Mouse DNA Methylation 2.1M Deluxe Promoter Arrays
 Format: 2.1MSource: UCSC Probe Length: 50-75mer Median Probe Spacing: 100bp Recommended Storage: Store arrays desiccated at room temperature. |
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| Description | Build | Promoter Upstream Tiling (bp) | Promoter Downstream Tiling (bp) | Number of CpG Islands | miRNA Promoters | Catalog Number | Pack Size | Workflow | Ordering* |
| Mouse DNA Methylation 2.1M Deluxe Promoter v2 Array | MM9 | 8000** | 3000 | 15969 | 599 (-15kb to mature miRNA) | 06532977001 | 1 Slide |  |
Contact Us to Purchase |
| 06533027001 | Dataset |  |
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| * Availability of products varies from country to country. ** There are approximately 24,507 promoters tiled on this array. |
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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, 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.
Workflow
DNA Methylation Delivery Workflow
- Purchase a NimbleGen catalog array or custom designed array of your choice.
- Prepare your MeDIP samples in your laboratory.
- Label the immunoprecipitated (IP) and Input DNA samples with Cy5 and Cy3 respectively, using a NimbleGen Dual-Color DNA Labeling Kit.
- Pool and hybridize the samples to the array using a NimbleGen Hybridization Kit and the NimbleGen Hybridization System 4.
- Wash the arrays using the NimbleGen Wash Buffer Kit.
- Scan the array using the 2-μm, high-resolution NimbleGen MS 200 Microarray Scanner.
- Analyze the data using DEVA software and visualize your MeDIP-chip results using SignalMap software.
DNA Methylation Service Workflow
- Purchase NimbleGen catalog arrays or custom designed arrays of your choice.
- Prepare your MeDIP 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.
