Roche NimbleGen | CGH | Other Designs

Chicken

	Format: 385K Source: UCSC Build: galGal3 Recommended Storage: Store arrays desiccated at room temperature.
Description		Catalog Number	Design Name	Probe Length	Median Probe Spacing
Whole Genome Tiling Array		B3791001-00-01	galGal3 WG CGH	50-75mer	2586bp

Cow

	Format: 385K Source: Bovine Genome Project (Baylor College of Medicine) Build: Btau3.1 Recommended Storage: Store arrays desiccated at room temperature.
Description		Catalog Number	Design Name	Probe Length	Median Probe Spacing
Whole Genome Tiling Array		B4491001-00-01	Btau31 WG CGH	50-75mer	5779bp

Caenorhabditis elegans

	Format: 385K Source: UCSC Build: CE2, WS120 Recommended Storage: Store arrays desiccated at room temperature.
Description		Catalog Number	Design Name	Probe Length	Median Probe Spacing
Whole Genome Tiling Array		B2144001-00-01	CE2 WG CGH	50-75mer	137bp

Dog

	Format: 385K Source: NCBI Build: canFam2, May 2005 Recommended Storage: Store arrays desiccated at room temperature.
Description		Catalog Number	Design Name	Probe Length	Median Probe Spacing
Whole Genome Tiling Array		B3679001-00-01	canFam2 WG CGH	50-75mer	4675bp

Drosophila melanogaster

	Format: 385K Source: UCSC Build: DM2, April 2004 Recommended Storage: Store arrays desiccated at room temperature.
Description		Catalog Number	Design Name	Probe Length	Median Probe Spacing
Whole Genome Tiling Array		B2440001-00-01	DM2 WG CGH	50-75mer	308bp

Plasmodium falciparum 3D7

	Format: 385K Source: NCBI Build: Dec 2004 Recommended Storage: Store arrays desiccated at room temperature.
Description		Catalog Number	Design Name	Probe Length	Median Probe Spacing
Whole Genome Tiling Array		B2028001-00-01	Plasmodium 3D7 WG CGH	50-75mer	48bp

Rat

	Format: 385K Source: Ensembl Build: RGSC 3.4, Ensembl July, 2005 Recommended Storage: Store arrays desiccated at room temperature.
Description		Catalog Number	Design Name	Probe Length	Median Probe Spacing
Whole Genome Tiling Array		B2432001-00-01	RN34 WG CGH	50-75mer	5303bp

Rhesus Monkey

	Format: 385K Source: UCSC Build: rheMac2 Recommended Storage: Store arrays desiccated at room temperature.
Description		Catalog Number	Design Name	Probe Length	Median Probe Spacing
Whole Genome Tiling Array		B4500001-00-01	rheMac2 WG CGH	50-75mer	6476bp

Saccharomyces cerevisiae

	Format: 385K Source: UCSC Build: Oct 2003 Recommended Storage: Store arrays desiccated at room temperature.
Description		Catalog Number	Design Name	Probe Length	Median Probe Spacing
Whole Genome Tiling Array		B2436001-00-01	2007-05-08 SCER WG CGH	50-75mer	12bp

Schizosaccharomyces pombe

	Format: 385K Source: NCBI Build: Jun 2005 Recommended Storage: Store arrays desiccated at room temperature.
Description		Catalog Number	Design Name	Probe Length	Median Probe Spacing
Whole Genome Tiling Array		B2441001-00-01	SPOM WG CGH	50-75mer	8bp

Zebrafish

	Format: 385K Source: UCSC Build: danRer4 Recommended Storage: Store arrays desiccated at room temperature.
Description		Catalog Number	Design Name	Probe Length	Median Probe Spacing
Whole Genome Tiling Array		B6057-00-01	Danio Zv6 WG CGH	50-75mer	3525bp

Custom

Please contact your Sales representative to Request a Quote or contact Technical Support with any questions about CGH custom array designs.

	NEW! 2.1M	NEW! 3x720K	NEW! 12x135K	385K	4x72K
Number of Arrays per Slide	1	3	12	1	4
Total Number of Probes	2,100,000	3 x 720,000	12 x 135,000	385,000	4 x 72,000
Source	Customer-defined
Build	Customer-defined
Probe Length	50-75mer
Probe Spacing	Uniform or mixed-density
Design Options	Whole-genome, single or multiple chromosomal regions per array.

To learn more about NimbleGen Array formats, please visit our Array Products page.

Literature

Brochures & Datasheets

NimbleGen Copy Number Variation (CNV) Arrays
Datasheet (PDF Format 1.4MB)
NimbleGen Human CGH Whole-Genome Arrays
Brochure (PDF Format 2.2MB)

User Guides

NimbleGen Arrays User’s Guide: CGH and CNV Arrays (Version 7.0)
User’s Guide (PDF Format 4.7MB)
NimbleGen Arrays User’s Guide: CGX Arrays (Version 2.0)
User’s Guide (PDF Format 5.7MB)

Downloads

Descriptions of HG18 Annotation Files
Datasheet (PDF Format 49KB)
Human Genome HG18 Annotation Files
Annotation Files (ZIP Format 11.2MB)
What files are included in this download?

Application Notes & Whitepapers

Array CGH using DNA from Formalin-Fixed Paraffin-Embedded (FFPE) Tissue Samples
Technical Note (PDF Format 2MB)
Detecting Copy Number Variants Associated with Basal Cell Carcinoma in an Arsenic-Exposed Population
Application Note (PDF Format 1.2MB)
High Resolution Copy Number Analysis of Parkinson’s Samples Using Nexus Copy Number and Roche NimbleGen Microarrays
Whitepaper (PDF Format 964KB)

For a complete listing of literature covering all Roche NimbleGen products and services please visit our literature page.

FAQ

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.