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Comparative Genomic Hybridization (CGH) measures DNA copy number differences between a test and reference genome. Roche NimbleGen offers ultra-high resolution CGH/CNV arrays with up to 2.1 million probes for comprehensive analysis of DNA copy number variation. In addition to the 2.1M array format, multiplex arrays are available for higher throughput and cost-effective analysis of either 3 or 12 samples on a single slide. Roche NimbleGen offers several types of CGH/CNV arrays for a variety of organisms to meet your specific research needs:
- Cytogenetics (CGX) Arrays for genome-wide analysis of DNA copy number changes with a subset of probes focused in disease-associated regions
- CNV Arrays for high-resolution CNV discovery and association studies
- CGH Whole-Genome Tiling Arrays for comprehensive, unbiased analysis of DNA copy number changes.
- CGH Whole-Genome Exon-Focused Arrays for genome-wide analysis of DNA copy number changes with a subset of probes focused in exon regions.
- CGH Custom Targeted Arrays for DNA copy number analysis of a whole genome, a single chromosomal region, or multiple loci of interest.
Whole-Genome Tiling 
| 3x720K Whole Genome Tiling New Design! |
| Description |
 |
Catalog Number |
Design Name |
Probe Length |
Median Probe Spacing |
| Whole Genome Tiling Array |
 |
05542081001 |
Mouse CGH 3x720K WG-T Arr Del |
50-75mer |
3537bp |
 |
05544149001 |
Mouse CGH 3x720K WG-T Arr Ser |
|
| 385K Whole Genome Tiling |
| Description |
|
Catalog Number |
Design Name |
Probe Length |
Median Probe Spacing |
| Whole Genome Tiling Array |
|
05542251001 |
Mouse CGH 385K WG-T Arr Del |
50-75mer |
5782bp |
|
05544319001 |
Mouse CGH 385K WG-T Arr Ser |
|
| 385K Whole Genome (4 Array Tiling Set) |
| Description |
|
Catalog Number |
Design Name |
Chromosome |
Tiling Start |
Tiling Stop |
| Whole Genome 4 Array Set |
 |
B4350-SET-01 |
MM8 WG CGH 4 |
See Below |
| Array 1 of 4 |
|
B4350-01-01 |
MM8 WG CGH 1 of 4 |
chr1 |
3,000,293 |
197,067,985 |
| chr2 |
3,007,234 |
181,924,958 |
| chr3 |
3,000,291 |
159,871,498 |
| chr4 |
3,007,126 |
109,660,570 |
| Array 2 of 4 |
|
B4350-02-01 |
MM8 WG CGH 2 of 4 |
chr4 |
109,663,130 |
155,028,692 |
| chr5 |
3,007,298 |
152,002,384 |
| chr6 |
3,000,436 |
149,524,578 |
| chr7 |
3,055,470 |
145,132,901 |
| chr8 |
3,027,760 |
132,084,028 |
| chr9 |
3,040,187 |
36,731,975 |
| Array 3 of 4 |
|
B4350-03-01 |
MM8 WG CGH 3 of 4 |
chr9 |
36,733,292 |
124,000,488 |
| chr10 |
3,000,293 |
129,951,542 |
| chr11 |
3,000,361 |
121,797,655 |
| chr12 |
3,009,912 |
120,462,673 |
| chr13 |
3,001,846 |
120,613,703 |
| chr14 |
3,102,049 |
65,206,768 |
| Array 4 of 4 |
|
B4350-04-01 |
MM8 WG CGH 4 of 4 |
chr14 |
65,209,422 |
123,961,988 |
| chr15 |
3,005,814 |
103,492,224 |
| chr16 |
3,016,968 |
98,252,181 |
| chr17 |
3,003,101 |
95,176,416 |
| chr18 |
3,000,301 |
90,735,078 |
| chr19 |
3,091,207 |
61,321,098 |
| chrX |
3,014,124 |
165,489,740 |
| chrY |
196 |
2,728,204 |
| chrY random |
67,462 |
14,576,508 |
|
| 385K Whole Genome (8 Array Tiling Set) |
| Description |
|
Catalog Number |
Design Name |
Chromosome |
Tiling Start |
Tiling Stop |
| Whole Genome 8 Array Set |
|
B4351-SET-01 |
MM8 WG CGH 8 |
See Below |
| Array 1 of 8 |
|
B4351-01-01 |
MM8 WG CGH 1 of 8 |
chr1 |
3,001,077 |
197,066,459 |
| chr2 |
3,006,344 |
123,959,628 |
| Array 2 of 8 |
|
B4351-02-01 |
MM8 WG CGH 2 of 8 |
chr2 |
123,962,199 |
181,926,640 |
| chr3 |
3,000,451 |
159,871,498 |
| chr4 |
3,006,937 |
108,173,152 |
| Array 3 of 8 |
|
B4351-03-01 |
MM8 WG CGH 3 of 8 |
chr4 |
108,173,698 |
155,029,642 |
| chr5 |
3,003,071 |
152,002,600 |
| chr6 |
3,000,436 |
123,746,411 |
| Array 4 of 8 |
|
B4351-04-01 |
MM8 WG CGH 4 of 8 |
chr6 |
123,747,011 |
149,525,430 |
| chr7 |
3,016,730 |
145,134,047 |
| chr8 |
3,027,760 |
132,084,028 |
| chr9 |
3,042,742 |
35,309,354 |
| Array 5 of 8 |
|
B4351-05-01 |
MM8 WG CGH 5 of 8 |
chr9 |
35,310,047 |
124,000,599 |
| chr10 |
3,008,904 |
129,951,974 |
| chr11 |
3,001,791 |
91,602,672 |
| Array 6 of 8 |
|
B4351-06-01 |
MM8 WG CGH 6 of 8 |
chr11 |
91,603,275 |
121,798,360 |
| chr12 |
3,027,081 |
120,462,673 |
| chr13 |
3,003,693 |
120,614,149 |
| chr14 |
3,207,139 |
64,109,628 |
| Array 7 of 8 |
|
B4351-07-01 |
MM8 WG CGH 7 of 8 |
chr14 |
64,110,901 |
123,962,871 |
| chr15 |
3,000,426 |
103,492,450 |
| chr16 |
3,138,900 |
98,252,181 |
| chr17 |
3,002,406 |
60,422,186 |
| Array 8 of 8 |
|
B4351-08-01 |
MM8 WG CGH 8 of 8 |
chr17 |
60,422,758 |
95,176,355 |
| chr18 |
3,002,382 |
90,736,224 |
| chr19 |
3,079,715 |
61,321,098 |
| chrX |
3,011,514 |
165,516,765 |
| chrY |
31 |
2,728,845 |
| chrY random |
21,465 |
14,500,280 |
|
Custom
Literature
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 |
| General |
| How is NimbleGen array technology different from other platforms? |
NimbleGen manufactures high-density DNA microarrays using its proprietary Maskless Array Synthesizer (MAS) technology. At the heart of the system is a Digital Micromirror Device (DMD) that uses a solid-state array of miniature aluminum mirrors to create “virtual masks” that replace the physical chromium masks used in traditional arrays. The DMD directs a pattern of UV light projected onto a microscope slide, which when coupled with UV-mediated DNA synthesis in a parallel, combinatorial manner, can generate up to 2.1 million unique probes on a single microarray. |
| How many features are included on a single array? |
Individual arrays are available in variety of formats with up to 2.1 million features. |
| Does NimbleGen offer CGH arrays in multiplex formats? |
Yes, we offer Human Whole Genome and custom eukaryotic arrays in 3x720K, 12x135K, and 4x72K formats. |
| What is the resolution of your arrays? |
Effective resolution varies according to the spacing of individual probes (generally 5-10x the median probe spacing). Our human whole-genome arrays enable resolution down to ~5kb on the 2.1M format. Custom targeted arrays enable higher density probe spacing in specified regions and detection of DNA copy number changes down to exon-level resolution. |
| Do NimbleGen array designs include non-coding regions of the genome? |
Yes - NimbleGen offers unbiased whole-genome tiling designs that include genic and intergenic regions. |
| Can NimbleGen design an array tailored to my specific research needs? |
Yes - specify genomic regions of interest and NimbleGen will design a custom array to meet your research needs. |
| What resolution scanner do I need? |
The NimbleGen MS 200 scanner set at 5 micron resolution is optimal for 385K arrays. The NimbleGen MS 200 scanner set at 2 micron resolution is optimal for 2.1M arrays. |
| Can NimbleGen CGH distinguish single vs. multi-copy amplifications? |
Yes. |
|
| Sample Processing |
| What are the sample requirements for CGH? |
1-5μg of high-quality unamplified gDNA is required. |
| What protocol does NimbleGen recommend for DNA isolation? |
Any protocol that provides high-quality gDNA. |
| What reference sample should I use? |
There are several options for choosing a reference sample. For example, for cancer studies choose an individual's own DNA (e.g. tumor vs. germline), DNA from a single individual, or pooled DNA from several individuals (NimbleGen can provide pooled male or female DNA). |
|
| Array Design |
| Are NimbleGen designs up-to-date with the latest genome builds? |
Yes, NimbleGen technology allows the rapid creation of new array designs based on the latest genome sequence. |
| Are designs based on earlier genome builds available? |
Yes. |
| Does NimbleGen offer non-human CGH designs? |
Yes - NimbleGen offers whole-genome designs for a wide range of organisms. In addition, NimbleGen can create custom designs for any genome (or region of genome) for which high-quality sequence is available. |
| Does NimbleGen use only non-unique probes? |
Generally only unique probes are included in array designs. However, NimbleGen Human Whole Genome v2.0 array designs contain non-unique probes for enhanced coverage of low-copy number repeat regions of the genome (e.g. segmental duplication). |
|
| Data Analysis |
| What software do I need to process NimbleGen CGH arrays in my own lab? |
Roche NimbleGen's NimbleScan and SignalMap software are required. |
| What software do I need to view my full service CGH data? |
Roche NimbleGen's SignalMap software is required for viewing CGH data in GFF format. A free, 30-day demo version of SignalMap is available for download. |
| Can I analyze my data using other software programs? |
Yes - NimbleGen data can be viewed and analyzed using a variety of commercially available software programs. |
| Can I view my data in the UCSC genome browser? |
Yes. |
| How do I get gene annotation information? |
NimbleGen provides a gene annotation track corresponding to your design. Additional annotation tracks can be viewed in the UCSC genome browser. |
|
| Array Delivery |
| Can I purchase NimbleGen arrays for use in my own lab or core facility? |
Yes. |
| Which CGH designs are available for array delivery? |
Whole-Genome and custom targeted array designs in any available array format. |
| What kits are availble for use with NimbleGen CGH microarrays? |
NimbleGen Hybridization, Wash Buffer, Array Processing Accessories, and Sample Tracking Control kits. Learn more about our kits... |
| Can I scan NimbleGen arrays using my Agilent scanner? |
The 5 micron Agilent scanner can work with NimbleGen arrays. |
| Does Roche NimbleGen offer training for array delivery customers? |
Yes, Roche NimbleGen Workshops are intensive, 2 to 4-day training programs designed to provide instruction in both the theory and practice of genomic and epigenomic research techniques using Roche NimbleGen high-density DNA microarrays. Click here to find out more. |
| Can I re-use NimbleGen CGH arrays? |
Roche NimbleGen offers a NimbleGen Array Reuse Kit that enables the stripping of NimbleGen CGH arrays so that they can be re-hybridized with newly-labeled test and reference genomic DNA. The success of array re-use is highly variable, depending on sample composition and hybridization conditions. Therefore, Roche NimbleGen does not guarantee the performance of the NimbleGen Array Reuse Kit. |
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