Molecular Devices GenePix 4100A User manual
GenePix®4100A Microarray Scanner
User Guide
5000449 D
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
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to designate those manufacturers' products as supplied by Molecular Devices for
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arising therefrom.
For research use only. Not for use in diagnostic procedures.
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© 2010 Molecular Devices, Inc.
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GenePix 4100A Microarray Scanner User Guide
5000499 D 3
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
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.
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Contents
Foreword . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Who This Manual Is For . . . . . . . . . . . . . . . . . . . . . . . . . 7
Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . 7
Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . 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 and Troubleshooting . . . . . . . . 21
Moving the Scanner . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Interlock Failure Symptoms . . . . . . . . . . . . . . . . . . . . . 23
Fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Appendix A Instrument Components. . . . . . . . . . . . . . . 25
Protective Enclosure . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Optics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Lasers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Optical Path. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
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
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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®4100A 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:
CAUTION! Indicates an operation that can cause damage to the
instrument, device, or data, if precautions are not followed.
Related Documentation
The customer documentation for the 4100A Microarray Scanner
includes the GenePix®Pro Software Reference Guide, Safety Practices
manual, and the GenePix®Pro Help.
WARNING! A warning indicates an operation that can cause
personal injury 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.
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Foreword
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1
Introduction
The GenePix®4100A 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
microarray 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 for each of the
two channels (13 minutes total time)
•5 μm resolution in approximately 13 minutes for each of the two
channels (26 minutes total time)
Scanner Features
•Can be configured with one or two internally installed
laser-excitation sources
•Sequential scanning of up to two wavelengths
•Precisely controlled automatic laser power monitoring with
pixel-by-pixel correction
•Data Scan pixel resolution from 5 μm to 100 μm
•Fast Preview Scan pixel resolution at 40 μm
•16-bit ultra-low-noise digitization
•Dynamic range of 104
•Two standard filters and an 8-position emission filter cartridge
with up to six additional pre-installed factory filters
•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
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Introduction
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Scanner Components
The main components of the 4100A Microarray Scanner are:
•Protective enclosure
•Optics
•Lasers
•Optical path
•Emission filters
•PMT (photo-multiplier tube)
•Status lights
Figure 1-1 GenePix 4100A Microarray Scanner
For detailed information about each component, see Instrument
Components on page 25.
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Table of contents
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