DNA Methylation
Roche NimbleGen provides the most sensitive and specific DNA methylation microarrays and services on the market. Affinity-based methods for enrichment of methylated DNA fragments, such as MeDIP (Methylated DNA immunoprecipitation) or the MBD (Methyl Binding Domain Protein) methods, are the preferred sample preparation methods for identifying methylated DNA on NimbleGen arrays. Coupled with one of these enrichment methods, our arrays and services offer:
- Precise identification of methylated DNA regions across whole genomes or within biologically focused regions including promoters and CpG islands.
- Highly sensitive detection of methylated CpGs due to use of long, isothermal (50-75mer) oligonucleotide probes.
- Comprehensive catalog collection of whole-genome tiling arrays and targeted Deluxe Promoter arrays for multiple organisms.
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 needs. Our whole-genome DNA methylation designs interrogate the non-repetitive regions of human, mouse, rat, chicken, dog, worm, fly, 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), 385K (385,000 probes on a single glass slide) and 4x72K (4 arrays with 72,000 probe each to test up to 4 samples on a single glass slide). 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. With the 4x72K arrays, you can increase sample throughput and lower the cost per sample for targeted DNA methylation analysis.
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: 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.
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/ |