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Targeted designs are for interrogating focused regions of the genome.
Compare Targeted Designs
Roche NimbleGen offers four types of targeted designs to suit your DNA Methylation analyses:
- 3x720K CpG Island Plus RefSeq Promoter Arrays are multiplex slides with 3 identical arrays per slide enabling the simultaneous analysis of 3 DNA Methylation samples for increased sample throughput. These arrays cover the annotated CpG islands as well as the promoters of the well characterized RefSeq genes derived from the UCSC RefFlat files and are available for human, mouse and rat. These arrays also include new positive, negative and non-CpG control regions to help facilitate assessment of array and sample performance.
- 385K CpG Island Plus Promoter Arrays are single array designs that include all UCSC-annotated CpG islands and with the following promoter regions for all RefSeq gene promoter regions: 1kb (human) and 1.8kb (mouse and rat). DNA methylation positive control regions, such as the HoxA gene cluster, H19/IGF2 cluster, KCNQ1 cluster, and the IGF2R gene are also included on the arrays.
- 385K Targeted Tiling Arrays offer fine tiling (5 bp median probe spacing) of select biologically significant areas. The Human HOX Array tiles through the HoxA, HoxB, HoxC, HoxD, β-globin and Xist genes. The Human and Dog ENCODE arrays tile through the biologically significant ENCODE pilot regions (HoxA, β-globin, Apo among others). The Human ncRNA (non-coding RNA) Array tiles through the promoters of the 462 miRNA genes, 362 snoRNAs and 89piRNA clusters as well as selected ENCODE regions.
- 4x72K Human ENCODE Array offers a higher throughput, lower cost solution for testing the quality of DNA methylation samples before moving to large-scale studies, or for screening focused targeted regions of interest, for up to 4 independent samples per slide.
Human
| 3x720K CpG Island Plus RefSeq Promoter |
| Description |
 |
Catalog Number |
Design Name |
Number of CpG Islands |
Promoter Upstream Tiling (bp) |
Promoter Downstream Tiling (bp) |
| Multiplex CpG Island Plus RefSeq Promoter Array |
 |
05924529001 |
Human Meth 3x720K CpG RfSq Prom Arr Del |
 |
05924600001 |
Human Meth 3x720K CpG RfSq Prom Arr Ser |
|
27,728 |
2440 |
610 |
| * Promoter number is calculated based on transcription start sites. Any transcription start sites on the same strand closer than 500bp are assumed to be transcribed from the one promoter. For a complete list of transcripts whose promoters are covered on each array, please contact Roche NimbleGen technical support. |
|
| 385K CpG Island Plus Promoter |
| Description |
|
Catalog Number |
Design Name |
Number of CpG Islands |
Promoter Upstream Tiling (bp) |
Promoter Downstream Tiling (bp) |
| Array 1 of 1 |
|
05543622001 |
Human Meth 385K Prom Plus CpG Arr Del |
|
05545668001 |
Human Meth 385K Prom Plus CpG Arr Ser |
|
28226 |
800 |
200 |
|
| 385K HOX Genes |
| Description |
|
Catalog Number |
Design Name |
Region* |
Chromosome |
Tiling Start |
Tiling Stop |
| Human HOX Array |
|
05543576001 |
Human Meth 385K HOX-T Arr Del |
|
05545617001 |
Human Meth 385K HOX-T Arr Ser |
|
HoxA |
chr7 |
26,886,173 |
27,032,857 |
| HoxB |
chr17 |
43,951,988 |
44,171,031 |
| HoxC |
chr12 |
52,603,895 |
52,730,355 |
| HoxD |
chr2 |
176,771,238 |
176,890,807 |
| ß-globin |
chr11 |
5,193,350 |
5,257,424 |
| Xist |
chrX |
72,673,922 |
73,027,348 |
| * Many other regions are also tiled on this design, contact Technical Support for the complete list. |
|
| 385K Non-Coding RNA |
| Description |
|
Catalog Number |
Design Name |
Regions |
Promoter Upstream Tiling (bp) |
Promoter Downstream Tiling (bp) |
| Non-Coding RNA Array |
|
05543584001 |
Human Meth 385K ncRNA Prom Arr Del |
|
05545625001 |
Human Meth 385K ncRNA Prom Arr Ser |
|
miRNA (462 genes) |
12500 |
7500 |
| snoRNA (375 genes) |
12500 |
7500 |
| piRNA (89 clusters) |
10000 |
10000 |
| select ENCODE regions (80bp spacing) |
|
|
|
| 385K ENCODE HG18 |
| Description |
|
Catalog Number |
Design Name |
Chromosome |
Probe Length |
Median Probe Spacing |
| Array 1 of 1 |
|
05543568001 |
Human Meth 385K ENC HG18 Tgt-T Arr Del |
|
05545609001 |
Human Meth 385K ENC HG18 Tgt-T Arr Ser |
|
Tiles All ENCODE Regions |
50-75mer |
60bp |
|
| 385K ENCODE HG17 |
| Description |
|
Catalog Number |
Design Name |
Chromosome |
Probe Length |
Median Probe Spacing |
| Array 1 of 1 |
|
05543550001 |
Human Meth 385K ENC HG17 Tgt-T Arr Del |
|
05545595001 |
Human Meth 385K ENC HG17 Tgt-T Arr Ser |
|
Tiles All ENCODE Regions |
50mer |
38bp |
|
| 4x72K ENCODE |
| Description |
|
Catalog Number |
Design Name |
Chromosome |
Probe Length |
Median Probe Spacing |
| Array 1 of 1 |
|
05543673001 |
Human Meth 4x72K ENC HG17 Tgt-T Arr Del |
|
Tiles biologically significant ENCODE Regions (HoxA, ß-globin, Apo, among others) |
50-75mer |
105bp |
|
Literature
Brochures & Datasheets
User Guides
Downloads
Application Notes & Whitepapers
For a complete listing of literature covering all Roche NimbleGen products and services please visit our literature page.
FAQ
| Hide All Topics Show All Topics |
| Sample Preparation |
| What kind of samples can be used on NimbleGen's DNA methylation arrays? |
These arrays are designed to detect differences between a sample enriched for methylated DNA and a control sample, such as total genomic DNA. We recommend samples enriched using affinity-based methods that utilize an anti-5-mC antibody or MBD proteins. We also accept enzyme based methods to detect DNA methylation, such as Hpa II tiny fragment enrichment by ligation-mediated PCR (HELP). |
| Do you have a recommended protocol for front-end sample processing for producing DNA fragments enriched for methylation? |
Yes, we recommend the MeDIP (methylated DNA immunoprecipitation) protocol (Nat Genet. 2005 Aug;37(8):853-62) followed by amplification if necessary. Please contact NimbleGen's Technical Services for a detailed sample preparation protocol. |
| What is the minimum amount of DNA required to perform a NimbleGen recommended MeDIP experiment? |
We recommend starting with 5μg high-quality genomic DNA. However, even smaller amount DNA can be used (1μg or even 200ng). The IP process generally yields 5-10% of the original starting DNA, and you can amplify your IP-ed DNA using whole genome amplification (WGA; kit available from Sigma) in order to obtain at least 4μg of DNA. |
| Do I need to amplify my MeDIP samples? |
We are able to use unamplified samples for labeling reactions if at least 2.5μg of enriched methylated DNA was obtained. Greater amounts of enriched DNA can be obtained by starting with more DNA and by pooling samples from multiple experiments. If amplifcation is necessary, we recommend using the WGA kit (Sigma, catalog #WGA2-50RXN) for MeDIP samples. We have routinely observed that the WGA method introduces little bias during the amplification. |
| What is the effect of CpG content on the MeDIP reaction? |
Studies by Weber et al. (Nat. Genet. 2005, 37(8):853-862) have shown that the more more methylated CpG dinucleotides within a given fragment, the more DNA that is immunoprecipitated. The increase immunoprecipitated material is due to the 5-methylcytidine antibody having more available epitopes (methylated CpG). |
| What are the sample requirements for DNA methylation arrays? |
We require 4μg DNA (although 2.5μg is acceptable) at a concentration of 250-500ng/μl with the majority of fragments greater than 200bp. The A260/A280 ratio should be at least 1.7 and the A260/A230 ratio should be at least 1.6. |
| Does NimbleGen perform front-end sample processing (e.g. IP and amplification)? |
No, NimbleGen is not currently set up to perform contract DNA methylation experiments for our customers. |
| Should I use a negative control and if so what should I use? |
Many of our customers do not use a negative control (e.g. nonspecific IgG antibody), but it is recommended if this is your first experiment with NimbleGen. You will want to have your negative control (IgG) co-hybridized with total DNA (input) in order to avoid a high signal/noise ratio that is often seen when the IgG sample is co-hybridized with the immunoprecipitated sample. |
| What should I use as a reference sample? |
The majority of our customers use total (input) sample as a reference. Using a nonspecific IgG is not a suitable reference. |
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| Array Design |
| Do we have a catalog CpG island array? |
Yes, we now offer our Human and Mouse 2.1M Deluxe Promoter Arrays for that include all annotated CpG islands and extensive coverage of all annotated gene and miRNA promoters. These arrays also include new positive, negative and non-CpG control regions to aid in assessment of experimental performance. (continue with previous info starting with) We also offer human, mouse, and rat CpG Island Plus Promoter arrays that include all UCSC annotated CpG islands plus 1kb human promoter or 1.8kb mouse promoter region of every RefSeq gene. Control tiled regions on the array include the HoxA cluster (methylation hotspot) and several imprinted loci, including H19/IGF2, KCNQ1, and IGF2R. |
| Are the probes designed from both strands? |
No, NimbleGen only designs probes based off of the forward strand. |
| How does NimbleGen address repetitive elements in the genome for DNA methylation designs? |
We have developed our own method of repeat masking which is dependent on the mean frequency of the 15-mers which make up each oligo. A table is made of the count of all 15-mers that appear in the genome, from both strands. Then a 15-mer window is slid along each oligo, looking up the count of each 15-mer in the table, and calculating the average count. A threshold is set, usually 100 for large eukaryotic genomes, and any probe that exceeds that threshold is eliminated from further consideration. Depending on the region of the genome being evaluated, approximately 20-25% of the DNA is excluded. For some designs we use conventional repeat masking, as done by the RepeatMasker program http://www.repeatmasker.org/). However, NimbleGen has no access to the repeat libraries necessary to use this application, so we rely on third parties to supply this type of masked sequence. We find, however, that RepeatMasker is often overly aggressive and can mask 50-55% of human DNA sequence. See the following paper for reference: Bioinformatics. 2006 Jan 15;22(2):134-41. WindowMasker: window-based masker for sequenced genomes; Morgulis A, Gertz EM, Schaffer AA, Agarwala R; National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services Building 38A, Room 1003N, 8600 Rockville Pike, Bethesda, MD 20894, USA. |
| What spacing do you recommend for DNA methylation designs? |
We recommend probe spacing of 100bp or less. |
| Can I get a graphical representation of all probes for a cataloged design that I am interested in so I can see what regions of the genome have coverage? |
Yes, we can generate this information in GFF format for all of catalog designs. You will need a copy of Roche NimbleGen's SignalMap software to view the GFF files. A free, 30-day demo version of SignalMap is available for download. |
|
| Data Analysis |
| Does NimbleGen normalize DNA methylation data? |
No, there is no normalization of DNA methylation data. However, we do scale the GFF files by subtracting the bi-weight mean for the log-ratio values from each log-ratio value. This effectively centers the log-ratio values around zero. |
| How does NimbleGen perform analysis on DNA methylation data? |
After scaled log2 ratio data is generated a modified ACME algorithm (Method Enzymol. 2006; 411:270-282) is employed where a fixed-length window is slid along the length of each chromosome, testing at each probe using a one-sided Kolmogorov-Smirnov (KS) test whether the surrounding window is enriched for high-intensity probes relative to the rest of the array. Each probe has a corresponding p-value score (-log10) and a threshold is set to select regions that are enriched (i.e. methylated) in the test sample. |
| Why is the data analysis for DNA methylation different from ChIP-chip? |
Since DNA methylation array data is often characterized by broad ranges of enrichment (whereas ChIP-chip data enrichment is more discrete) a different method to identify peaks from scaled log2-ratio data must be employed. |
| How do I validate a genome-wide DNA methylation array experiment? |
Common methods include bisulfite sequencing (single nucleotide resolution) to validate methylation status of all CpG dinucleotides within a peak called on the array, combined bisulfite restriction analysis (COBRA, determine percent methylation), and quantitative PCR to validate MeDIP array results by accurately measuring enrichment of methylated DNA fragments. |
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| Deliverables |
| Can I get the images for my data? |
Yes, we can supply you with the raw data array images (.tif) upon request. Scaled log2-ratio data (.gff) files and peak (.gff) files are included in your deliverable data. |
| Can I get a graphical representation of all probes for a cataloged design that I am intersted in so I can see what regions of the genome have coverage? |
Yes, we can generate this information in GFF format for all of the catalog designs. You will need a copy of Roche NimbleGen's SignalMap software to view the GFF files. A free, 30-day demo version of SignalMap is available for download. |
| Does NimbleGen generate reports listing the most significant binding/modification events for my DNA methylation experiment? |
Yes, we are including two summary reports that map the peaks from your DNA methylation data relative to the transcription start site of a gene. For instance, if a peak is called within the promoter region of a gene, the report will give the approximate location of the peak as a negative position (upstream of the start site) or positive position (downstream). Also included are accession number of the gene, gene ID, chromosome position, among others. These reports will help narrow down the genomic regions you should be looking at when moving forward to validate your DNA methylation data (e.g. bisulfite sequencing or qPCR). |
|
| Benefits |
| Why should I use a genome-wide approach to study DNA methylation? |
NimbleGen's DNA methylation analysis arrays allow you to map DNA methylation across your genome of interest genome in an unbiased fashion, compare differential methylation patterns between cells, tissues, and tumors, and identify prognostic markers. |
| How sensitive are NimbleGen's DNA methylation arrays? |
Our arrays, when coupled with MeDIP, can readily detect as little as 2 methylated CpG dinucleotides per fragment. |
| What is the reproducibility of NimbleGen DNA methylation analysis arrays? |
While not fully validated by NimbleGen scientists, Weber et al. (Nat. Genet. 2007, 39(4):457-466) observed highly reproducible DNA methylation data between biological replicates (R = 0.92 for WI38 cells and R = 0.95 and 0.91 for sperm) when using MeDIP coupled with NimbleGen human promoter arrays. |
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