05-0052 IQ5_GUIDE4-6-05.

qxp 4/6/2005 10:31 AM Page 2

iQ 5 ™

Multicolor Real-Time PCR

Detection System
Installation Guide
and System Manual
05-0052 IQ5_GUIDE4-6-05.qxp 4/6/2005 10:31 AM Page 3

The iQ5 Real-Time PCR Detection System

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Section 1
Safety Information
Important: Read this information carefully before using the iQ5 System.

Grounding
Always connect the iQ5 optics module to a three-prong, grounded AC outlet using the
AC power cord provided with the system. Do not use an adaptor to a two-terminal
outlet. Always ensure power switch is set to the off position when connecting or
disconnecting power cords for the iQ5 system.

Handling
Handle all components of the iQ5 system with care and with clean, dry hands at all
times. The optical system contains mirrors and lenses that may shatter if the unit is
dropped or struck with great force. If the unit is damaged, such that internal
components or wires are exposed, contact your local Bio-Rad office immediately, do
not attempt to repair or power on the instrument.

Service
The only user-serviceable parts of the iQ5 optics module are the lamp and filters. Call
your local Bio-Rad office for all other optics module and thermal cycler related service.
When replacing the lamp or filters, open only the outer casing of the iQ5 optics module.
The camera lamp may get extremely hot during system operation, do not attempt to
remove the lamp without powering off the instrument and allowing the system to cool
for at least 15 minutes. To prevent skin burns and fire hazards, do not attempt to
operate the iQ5 system while the camera case is open. Do not open the casing of
the iQ5 optics module when the instrument is in use.

Temperature
For normal operation, the maximum ambient temperature should not exceed 40°C
(see Appendix A for specifications). To ensure adequate cooling of the system,
maintain a clearance of at least 4 inches around the sides of the iQ5 optics module.
Do not block the fan vents near the lamp, as this may lead to improper operation or
cause physical damage to the iQ5 detector. Do not operate the iQ5 optics module in
extreme humidity (>90%) or where condensation can short internal electrical circuits or
fog optical elements.

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Notice
This Bio-Rad instrument is designed and certified to meet EN-61010 safety standards.
EN-61010-certified products are safe to use when operated in accordance with the
instruction manual. This instrument should not be modified in any way. Alteration of
this instrument will:
• Void the manufacturer’s warranty
• Void the EN-61010 safety certification
• Create a potential safety hazard
Bio-Rad is not responsible for any injury or damage caused by the use of this
instrument for purposes other than those for which it is intended, or by modifications
to the instrument not performed by Bio-Rad or an authorized agent.
The iCycler® thermal cycler and iQ5 real-time PCR detection system are intended for
laboratory research applications only.

~
~
!

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Section 2
iQ5 System Installation
2.1 Preparing for the Installation Process
The iQ5 system should be installed on a clean, dry, level surface. Identify an
appropriate work area for the installation process prior to unpacking any system
components. The entire installation process should take approximately 15 minutes
to complete.
System Checklist
❑ iQ5 Optics Module (170-9751), 1 box
❑ Power cord
❑ iQ5 optics module
❑ iQ5 software installation disk (170-9753)
❑ Amplification tech notes CD (version 1.0)
❑ iCycler Chassis (170-8701), 1 box
❑ Power cord
❑ iCycler chassis
❑ iCycler thermal cycler operating instructions
❑ iQ5 Optical Kit (170-9752), 1 box
❑ Optical reaction block
❑ Modified sliding rear cover for iCycler thermal cycler
❑ Serial cable
❑ USB cable
❑ Filter extraction tool
❑ Optical tape applicator tools (3)
❑ iQ5 optics support bracket
❑ Support bracket screws
❑ Hex driver
❑ Hex screws
❑ Spare part: halogen lamp
❑ iQ Calibration Kit (170-8792), shipped on dry ice
❑ External well factor solution
❑ 1x calibration dye solutions (9 dyes, 3 tubes of each dye)
Contact your local Bio-Rad office if any system components are missing or damaged.
In addition, the following accessories are required to complete the installation process:
• Scissors • Optical-quality sealing film or tube caps
• #2 Phillips screwdriver • Calibrated micropipet(s)
• Optical-quality PCR plates or tubes • Aerosol barrier pipet tips

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Handle the iQ5 optics module and iCycler thermal cycler with care and with clean, dry
hands during unpacking and assembly. Do not handle the iQ5 system components
with wet hands. Refer to Section 1 of this guide for additional safety information.
2.2 Installing the Optics Module on the iCycler Chassis
1. Remove the existing rear
cover from the iCycler chassis
by sliding the cover towards
the front of the iCycler base
(Figure 2.1).
2. Install the modified sliding
rear cover provided with the
optical reaction block,
ensuring that the notch is
oriented towards the rear of
the iCycler thermal cycler.
Fig. 2.1. Slide the rear cover forward to remove it.
3. Push the sliding rear cover on
top of the chassis as far back
as possible.
4. Rotate the green latches
on the optical reaction block
up towards the open lid.
5. Lift the optical reaction block
by the handle and install it
onto the chassis. Lower the
front portion of the reaction
block so that it engages
with the chassis before the
Fig. 2.2. Engage front portion of reaction block with
rear portion. The rear of the chassis.
block lid should fit over the
front lip of the sliding rear cover (Figure 2.2).
6. Secure the optical reaction block in place by rotating the green latches down-
ward.
7. Close the optical lid.

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2.3 Installing the

Support Bracket
A support bracket with roller is
provided for the iQ5 optics module.
It is mounted to the rear of the
iCycler thermal cycler as shown
in Figure 2.3.
Align the optics module support
bracket with the two holes on the
rear of the iCycler thermal cycler.
Using a #2 Phillips screwdriver,
Fig. 2.3. Secure the support bracket to the rear of the
adjust the height of the bracket iCycler chassis.
with two of the appropriate screws
provided with the system
accessories. Both of the screws
should be approximately in the
center of the slots on the bracket.
2.4 Installing the iQ5 Optics
Module
1. Remove the plastic sheath
and protective label from the
optics module and place the
optical module on a flat
surface, taking care not to
Fig. 2.4. Slide module onto U-bracket.
touch the inside of the nose
portion of the module.
2. Remove the protective label from the optical lid.
3. Slide the optics module onto the U-bracket as shown in Figure 2.4.
4. Secure the optics module to the U-bracket using the two long, thin hex screws
and the hex driver provided.
5. After the optics module has been installed, confirm that the optics module and lid
assembly can be opened and closed readily.
If the lid is difficult to open, lower the support bracket slightly before
tightening the bracket mounting screws.
If the lid is difficult to close, try raising the support bracket slightly before
tightening the rear screws.

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2.5 Connecting Power and Communication Cables to the iQ5 System

Before connecting any
communication or power cables to
the system, confirm that the power
switch for the iCycler thermal cycler
and the iQ5 optics module are in
the OFF position.
1. Close the optical reaction
block by sliding the lid forward
and pressing down on the lid
handle. On the right side of
the optics module are three
connectors (Figure 2.5). Fig. 2.5. Optics module connectors.

2. Using the cables provided in

the iQ5 Optical Kit, establish
power and communication
with the computer as follows:
Recessed 3-pin power
connector — Connect the
supplied power cord between the
optics module and a grounded
power outlet. This connection
provides power only to the optical
module; a separate power cord
must be connected to the iCycler Fig. 2.6. The serial connector.
thermal cycler.
Serial connector — A serial connector is located at the rear of the iCycler thermal
cycler (Figure 2.6). Connect the serial cable to the rear of the iCycler chassis and to
the serial port on the side of the iQ5 optics module. This connection enables
communication between the iQ5 software and the iCycler thermal cycler.
USB port connector — Connect the supplied USB cable between the iQ5 optics
module and a USB 2.0 high-speed enabled port on the computer. Data are
transferred to the computer via this cable. This single connection directs the operation
of both the iQ5 optics module and the iCycler thermal cycler by the iQ5 Optical
System Software.
At the right rear corner of the optical reaction block is a single connector:
Positive docking connector — This self-aligning connector is secured into place
when the iQ5 optics module is installed on the iCycler chassids. This connection
senses when the lid handle is lifted.

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2.6 Installing the iQ5 System Software

Locate the software installation disk provided with the iQ5 system. This installation
disk is compatible with computers running Windows XP and Windows 2000
operating systems.
1. Insert the iQ5 Optical System Software installation CD in a CD-ROM drive.
2. If the installation program does not begin automatically, select Run… from the
Start menu and then type “X:\Setup”, where X is the drive letter of the CD-ROM
drive. For example, if the CD-ROM is the E drive, type “E:\Setup”.
3. Follow all screen prompts to finalize the installation.
Certain configurations of Windows 2000 and XP initialize new folders by assigning
Read and Execute permission for the members of the Users group. If you have this
type of operating system and this is a first-time installation, the administrator must
change the protection on the Program Files/Bio-Rad folder or the Program Files/
Bio-Rad/iQ5 folder so that you can save protocol, plate setup, and data files.
If, after changing the protection on either of these folders, it is still not possible to
write to the folders beneath Program Files/Bio-Rad/iQ5, check the properties of each
individual folder to be sure that under the Securities tab, the box is checked that
allows inheritable permissions to propagate to that folder.
2.7 Initializing the iQ5 Instrument
Before using the iQ5 system for the first time, five procedures must be performed
on the new instrument: Camera Driver Installation, Mask Alignment, Background
Calibration, Persistent Well Factor Collection, and Pure Dye Calibration.
1. Power on the iCycler thermal cycler and the iQ5 optics module.
2. Follow all screen prompts to finalize the camera driver installation.
3. Allow the instrument optics to warm up for 20 min prior to performing
the Mask Alignment, Background Calibration, Persistent Well Factor Collection, or
Pure Dye Calibration procedures.
4. Open the iQ5 system software by double-clicking on the shortcut icon
located on the Windows desktop, or by selecting the iQ5 program icon from the
Bio-Rad folder of the Windows Start menu.
Refer to the Help section of the iQ5 Optical System Software for detailed directions on
the procedures and materials required to perform Mask Alignment, Background
Calibration, Persistent Well Factor Collection, and Pure Dye Calibration.

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Section 3
iQ5 Optical System Components
The optics module houses the excitation system and the detection system
(Figure 3.1). The excitation system consists of a fan-cooled, 50 W tungsten-halogen
lamp, a heat filter (infrared-absorbing glass), a six-position filter wheel fitted with five
optical filters and one opaque filter “blank”, and a dual mirror arrangement that allows
simultaneous illumination of the entire sample plate. The excitation system is physically
located on the right front corner of the optics module, with the lamp shining from
right to left, perpendicular to the instrument axis. Light originates at the lamp, passes
through the heat filter and a selected color filter, and is then reflected onto the 96-well
plate in the thermal cycler by a set of mirrors. This light source excites the fluorescent
molecules in the wells.

CCD

CCD lens
Excitation
Emitter filter wheel
filter wheel
IR filter

Lamp

Mirror

Lid lens

Heater glass

Sample

Fig. 3.1. Representation of the optical system layout. The detection system occupies the rear portion of
the optics module housing. The primary detection components include a six-position emission filter wheel
and a CCD detector. The emission filter wheel is identical to the wheel in the excitation system and is fitted
with five colored-emission filters and one opaque filter “blank”. Fluorescent light from the wells passes
through the emission filter and is then detected by the CCD.

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Appendix A
iQ5 System Specifications
Input power 100–250 VAC ± 10%, 50–60 Hz, 250 W max, 95 W typical
Operating temperature 5–40°C
Storage temperature –20 to 40°C
Humidity 0–90%, noncondensing
Dimensions, optics module 29.3 x 38.74 x 20.3 cm (11.5 x 15.25 x 8.75")
(W x D x H)
Weight, optics module 6.3 kg (13.9 lb)
Data communication USB 2.0 high speed
Regulatory compliance EN-61010, NRTL

Appendix B
Computer Specifications
A computer with the following system specifications is required to run the
iQ5 real-time PCR detection system.
Minimum Computer Specifications
• Pentium or comparable processor, 1.0 GHz or faster
• Windows 2000 or Windows XP operating system
• Internet Explorer browser (version 5.0 or higher)
• 512 MB RAM
• 10 GB hard drive
• CD-ROM drive
• Mouse
• 1,024 x 768 x 256 colors minimum screen resolution
• USB 2.0 high-speed communications port
Recommended Computer Specifications
To ensure optimal performance of the iQ5 system and software, connect the iQ5
instrument to a computer with the following specifications:
• Pentium or comparable processor, 2.0 GHz or faster
• Windows XP operating system
• Internet Explorer browser (version 5.0 or higher)
• 512 MB RAM
• 20 GB hard drive
• CD-RW drive
• Mouse

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• 1,024 x 768 x 256 colors minimum screen resolution

• At least 4 USB 2.0 high-speed communications ports
The following system accessories are also recommended:
• USB-compatible color printer
• Excel software
• High-speed modem with an Internet connection (suggested for downloading
new releases)
• Uninterruptible power supply: at least 1,000 W for the base iCycler thermal cycler,
650 W for the computer, and 250 W for the iQ5 module

Appendix C
Ordering Information
Catalog # Description
System Configuration
170-8701 iCycler Chassis, includes iCycler base, power cord, quick reference
cards, instruction manual
170-9750 iQ5 Optical System, includes optics module, software CD-ROM,
5 installed filter sets, 96-well reaction module, calibration solutions,
optical-quality 96-well PCR plates, communication cables, power cord,
instruction manual
Accessories
223-9441 96-Well 0.2 ml Thin-Wall PCR Plates, 25
223-9443 96-Well 0.2 ml PCR Plate Caps, for 223-9441, 300
223-9444 Optical-Quality Sealing Tape, optimized for use with 223-9441,
100 sheets
170-8756 Replacement Halogen Lamp
170-9753 iQ5 Software Installation Disk
170-9761 iQ5 Filter Set, FAM/SYBR dyes
170-9762 iQ5 Filter Set, VIC/HEX/TET dyes
170-9763 iQ5 Filter Set, Cy3/TAMRA dyes
170-9764 iQ5 Filter Set, ROX/Texas Red dyes
170-9765 iQ5 Filter Set, Cy5 dyes
Calibration Solutions
170-8792 iCycler iQ Calibration Kit, shipped on dry ice
170-8794 External Well Factor Solution
170-8793 FAM Calibrator Solution, 1.5 ml tubes, 5
170-8795 HEX Calibrator Solution, 1.5 ml tubes, 5
170-8797 Cy5 Calibrator Solution, 1.5 ml tubes, 5
170-8799 Texas Red Calibrator Solution, 1.5 ml tubes, 5

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Appendix D
Care and Maintenance
Cleaning the Unit
Take care not to spill liquids onto or into the iCycler thermal cycler or the iQ5 optics
module.
The outer casing of the instrument may be cleaned using a soft, lint-free cloth
and water.
Replacing the Lamp
Before replacing the lamp, turn the instrument off and allow it to cool for at
least 15 min.
The lamp is located on the right side of the optics module, (Figure D.1).
To replace the lamp:
1. Turn off the power to the optics module.
2. Reach behind the iQ5 optics module and unscrew the short fastener that secures
the lid of the module in place.
3. Using a gentle pressure with both hands, push inward on the rear vents located
on the top half of the iQ5 casing. Lift upward to remove the cover of the optics
module.
4. Push up on the lamp spring
clip to release the lamp from
the bracket.
5. Lift the lamp out of the socket.
6. Install the new lamp using the
reverse of steps 1–5. Hold the
new lamp by the outer
reflector and do not touch the
bulb. Be sure the spring clip is
down before inserting the
lamp into the socket. Push the
lamp firmly into the bracket, Fig. D.1. Replacing the lamp.
then close the case and
secure the lid.

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iQ5 Filter Description and Installation Instructions

The filters designed for use in the
iQ5 optics module are made of
glass and mounted in plastic holders
(see Figure D.2). The filter holders
are held in either the excitation or
emission filter wheel of the iQ5
optics module. Each filter wheel
holds six filters. Every position in a
filter wheel must have a filter or an
opaque filter blank to avoid damage
to the CCD detector. The first
position in each filter wheel is
designated as the "home" position
Fig. D.2. Filter in filter holder.
and must always contain an
opaque filter blank. Filters can be removed for cleaning or replacement. If a filter
shatters or breaks during the installation process, contact your local Bio-Rad office
immediately for service, do not attempt to remove the broken components from the
interior of the camera housing.
It is critically important that the excitation and emission filters are in the
correct positions in the filter wheels, please confirm that the filters are in the
proper location after cleaning or replacing filters in the iQ5 optics module.
The table below summarizes the positions of the filter pairs, their optical characteristics, and
the recommended fluorophores with which they are compatible.
Position Excitation Emission Recommended Fluorophores
2 490/20X 530/30M Fluorescein (FAM),SYBR Green I
3 530/30X 575/20M HEX, TET, VIC, JOE
4 545/30X 585/20M TAMRA/Cy3
5 575/30X 620/30M Texas Red, ROX
6 635/30X 680/30M Cy5, LC640
Note: The filter designation 490/20X indicates that this filter will allow light between 480
and 500 nm to pass through. The first number, 490, indicates the center of the wavelength
of light. The second number, 20 indicates the total breadth of wavelengths of light that can
pass through it. The letter "X" indicates that the filter is specified for excitation only, and the
letter "M" indicates emission only types of filters. Excitation and emission filters are not
interchangeable.

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To access the existing filters, proceed as follows:

1. Turn off the power to the optics module.
2. Reach behind the iQ5 optics module and unscrew the short fastener that secures
the lid of the module in place.
3. Using gentle pressure and both hands, push inward on the rear vents
located on the top half of the iQ5 casing. Lift upward to remove the cover
of the optics module.
4. To access the excitation filter
wheel, remove the black plug
from the slot located near the
lamp, at the right-hand side of
the optics module. To access
the emission filter wheel,
remove the plug from the slot
located at the top of the
instrument (see Figure D.3).
5. Turn the filter wheels to the
desired positions using the
Fig. D.3. Installing the filter.
supplied ball-end hex
driver. As long as the power to the optics module is off, the filter wheels may be
turned freely in either direction.
6. To remove a filter, grasp it on both sides with the filter removal pliers and squeeze
the tab in; gently pull the filter up and out.
7. To insert a filter, grasp the filter with the pliers and insert it into a vacant slot. For
the excitation filters, the tab on the filter should face toward the front of the
instrument. For the emission filters, the tab on the filter should face the right of
the instrument. Be sure that every position in the filter wheel has either an
excitation or emission filter or a filter blank before powering on the system.
8. After the filters or filter blanks have been inserted, replace the rubber plugs over
the slots of the filter wheels.
9. Realign the tabs on the front end of the iQ5 optics module cover with the tabs on
the main housing. Lower the cover until the top half of the camera housing snaps
into place.
10. Replace the screw in the rear of the optics module to secure the casing.

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Appendix E
Installing New Versions of Firmware
Bio-Rad is committed to continuous improvement in iCycler features. Towards that
end, the iCycler firmware will be upgraded to offer new features on a regular basis.
We will make a firmware upgrade disk available at the time of each new release
and announce the release on our web site, discover.bio-rad.com. The iCycler
thermal cycler is upgraded via a serial port connection to a PC computer, or via a
serial port pass-through with the iQ5 USB connection. The computer serial port
must support a 57,600 baud rate. The connection may be made with a standard
9-pin serial cable. The iCycler firmware upgrade kit may be ordered from Bio-Rad
using part number 170-8737.

Upgrading the iCycler Firmware

A recent version of the iCycler firmware and a related utility are contained on the
iQ5 software installation CD provided with the iQ5 system. To complete a firmware
upgrade of older iCycler instruments, follow the directions below to copy the iCycler
upgrade files from installation CD to the computer connected to the iQ5 system.
1. Connect the 9-pin serial cable from the serial port located at the rear of the
iCycler instrument to the iQ5 optics module, ensuring that the iQ5 optics module
is connected to a computer via USB.
2. Close any other application that may have already established communication
with the iCycler base unit (for example, IQ5.EXE or the iCycler report
utility software).
3. Use Windows Explorer to create a new folder on the C: drive. Name this new
folder “PC Firmware Upgrade”.
4. Open the CD directory \base unit\firmware upgrade and copy the files
UPGRADE.EXE and ICYCPROG.BIN to the Firmware Upgrade folder
created in step 3.
5. From Windows Explorer, open the Firmware Upgrade folder now located on the
C: drive and double-click on UPGRADE.EXE. The utility will open and establish
communication with the iCycler instrument through the serial port connection
bridged by the iQ5 optics module.
6. Each new version of firmware is assigned a higher version number than the
previous version. The UPGRADE.EXE utility will detect the version number of the
installed firmware and display this information for comparison to the version ready
for download. Download of a new firmware program will not proceed until the
user enters “y” after reviewing the firmware version information.

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The upgrade utility will display the following information:

Old program version: _____
New program version: _____
Proceed with download? y / n
Enter “y” to proceed with the download if the new program version has a
HIGHER number than the old program version before proceeding with download.
Enter “n” if the new program version is the same or LOWER than the old
program version. Entering “n” will exit and close the UPGRADE.EXE utility.
Once the download is complete, the UPGRADE.EXE utility will display a
message confirming that the upgrade has been successfully completed.
The UPGRADE.EXE utility will automatically shut down and restart the iCycler
instrument in order to complete the installation of the new firmware.

Appendix F
System Warranty
The iQ5 real-time PCR detection system is warranted against defects in materials and
workmanship. For specific warranty information, contact your local Bio-Rad office.
If any defects should occur during the warranty period, Bio-Rad will replace the
defective parts without charge. However, damage or defects resulting from any of the
following causes are specifically excluded:
1. Improper operation.
2. Use of improper solvent or sample.
3. Use with tubes, plates, or sealing materials not specified by Bio-Rad Laboratories
for use with the iQ5 real-time PCR detection system.
4. Deliberate or accidental misuse.
5. Repair or modifications done by anyone other than Bio-Rad Laboratories.
6. Natural disaster of any kind.
The warranty does not apply to fuses.
For inquiry or request for repair service, contact Bio-Rad Laboratories after confirming
the model and serial number of your instrument. For technical support, call your local
Bio-Rad office, or in the US, call 1-800-4BIORAD (1-800-424-6723), or visit us on the
Web at discover.bio-rad.com

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Appendix G
iCycler® Thermal Cycler Authorization Statement
This instrument, Serial No. ________________, is an Authorized Thermal Cycler.
Its purchase price includes the up-front fee component of a license under United
States Patent Nos. 4,683,195, 4,683,202 and 4,965,188, owned by Roche Molecular
Systems, Inc., and under corresponding claims in patents outside the United States,
owned by F. Hoffmann-La Roche Ltd, covering the Polymerase Chain Reaction
(“PCR”) process, to practice the PCR process for internal research and development
using this instrument. The running royalty component of that license may be
purchased from Applied Biosystems or obtained by purchasing Authorized Reagents.
This instrument is also an Authorized Thermal Cycler for use with applications licenses
available from Applied Biosystems. Its use with Authorized Reagents also provides a
limited PCR license in accordance with the label rights accompanying such reagents.
Purchase of this product does not itself convey to the purchaser a complete license
or right to perform the PCR process. Further information on purchasing licenses to
practice the PCR process may be obtained by contacting the Director of Licensing,
Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California 94404, USA.
No rights are conveyed expressly, by implication or estoppel to any patents on
real-time PCR.
Applied Biosystems does not guarantee the performance of this instrument.

Cy is a trademark of Amersham Biosciences. Excel, Internet Explorer, Windows, and Windows 2000 and XP
are trademarks of Microsoft Corporation. Pentium is a trademark of Intel Corporation. Phillips is a trademark of
Phillips Screw Company Corporation. SYBR and Texas Red are trademarks of Molecular Probes, Inc.

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05-0052 IQ5_GUIDE4-6-05.qxp 4/6/2005 10:31 AM Page 1

Bio-Rad
Laboratories, Inc.

Life Science Web site www.bio-rad.com USA (800) 4BIORAD Australia 02 9914 2800
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