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 needs. Our whole-genome DNA methylation designs interrogate the non-repetitive regions of human, mouse, rat, and plant genomes at intervals ranging from <100bp to 255bp for unbiased discovery of methylated DNA regions. Arrays focused on biologically significant genomic regions are also available including promoter/CpG island array designs and promoter only designs aimed at well characterized promoter regions. For custom designs, researchers can specify their regions of interest for fine-tiling of genomic regions or promoters or design a tailored array with their own probe designs.

High-Resolution, High-Throughput Analysis of DNA Methylation

NimbleGen high density DNA methylation microarrays are available in three 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). The 2.1M high density microarrays enable coverage of the entire non-repetitive human genome at 100bp spacing using only 10 slides - greatly simplifying whole genome analysis. Now with the 3x720K and 4x72K arrays, you can increase sample throughput and lower the cost per sample for targeted DNA methylation analysis.

Figure 1

Figure 1: Detection of Differential DNA Methylation using the Three New Human DNA Methylation 2.1M Designs - MeDIP samples from OT (maternally-derived ovarian teratoma cells) and CHM (paternally-derived hydatidiform mole) cells were labeled with Cy5 and the control (input) DNAs with Cy3, pooled and technical replicates were hybridized to the three different human array designs. Raw data were analyzed using NimbleScan software and the P-values estimating the significance of enrichment were visualized using SignalMap software. The black horizontal bar indicate the regions tiled on the different array designs. The red box highlights the differentially methylated region between the OT and CHM samples, which was easily identified using all three array designs. The blue box highlights a region of DNA methylation detected on the whole-genome tiling design with 100bp probe spacing but not in the whole-genome economy design with 205bp probe spacing illustrating the greater detection sensitivity possible using arrays with 100bp probe spacing.

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 DNA methylation array experiments using a two-color protocol, where input control and MeDIP samples are co-hybridized to the same array, inter-array variation is eliminated. As a result, NimbleGen DNA Methylation Arrays can readily detect as low as two methylated CpGs in a 500 bp fragment.

Easy-to-use Graphical View of Data Facilitates Discovery

Roche NimbleGen’s SignalMap software enables you to visually interpret your data and perform peak finding. SignalMap’s graphic representation of your data aids in the discovery of methylated or unmethylated DNA regions and well as differentially methylated DNA regions between samples. A free, 30-day demo version of SignalMap software is available for download.

Figure 2

Figure 2: Identification of DNA Methylation Using NimbleGen Arrays - From the raw data, NimbleGen generates scaled log₂-ratio data for IP/input. A statistical method is used to generate p-value enrichment data for each probe; peaks (methylated regions) are then generated based on the p-value data. NimbleGen also provides gene annotations and CpG island annotations.

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

NimbleGen DNA Methylation 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.

DNA Methylation Delivery Workflow

1. Purchase a NimbleGen catalog array or custom designed array of your choice.
2. Prepare your MeDIP 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 MeDIP-chip results using SignalMap software.

DNA Methylation Service Workflow

1. Purchase NimbleGen catalog arrays or custom designed arrays of your choice.
2. Prepare your MeDIP 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 DNA Methylation analysis. Software available from NimbleGen includes:

• DEVA automates the feature extraction, primary data analysis, and visualization process for Roche NimbleGen DNA Methylation 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, p-value, and peak data generated by NimbleScan. Graphical representation of your data aids the discovery of epigenetic and transcriptional regulation, including DNA hypermethylation within a target genome and the correlation of promoter and genic methylation with gene expression. 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 DNA Methylation 2.1M Whole-genome Tiling and Deluxe Promoter Arrays
  Sales Flyer (PDF Format 1.4MB)
• NimbleGen DNA Methylation 4x72K Array Delivery
  Sales Flyer (PDF Format 312KB)

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 Functionally Annotating Your DNA Methylation Data (Version 1.2)
  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

• NEW! NimbleGen arrays and LightCycler® 480 System: A complete workflow for DNA methylation biomarker discovery and validation
  Application Note (PDF Format 1.7MB)
• Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line
  Application Note (PDF Format 914KB)
• Genome-Wide Screen of Promoter Methylation Identifies Novel Markers in Melanoma
  Application Note (PDF Format 2.7MB)