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Comparative Genomic Hybridization (CGH) measures DNA copy number differences between and test and reference genome. NimbleGen offers two types of CGH array products: whole-genome and custom targeted arrays. Whole-genome arrays measure DNA copy number gains and losses across entire genomes, while custom targeted arrays can interrogate a single chromosomal region or multiple loci of interest. In addition, custom designs can be created with either uniform or mixed-density probe spacing.
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 |
 |
B8443-00-01 |
MM9 CGH 3x720K WG Tiling |
|
| 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 |
|
B4254-00-01 |
MM8 WG CGH |
|
| 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 NimbleGen offer training for array delivery customers? |
Yes - NimbleGen offers on-site Training Workshops at our Madison, WI location. |
| Can I strip and re-use my CGH microarray? |
Yes - NimbleGen offers an array re-use kit for stripping and re-hybridizing arrays. |
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