Molecular Devices GenePix 4000B User Manual

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GenePix® 4000B Microarray Scanner

User Guide

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October 2010

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This document is provided to customers who have purchased Molecular Devices, Inc.
(“Molecular Devices”) equipment, software, reagents, and consumables to use in the
operation of such Molecular Devices equipment, software, reagents, and
consumables. This document is copyright protected and any reproduction of this
document, in whole or any part, is strictly prohibited, except as Molecular Devices
may authorize in writing.

Software that may be described in this document is furnished under a license
agreement. It is against the law to copy, modify, or distribute the software on any
medium, except as specifically allowed in the license agreement. Furthermore, the
license agreement may prohibit the software from being disassembled, reverse
engineered, or decompiled for any purpose.

Portions of this document may make reference to other manufacturers and/or their
products, which may contain parts whose names are registered as trademarks and/or
function as trademarks of their respective owners. Any such usage is intended only
to designate those manufacturers' products as supplied by Molecular Devices for
incorporation into its equipment and does not imply any right and/or license to use
or permit others to use such manufacturers' and/or their product names as
trademarks.

Molecular Devices makes no warranties or representations as to the fitness of this
equipment for any particular purpose and assumes no responsibility or contingent
liability, including indirect or consequential damages, for any use to which the
purchaser may put the equipment described herein, or for any adverse circumstances
arising therefrom.

For research use only. Not for use in diagnostic procedures.

The trademarks mentioned herein are the property of Molecular Devices, Inc. or their
respective owners. These trademarks may not be used in any type of promotion or
advertising without the prior written permission of Molecular Devices, Inc.

Product manufactured by Molecular Devices, Inc.

1311 Orleans Drive, Sunnyvale, California, United States of America 94089.

Molecular Devices, Inc. is ISO 9001 registered.

© 2010 Molecular Devices, Inc.

All rights reserved.

Printed in the USA.

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Licensing Notice

Molecular Devices is not licensed under any patents owned by Oxford Gene Technology
Limited (“OGT”), covering oligonucleotide arrays and methods of using them to analyze
polynucleotides. The purchase of Molecular Devices products does not convey any license
under any of OGT’s patent rights, including any right to make or use oligonucleotide
arrays under OGT’s patents.

Customers may use Molecular Devices products to analyze oligonucleotide arrays
according to OGT’s patented methods if those arrays have either been purchased from
OGT’s licensed suppliers, or have been made by the customer under a license from OGT.

Please contact OGT to enquire about a license under OGT’s patents at
[e-mail].

USE OF THIS INSTRUMENT WITH MICROARRAYS MAY REQUIRE A LICENSE FROM ONE OR
MORE THIRD PARTIES THAT HAVE PATENTS RELEVANT TO SUCH USE. MOLECULAR
DEVICES DOES NOT SUGGEST OR PROMOTE THE USE OF THIS INSTRUMENT IN A
MANNER THAT INFRINGES ON THE PATENT RIGHTS OF A THIRD PARTY. YOU ARE
ENCOURAGED TO EVALUATE WHETHER A LICENSE IS REQUIRED FOR YOUR SPECIFIC
APPLICATION OF THIS INSTRUMENT. COMPANIES THAT HAVE INTELLECTUAL PROPERTY
RIGHTS IN THE POTENTIAL FIELD OF APPLICATION OF THIS INSTRUMENT INCLUDE
WITHOUT LIMITATION, AFFYMETRIX, INC. (“AFFYMETRIX”), AGILENT, AND OXFORD
GENE TECHNOLOGY. THIS INSTRUMENT HAS NOT BEEN LICENSED OR APPROVED FOR
DIAGNOSTIC APPLICATIONS.

THE USE OF THIS INSTRUMENT IN CONNECTION WITH MICROARRAYS MAY BE WITHIN
THE SCOPE OF PATENTS HELD BY AFFYMETRIX. TO THE EXTENT THAT AFFYMETRIX
PATENT RIGHTS ENCOMPASS THIS INSTRUMENT OR ITS USE, AFFYMETRIX HAS
GRANTED A LIMITED PATENT LICENSE FOR RESEARCH USE ONLY AND NOT FOR USE IN
DIAGNOSTIC PROCEDURES. SUCHLICENSE, IF APPLICABLE, IS LIMITED TO USE OF THIS
INSTRUMENT WITH SPOTTED MICROARRAYS SEPARATELY LICENSED BY AFFYMETRIX.
NO LICENSE IS CONVEYED, BY IMPLICATION, ESTOPPEL OR OTHERWISE, TO USE THIS
INSTRUMENT WITH MICROARRAYS MADE USING IN SITU OR PHOTOLITHOGRAPHIC
SYNTHESIS. NO OTHER LICENSE IS CONVEYED, BY IMPLICATION, ESTOPPEL OR
OTHERWISE, UNDER ANY AFFYMETRIX PATENT OR OTHER INTELLECTUAL PROPERTY
RIGHT.

This instrument is licensed by Affymetrix under the following patents: U.S. Patent Nos.
5,578,832;5,631,734; 5,834,758; 5,936,324; 5,981,956; 6,025,601; 6,141,096;
6,171,793; 6,185,030; 6,201,639;6,207,960; 6,218,803; 6,225,625; 6,252,236;
6,262,838; 6,335,824; 6,403,320; 6,403,957, 6,407,858;6,472,671; 6,490,533;
6,545,264; 6,597,000; 6,643,015; and 6,650,411.

GenePix 4000B Microarray Scanner User Guide

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Contents

Foreword . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Who This Manual Is For . . . . . . . . . . . . . . . . . . . . . . . . . 7

Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . 7

Chapter 1 Principles of Operation . . . . . . . . . . . . . . . . . . 9

Scanner Features. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Scanner Components . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Scanner Specifications . . . . . . . . . . . . . . . . . . . . . . . . . 11

Site Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Chapter 2 Installation and Operation . . . . . . . . . . . . . . 13

Unpacking the scanner and positioning it on the bench. . . 13

Installing the Software . . . . . . . . . . . . . . . . . . . . . . . . . 16

Turning on the Scanner . . . . . . . . . . . . . . . . . . . . . . . . 17

Inserting a Slide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Shutting Down the Scanner. . . . . . . . . . . . . . . . . . . . . . 19

Chapter 3 Maintenance & Troubleshooting . . . . . . . . . . 21

Moving the Scanner . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Interlock Failure Symptoms . . . . . . . . . . . . . . . . . . . . . 23

Fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Appendix A Instrument Components. . . . . . . . . . . . . . . 25

Protective enclosure . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Optics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Lasers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Optical Path. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Emission Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

PMT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Status Lights . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Appendix B Instrument Performance Factors . . . . . . . . 29

Spatial Resolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Dynamic Range and Detection Limit . . . . . . . . . . . . . . . . 31

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Contents

Appendix C Warranty and Service . . . . . . . . . . . . . . . . . 33

Standard Warranty . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Out-of-Warranty Repair Service . . . . . . . . . . . . . . . . . . 33

Optional Service Agreement. . . . . . . . . . . . . . . . . . . . . 33

Technical Support. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

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Foreword

The foreword describes the intended audience for the manual. It
defines the typographical conventions used in the manual and lists the
related documentation.

Who This Manual Is For

This manual is written for the GenePix® 4000B Microarray Scanner user.
The manual contains the information required to install the scanner,
turn it on, and perform maintenance procedures.

Conventions

Within the scope of this manual, the following typographical
conventions are used:

WARNING! A warning indicates an operation that can cause
personal injury if precautions are not followed.

CAUTION! Indicates an operation that can cause damage to the

instrument, device, or data, if precautions are not followed.

Tip! Provides useful information that helps apply the techniques and
procedures in the text to your specific needs, and provides shortcuts,
but is not essential to the completion of a procedure.

Note: Provides essential information for the completion of a procedure.

Related Documentation

The customer documentation for the GenePix 4000B Microarray
Scanner includes the GenePix® Pro Software Reference Guide, Safety
Practices manual, and the GenePix® Pro online Help.

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Foreword

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Principles of Operation

The GenePix® 4000B Microarray Scanner uses a laser-excitation based
fluorescence scanning and imaging system. The laser-based scanning
system operates by slowly moving the slide in the Y–direction, while
the slide is rapidly scanned in the X–direction. The design of the
scanner allows you to scan a 25 mm by 75 mm slide at up to two
wavelengths:

• 10 μm resolution in approximately 6.5 minutes

• 5 μm resolution in approximately 13 minutes

Scanner Features

• Two internally installed laser-excitation sources

• A user-attenuated lasers allowing 10%, 33%, and 100%

transmission

• Simultaneous scanning of two wavelengths

• User-adjustable focus

• Precisely controlled automatic laser power monitoring with

pixel-by-pixel correction

• Data Scan pixel resolution from 5 m to 100 μm

• Fast Preview Scan pixel resolution at 40 μm

• 16-bit ultra-low-noise digitization

• Dynamic range of 10

• Two filters (670DF40 and 575DF35)

• Capacity for one standard 1 inch by 3 inch (25 mm by 75 mm,

or 26 mm by 76 mm) microscope slide-based microarray

• Full integration with GenePix Pro Software and Acuity®

Microarray Informatics Software

1

4

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Principles of Operation

Scanner Components

The main components of the GenePix 4000B Microarray Scanner are:

• Protective enclosure

• Optics

• Lasers

• Optical path

• Emission filters

• PMTs (photo-multiplier tubes)

• Status lights

• External power supply

.

Figure 1-1 GenePix® 4000B Microarray Scanner

For detailed information about each component, see Instrument

Components on page 25.

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Scanner Specifications

Table 1-1 Specifications

Sample type Standard microscope slides (1 inch by 3 inches, 25

Maximum scan area 22 mm by 72 mm

Maximum resolution 5 μm

Scan mode and order Simultaneous scanning of two wavelengths

Detector Dual PMTs

Signal digital output 16-bit

Image format Single or multi-image TIFF

Computer interface USB 2.0

Scan time 6.5 minutes at 10 μm resolution

Dynamic range Four orders of magnitude

Uniformity Plus or minus 10%

Dimensions 13 inches wide by 8.7 inches high by 17.4 inches long

Weight 35.8 lb (16.2 kg)

Power supply Line voltage: 85 to 264 VAC (110 to 340 VDC)

Line frequency 50 to 60 Hz

Power 85 W, Fuse: 2.0 A slow. 5 to 20 mm

GenePix 4000B Microarray Scanner User Guide

mm by 75 mm or 26 mm by 76 mm; 0.9 to 1.2 mm
thick)

(36 cm by 22 cm by 44 cm).

universal voltage input

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