Molecular Devices GenePix 4300A User manual

GenePix®4300A/4400A
High-Resolution Microarray Scanner
User Guide
0112-0173 B
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
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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.
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.
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.
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GenePix Microarray Scanner User Guide
0112-0173 B 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
[email protected].
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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4 0112-0173 B
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0112-0173 B 5
Contents
Foreword . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Who This Manual Is For . . . . . . . . . . . . . . . . . . . . . . . . . 7
Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . 7
Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Scanner Features. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Scanner Components . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Protective enclosure . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Optics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Lasers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Optical Path. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Emission Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
PMT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Status Lights . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Scanner Specifications . . . . . . . . . . . . . . . . . . . . . . . . . 14
Site Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Chapter 2 Installation . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Unpacking the scanner and positioning it on the bench. . . 17
Installing the Software . . . . . . . . . . . . . . . . . . . . . . . . . 20
Turning on the Scanner . . . . . . . . . . . . . . . . . . . . . . . . 21
Inserting a Slide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Shutting Down the Scanner. . . . . . . . . . . . . . . . . . . . . . 23
Chapter 3 Maintenance & Troubleshooting . . . . . . . . . . 25
Moving the Scanner . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Installing Custom Filters . . . . . . . . . . . . . . . . . . . . . . . . 27
Interlock Failure Symptoms . . . . . . . . . . . . . . . . . . . . . 34
Fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
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Contents
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Appendix A Warranty and Service . . . . . . . . . . . . . . . . . 35
Standard Warranty . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Out-of-Warranty Repair Service . . . . . . . . . . . . . . . . . . 35
Optional Service Agreement. . . . . . . . . . . . . . . . . . . . . 35
Technical Support. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
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0112-0173 B 7
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®4300A/4400A High-Resolution
Microarray Scanner user. It 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 may cause damage to the
instrument, device, or data, if the precautions are not followed.
Related Documentation
The customer documentation for the GenePix 4300A/4400A Microarray
Scanner includes the GenePix®Pro Software Reference Guide, Safety
Practices manual, and the GenePix®Pro online Help.
WARNING! A warning indicates an operation that may 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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0112-0173 B 9
1
Introduction
The GenePix®4300A/4400A Microarray Scanner uses a laser-excitation
based fluorescence scanning and imaging system. The laser-based
scanning system uses a patent-pending mechanical design, and
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
scanning up to four wavelengths of a 25 mm by 75 mm slide at:
•5 m resolution for the 4300A in approximately 30 minutes for
all four channels
•2.5 m resolution for the 4400A in approximately 60 minutes for
all four channels
Scanner Features
•Up to four internally installed laser-excitation sources
•Gradient neutral density wheel permitting 5 to 100 % laser
transmission
•Data Scan resolution from 5 to 100 m for the 4300A, or 2.5 to
100 m for the 4400A.
•Fast Preview Scan at 40 m
•16-bit ultra-low noise digitization
•Dynamic range of 104
•Easy-access 16-position emission filter cartridge with standard
filters for each pre-installed laser
•Standard 1 inch by 3 inch (25 mm by 75 mm) microscope slides
•Full integration with GenePix Pro Microarray Software and
Acuity®Microarray Software
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Introduction
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Scanner Components
The main components of the GenePix 4300A/4400A Microarray Scanner
are:
•Protective enclosure
•Optics
•Lasers
•Optical Path
•Emission Filters
•PMT (photo-multiplier tube)
•Status lights
.
Figure 1-1 GenePix 4300A/4400A Microarray Scanner
Protective enclosure
The protective enclosure protects the user from exposure to laser
radiation, high voltage, and moving parts.
WARNING! Laser Hazard! Do not remove the protective
enclosure. Operating the scanner with the protective enclosure
removed exposes the user to laser radiation.
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GenePix Microarray Scanner User Guide
0112-0173 B 11
Optics
The GenePix 4300A/4400A Microarray Scanner uses a laser-excitation
based fluorescence scanning and imaging system. The optical system
can be considered in terms of excitation light, mirrors, lenses, filters,
and photo-detection.
Lasers
In the GenePix 4300A/4400A Microarray Scanner standard
configuration, laser excitation is provided by individual 532 nm and 635
nm lasers. These wavelengths correspond to the ideal wavelengths
used to excite the fluorophores Cy3 and Cy5 (GE Healthcare), or other
fluorophores with similar fluorescent characteristics. The individual
lasers have been selected because of their superior optical performance
and reliability. Since the performance of such lasers is often sensitive to
external temperature fluctuations, the scanner uses an active
temperature stabilization design to minimize temperature-based laser
fluctuations. Furthermore, each laser has integrated output monitoring
feedback to compensate for fluctuations in photon output, ensuring
consistency in measured fluorescence.
The scanner can be configured with two additional lasers for a total of
four installed laser light sources. A blue laser with 488 nm excitation
can be used with fluorescein and similar dyes, and a yellow laser with
594 nm excitation can be used with Texas Red and similar dyes.
Optical Path
Excitation laser light is directed onto the slide after passing through a
series of filters and mirrors. While laser light is by definition very
narrow band, the GenePix 4300A/4400A Microarray Scanner employs
additional optical filters to make sure that no spurious excitation light is
directed onto the slide. If the laser light impinges on an appropriate
fluorophore bound on the slide, emission light of a longer wavelength is
emitted. These emission photons are directed back through the optical
system where they pass through another bandpass filter before
reaching the photodetector.
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Introduction
12 0112-0173 B
Emission Filters
The GenePix 4300A/4400A Microarray Scanner is available in standard
configuration with either two or four lasers. The scanner can be custom
configured with one to four lasers. Each laser (red, yellow, green, and
blue) includes a matching emission filter pre-installed in the sixteen-
position filter cartridge.
Four positions in the filter cartridge are reserved for the standard
emission filters.
•Position 1 – red (661 to 690 nm)
•Position 5 – yellow (619–641 nm)
•Position 9 – green (562–596 nm)
•Position 13 – blue (513–555 nm)
These filters are not accessible, however, the remaining twelve
positions are available for custom filter installation.
Each standard emission filter is optimized for the emission spectrum of
the respective dye, designed to reject laser light at OD 8 (optical
density) for each respective laser excitation, and reject broad-spectrum
light at OD 5.
For specific information on custom filters and their applications, refer to
the filter manufacturer’s website.
•Semrock Inc.: www.semrock.com
•Chroma Technology Corp: www.chroma.com
PMT
The GenePix 4300A/4400A Microarray Scanner uses a high-sensitivity,
low-noise PMT to detect the emitted fluorescent light. A PMT converts
incident photons into electrons through the photoelectric effect. When
an incident photon impinges on the active surface of the PMT (the
photocathode), an electron is generated. The electron flows through a
series of electron multipliers (dynodes) to the anode. The amount of
current that flows from the anode is directly proportional to the number
of photons at the photocathode.
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GenePix Microarray Scanner User Guide
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Status Lights
Three lights on the front of the GenePix 4300A/4400A Microarray
Scanner indicate status.
•Device standby
•Scanning
•Eject
.
Table 1-1 Status lights
Item Name Description
1 Device standby The scanner is powered up and ready to scan a
slide
2 Scanning The slide is in the load position and is being
scanned
3 Eject The slideholder is ready to be unloaded
1
2
3
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Introduction
14 0112-0173 B
Scanner Specifications
Table 1-2 Specifications
Sample type Standard microscope slides (1 inch by 3 inches, 25 mm
by 75 mm; 0.9 to 1.2 mm thick)
Maximum scan area 22 mm by 72 mm
Maximum resolution 5 m for the 4300A, 2.5 m for the 4400A
Scan mode and
order
Sequential scan of user-configured wavelengths
Detector PMT
Signal digital output 16-bit
Image format Single or multi-image TIFF
Computer interface USB 2.0
Scan time Four minutes per channel for full size scan area at 10
m resolution
Dynamic range Four orders of magnitude
Rotational
uniformity
Less than 4% non-uniformity
Dimensions 16.9 inches wide by 25.6 inches long by 13.4 inches
high (43 cm by 65 cm by 34 cm).
Weight 99 lb (45 kg)
Power supply Line voltage: 85 to 264 VAC (110 to 340 VDC) universal
voltage input
Line frequency 50 to 60 Hz
Power 85 W, Fuse: 2.0 A slow. 5 to 20 mm
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GenePix Microarray Scanner User Guide
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Site Requirements
Table 1-3 Site Requirements
Temperature 50 to 86º F (15 to 30º C)
Humidity 5 to 95% non-condensing
Power Universal input 50 to 60 Hz, 100 to 240 VAC, 2A max
Space 25.6 inches deep by 16.9 inches wide by 13.4 inches high (65
cm by 43 cm by 34 cm). An additional 6 inches (15.2 cm) for
clearance.
Bench support Sufficient to support 99 lbs (45 kg) with minimal vibration
Power supply Line voltage: 85 to 264 VAC (110 to 340 VDC) universal
voltage input
Line
frequency
50 to 60 Hz
Power 2.0 A
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Introduction
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0112-0173 B 17
2
Installation
The GenePix®4300A/4400A Microarray Scanner should be unpacked
and in position on a flat level surface before performing any of the
installation procedures. Perform the procedures in the following order.
•Unpack the scanner and position it on the bench
•Install the software
•Turn on the scanner
•Insert a slide
Unpacking the scanner and positioning it on the bench
The GenePix 4300A/4400A Microarray Scanner is packed in a specially
designed crate. Retain the crate and the packing materials. In the
event the scanner requires repair, you must return it to Molecular
Devices in the original packaging. If the crate has been damaged in
transit, you must retain it for inspection by the carrier.
WARNING! Shock Hazard. In an emergency, users must be
able to safely disconnect the mains power cable without
moving the scanner. Locate the scanner so that either the
power outlet or the scanner’s appliance connector is
accessible.
WARNING! The scanner weighs approximately 99 pounds (45
kg). To avoid potential injury, a minimum of two people are
needed to lift the scanner.
WARNING! Biohazardous Material. Do not operate the scanner
in an environment where potentially damaging liquids or gases
are present, or in a room with a temperature below 15° C.
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Installation
18 0112-0173 B
To unpack the scanner and position it on the bench
1. Open the crate and remove any foam blocks used to protect the
scanner from excessive shock and vibration during shipping.
CAUTION! Do not touch or loosen any screws or parts other than those
specifically described in the instructions. Doing so may cause
misalignment and voids the scanner warranty.
2. Lift the scanner using the molded lifting handgrips, and then
place the scanner on a flat level surface, away from direct
sunlight, dust, drafts, vibration, and moisture. Carefully move
the scanner to its final position.
Note: Do not tilt or slide the scanner when transferring it from
the crate to its final position on a bench or desk.
Table 2-1 Lifting handgrips
Item Name Description
1 Lifting handgrip Lifting handgrips are molded into
each side of the base of the
protective enclosure
1
1
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GenePix Microarray Scanner User Guide
0112-0173 B 19
3. Plug the USB cable into the USB type B port on the back of the
scanner, and the USB type A port on the control computer.
.
4. Plug the mains power cable into the port on the back of the
scanner, and the lab’s power outlet.
Molecular Devices recommends you use a surge protector
between the mains power cable and the power outlet.
Tip! For proper ventilation and cooling, leave at least six inches
of space between the back of the scanner and the nearest
object or surface.
Table 2-2 Connections on back of the scanner
Item Name
1 Mains power supply connection
2 USB type B port
12
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Installation
20 0112-0173 B
Installing the Software
Before operating the scanner, you must install the GenePix Pro
Microarray Software on a Windows based control computer.
To install the software
1. Locate the GenePix Pro Software CD.
2. Read the supplied software installation instructions.
3. Insert the GenePix Pro Software CD into the computer. Follow
the InstallShield Wizard instructions to install the GenePix Pro
Software.
CAUTION! Do not to insert the security key into the control computer
until after the GenePix Pro Software has been installed.
4. Install the security key. For more information, refer to the
GenePix®Pro Software Reference Guide included with the
GenePix Pro Software.
Note: You must be fully aware of the information contained in
the GenePix®Pro Software Reference Guide to ensure a
successful software installation. The installation instructions are
provided in hard copy, and soft copy on the GenePix®Pro
Software CD.
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