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
consumables. This document is copyright protected and any reproduction of this
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function as trademarks of their respective owners. Any such usage is intended only
to designate those manufacturers' products as supplied by Molecular Devices for
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or permit others to use such manufacturers' and/or their product names as
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equipment for any particular purpose and assumes no responsibility or contingent
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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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advertising without the prior written permission of Molecular Devices, Inc.
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GenePix 4100A Microarray Scanner User Guide
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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
[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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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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5000499 D 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®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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GenePix 4100A Microarray Scanner User Guide
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Scanner Specifications
Table 1-1 Specifications
Sample type Standard microscope slides (1 inch by 3 inches, 25
mm by 75 mm, or 26 mm by 76 mm; 0.9 to 1.2 mm
thick)
Maximum scan area 22 mm by 72 mm
Maximum resolution 5 μm
Scan mode and order Sequential scanning of up to two wavelengths
Detector Single PMT
Signal digital output 16-bit
Image format Single or multi-image TIFF
Computer interface USB 2.0
Scan time 6.5 minutes per channel for full size scan area at 10
μm resolution
Dynamic range Four orders of magnitude
Uniformity Plus or minus 5%
Dimensions 14 inches wide by 14 inches long by 11.5 inches high
(36 cm by 36 cm by 29 cm).
Weight 40 lb (18 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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Introduction
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Site Requirements
Table 1-2 Site Requirements
Temperature 50 to 86ºF (15 to 30ºC)
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 40 lbs (18 kg) with minimal vibration
Uninterruptible
power supply
(UPS)
We recommend the use of a 325 VA UPS
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2
Installation and Operation
The GenePix®4100A 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 4100A Microarray Scanner is packed in a specially designed crate.
Retain the crate and the packing materials. In the event the microarray
scanner requires repair, you must return it 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 main 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 40 pounds (18 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 and Operation
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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 can cause
misalignment and voids the scanner warranty.
2. Lift 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.
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.
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GenePix 4100A Microarray Scanner User Guide
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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 main power cable into the port on the back of the
scanner, and the lab’s power outlet.
We recommend you use a surge protector between the main
power cable and the power outlet.
Figure 2-1 Connections on back of the scanner
Item Name
1 USB type B port
2 Main power switch
3 Main power supply connection
1
3
2
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Installation and Operation
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Installing the Software
Before operating the scanner, you must install the GenePix Pro
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, see 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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GenePix 4100A Microarray Scanner User Guide
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Turning on the Scanner
Proper startup of the 4100A Microarray Scanner includes a functional
checkout procedure to confirm that the scanner is performing according
to the specifications established during commissioning before the
scanner left the factory.
To turn on the scanner
1. Make sure the slide door is closed.
2. Turn on the scanner power switch.
3. Turn on the control computer.
4. Click Start > Programs > Molecular Devices > GenePix
Pro, and then click the Report tab.
5. Click Functional Checkout in the Hardware Diagnostics
Reports area, and follow the steps in the Wizard.
The GenePix Pro Software automatically logs hardware
performance events into the Hardware Diagnostics Report every
two hours during operation.
Inserting a Slide
The slide holder is a precision component designed to ensure proper
focusing and field uniformity. Improper handling can damage the slide
holder and affect imaging performance.
CAUTION! Never touch the slide holder while it is moving. Never force
the slide holder closed, or apply significant pressure to it.
To insert a slide
1. Raise the slide door.
The slide holder moves forward into the load position.
2. Raise the top of the slider holder.
3. With the slide held between your thumb and finger, carefully
place the slide, feature-side down into the slide holder.
Note: For optimum performance, allow the 4100A Microarray
Scanner to warm up for 15 minutes before scanning slides with
the GenePix Pro Software.
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Installation and Operation
18 5000499 D
.
.
Note: Make sure the barcode on the slide is facing the
front of the scanner.
Figure 2-2 Slider holder
Ite
mName Description
1 Slide door In raised position
2 Slide holder In load position
3 Slide Place feature-side down
4 Barcode Barcode is facing the front of the scanner
2
3
4
1
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GenePix 4100A Microarray Scanner User Guide
5000499 D 19
4. Lower the top of the slide holder.
CAUTION! Make sure the top of the slide holder is lowered before
closing the slide door.
5. Close the slide door.
The slide holder moves into the scan position.
Shutting Down the Scanner
Proper shutdown of the 4100A Microarray Scanner ensures the scanner
or software are not damaged.
To shut down the scanner
1. Close the GenePix Pro Software.
2. Turn off the scanner power switch.
3. Turn off the control computer.
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Installation and Operation
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