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NimbleExpress™ Array Program

The NimbleExpress™ Array Programis a rapid, cost-efficient solution forsmaller expression studies such asresearch that may require frequentrevision of array designs, rapid proto-typing of design concepts, or experi-ments that require fewer numbers ofcustomized arrays. Each NimbleExpressArray can accommodate probe sets forup to 12,000 transcripts. The advantagesof NimbleExpress arrays include:

• Flexible manufacturing• Low minimum order of 10 arrays • Complementary to GeneChip®

brand arrays • Available for multiple applications

Manufactured by NimbleGen™ Systems,Inc., for Affymetrix, NimbleExpressarrays are compatible with theGeneChip® System and complementthe GeneChip CustomExpress™ productline. Together, these arrays form arobust portfolio of custom solutions,enabling researchers to quickly andcost-efficiently study any number oftranscripts from any organism on aGeneChip array.

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Data Sheet

NimbleExpress™ Array Program

Introduction

NimbleExpress™ Arrays contain up to

282,000 unique oligos and are useful microar-

ray tools for a variety of applications. For gene

expression studies, these arrays can accommo-

date up to 12,000 genes, which are each inter-

rogated with 11 probe pairs. NimbleExpress

arrays are an ideal choice for pilot experiments

or other research that requires smaller lots

of highly customized arrays. They provide

researchers with an efficient method of per-

forming a variety of applications on a smaller

scale, such as custom expression analysis,

whole-genome analysis of smaller organisms,

and applications requiring tiling arrays.

Applications

NimbleExpress arrays can be used for many

microarray applications, including:

··Whole-genome expression profiling

··Multiple-genome expression profiling

··Genome tiling arrays

··Preliminary experiments prior to design-

ing a GeneChip® CustomExpress™ Array

·· Iterative experiments, where frequent

array design updates are required

NimbleExpress Arrays are produced by

NimbleGen™ Systems, Inc. (Madison, WI)

for Affymetrix, using a flexible, maskless pho-

tolithography manufacturing technology to

create customized high-quality microarrays.

FAST, FLEXIBLE ARRAY PROGRAM

Because NimbleExpress arrays are manufac-

tured with a flexible, maskless photolitho-

graphic process, the minimum order size is

only ten arrays. Additionally, NimbleExpress

arrays are produced and shipped within four

weeks of design completion. These benefits

make the NimbleExpress arrays ideal for pilot

studies, allowing researchers to begin experi-

ments within weeks of submitting an array

design. Benefits of NimbleExpress arrays:

··Flexible manufacturing, which allows

researchers to test new design strategies

with frequent revisions

··Low minimum order of 10 arrays, which

offers an affordable custom array solution

··Complementary to GeneChip arrays,

which enables all arrays to be run on the

same instrument platform

··Design strategies for multiple applications,

including gene expression, tiling, and

custom applications

··Flexibility to begin pilot designs before

ordering a larger GeneChip

CustomExpress Array

NIMBLEEXPRESS ARRAY MANUFACTURINGPROCESS

NimbleExpress arrays are manufactured using

photo deprotection chemistry with a

Maskless Array Synthesizer (MAS) system. A

key component of the MAS device is a Digital

Micromirror Device (DMD), similar to the

technology used in high-quality computer

Product Content Capacity Application Ideal for

NimbleExpress™ 12,000 probe sets Expression, tiling, – Fewer than 40 arraysArray (11pp/sequence) and custom – Low-medium content

282,000 features applications arrays

CustomExpress™ 520-61,000 probe sets Expression, tiling, – High volume orders Array (11pp/sequence) and custom >40 arrays

Up to 1.3 million features applications – Low-high contentarrays

projection equipment. Using a solid-state

array of miniature aluminum mirrors, which

are each individually controlled, the DMD

enables an oligo synthesis process that is sim-

ilar to the photolithography process used to

create GeneChip brand microarrays. This

maskless MAS process can be changed or

updated easily as experiments evolve. For

more information on the MAS manufacturing

process, please refer to www.nimblegen.com.

Each NimbleExpress microarray is individ-

ually produced and quality control tested.

After array synthesis, NimbleExpress arrays

are packaged in an Affymetrix® GeneChip

cartridge for use with the GeneChip reagents,

hybridization oven, fluidics station, and scan-

ner. Standard NimbleExpress expression arrays

are designed using Affymetrix proven probe

set selection algorithms. Certain arrays for

customized applications may be designed by

NimbleGen.

ARRAY DESIGN TECHNICAL SUPPORT

Technical support regarding the design of

NimbleExpress expression arrays is available

through the Affymetrix Chip Design Group.

Certain non-standard arrays may be designed

in direct consultation with NimbleGen.

Please contact chip_design@affymetrix.com

for more information about NimbleExpress

or CustomExpress Array design options.

SUBMIT DESIGN DATA

The GeneChip® CustomExpress™ Array Design

Guide offers instructions for preparing the

design request form and files such as sequence

lists, special instruction, pruning, and control

files. Additionally, a free Design Checker

software tool is available to help proofread

your sequences prior to the submission of

your array design. The GeneChip®

CustomExpress™ Array Design Guide and the

Design Checker tool are available for down-

load from www.affymetrix.com.

PROBE SELECTION

In general, NimbleExpress array probes are

selected by the Affymetrix Chip Design

Group using the same algorithms used to

design Affymetrix GeneChip catalog arrays.

Where appropriate, certain non-standard

designs may be designed directly by

NimbleGen in direct consultation with

customers. Affymetrix will facilitate these

G E N E E X P R E S S I O N M O N I T O R I N G

A F F Y M E T R I X fi P R O D U C T FA M I LY > A R R AYS

GG

UV Light

Digital micromirrors

photolabileprotectinggroup

=

G G

Add

G

RepeatG G

A . . . . .

A . . . . .

G . . . . . . . . .

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G GG GC

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CC

C

Figure 1: Photolithographic manufacturing process for NimbleExpress™ arrays. (Courtesy ofNimbleGen™ Systems, Inc.)

designs, so please contact your Affymetrix

Account Manager with any design proposals

you are considering.

G E N E E X P R E S S I O N M O N I T O R I N G

A F F Y M E T R I X fi P R O D U C T FA M I LY > A R R AYS

Array format 12,000 probe sets (11 pp/set) 282,000 features

Scanner requirements GeneArray® 2500, GeneChip® Scanner 3000

Feature size 17 µm

Probe pairs/gene for expression arrays 11 recommended

Oligo length 25-mer recommended

Hybridization controls bioB, bioC, bioD, and cre

Poly-A controls dap, lys, phe, and thr

Maintenance genes For each species represented where Affymetrixhas a catalog array, the species-specific controlswill be added to your design. You may specifyas many additional controls as you wish.

Critical Specifications

NimbleExpress™ Array Image

RUN ARRAYS AND ANALYZE DATA

Typical NimbleExpress expression arrays are

compatible with the protocols in the

GeneChip® Expression Analysis Technical

Manual and can be run on the GeneChip®

Instrument system. NimbleExpress arrays

may also be customized for new applications

that are not currently supported by

Affymetrix reagents or analysis software.

Results can be mined with standard

GeneChip® software or exported for further

analysis in third-party software packages.

Technical support is available from Affymetrix

technical support.

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Ordering Information

AFFYMETRIX UK Ltd

Voyager, Mercury Park,Wycombe Lane, Wooburn Green,High Wycombe HP10 0HHUnited KingdomTel: +44 (0) 1628 552550Fax: +44 (0) 1628 552585saleseurope@affymetrix.comsupporteurope@affymetrix.com

AFFYMETRIX, INC.

3380 Central ExpresswaySanta Clara, CA 95051 USATel: 1-888-DNA-CHIP (1-888-362-2447)Fax: 1-408-731-5441sales@affymetrix.comsupport@affymetrix.com

www.affymetrix.com

AFFYMETRIX JAPAN K.K.

Mita NN Bldg., 16 F 4-1-23 Shiba, Minato-ku, Tokyo 108-0014 Japan Tel: +81-(0)3-5730-8200 Fax: +81-(0)3-5730-8201 salesjapan@affymetrix.com supportjapan@affymetrix.com

For research use only.

Not for use in diagnostic procedures.

Part No. 701665 Rev. 1

©2004 Affymetrix, Inc. All rights reserved. Affymetrix®,GeneChip®, ®, ®, ®, HuSNP®, Jaguar™, EASI™, MicroDB™, GenFlex®, CustomExpress™, CustomSeq™, NetAffx™, NimbleExpress™,

‘Tools to take you as far as your vision™’, and ‘The Way Ahead™’ are trademarks owned or used by Affymetrix, Inc. Array products may be covered by one or more of the following patents and/or sold

under license from Oxford Gene Technology: U.S. Patent Nos. 5,445,934; 5,744,305; 6,261,776; 6,291,183; 5,700,637; 5,945,334; 6,346,413; 6,399,365; and 6,610,482; and EP 619 321; 373 203 and other U.S.

or foreign patents. GeneArray is a registered trademark of Agilent Technologies, Inc.

Please visit www.affymetrix.com. todownload a copy of the CustomExpress™

Array Design Guide to assist you in yourdesign strategy and preparation of yoursequence files. Your Affymetrix AccountManager can help you decide which arrayprogram will best suit your needs and willprovide you with a quote for your design.

NimbleExpress™ ArrayProgram

To Order

North America

888-DNA-CHIP 888-362-2447

Europe

+44 (0) 1628 552550

Japan

+81-(0)3-5730-8200