
  Find out more about CEAS...
• Guide to Functionally Annotating Your ChIP-chip Data
  DAVID User’s Guide (PDF Format 274KB)
  Find our more about DAVID...

Downloads

• 385K HG18 Tiled Promoters
  List of HG18 genes whose promoters are tiled on 385K Promoter Arrays (Excel Format 13.2MB)
• 385K MM8 Tiled Promoters
  List of MM8 genes whose promoters are tiled on 385K Promoter Arrays (Excel Format 11.3MB)

Application Notes & Whitepapers

• Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line
  Application Note (PDF Format 914KB)
• Using Chromatin Immunoprecipitations (ChIP) to Determine Protein Binding Sites on DNA
  Whitepaper (PDF Format 436KB)