GeneAmp PCR System 9700 User manual

GeneAmp®PCR System 9700
0.5mL Sample Block Module
User’s Manual

© Copyright 2006, 2010 Applied Biosystems. All rights reserved.
Information in this document is subject to change without notice. Applied Biosystems assumes no responsibility for any errors that may appear in this
document.
APPLIED BIOSYSTEMS DISCLAIMS ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT, EXPRESSED OR IMPLIED, INCLUDING
BUT NOT LIMITED TO THOSE OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. IN NO EVENT SHALL APPLIED
BIOSYSTEMS BE LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY, OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR
SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING
FROM THIS DOCUMENT, INCLUDING BUT NOT LIMITED TO THE USE THEREOF.
NOTICE TO PURCHASER:LIMITED LICENSE
The combination of the GeneAmp®PCR System 9700 Sample Block Module with a GeneAmp®PCR System 9700 Base Unit is licensed under patent
claims for thermal cycler apparatus and counterpart patent claims in other countries. No other rights are conveyed expressly, by implication, or by
estoppel. Further information on purchasing licenses may be obtained by contacting the Director of Licensing, Aplied Biosystems, 850 Lincoln Centre
Drive, Foster City, California 94404, USA.
TRADEMARKS:
AB (Design), Applied Biosystems, and MicroAmp are registered trademarks, Applera and Celera Genomics are trademarks of Applera Corporation or
its subsidiaries in the U.S. and/or certain other countries.
GeneAmp is a registered trademark of Roche Molecular Systems, Inc.
All other trademarks are the sole property of their respective owners.
Part Number 4307808 Rev. D
06/2010

Contents
i
1 0.5-mL Sample Block Module
Safety and Regulatory Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
General Symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
Electrical Safety Testing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
Instrument Labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
Operating Precautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-3
Precautions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-3
Grounding and Electrical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4
Voltage Quality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4
Input/Output Connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4
Physical Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4
Pollution Category. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-5
Instrument Storage. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-5
Communautes Europeennes (CE) Compliance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-5
FCC Compliance (U.S.). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-5
Routine Maintenance for Safe Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-5
Technical Support. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-6
To Reach Us On the Web. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-6
Hours for Telephone Technical Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-6
To Reach Us by Telephone or Fax in North America . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-6
Documents-on-Demand. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-7
To Reach Us by E-Mail . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-8
Regional Offices Sales and Service. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-8
About the 0.5-mL Sample Block Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-11
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-11
Diagram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-11
Sample Block. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-12
Heated Cover . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-13
Peltier Heating/ Cooling Unit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-13
Modules, Accessories, and Disposables. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-14
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-14
Ordering. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-14
Installing the 0.5-mL Sample Block Module. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-15
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-15
Installing the Sample Block Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-16
Loading Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-17
Loading Samples: Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-17
Reaction Tube/Frame Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-17

ii
Loading Samples into the Reaction Tubes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-17
Placing the Reaction Tubes into the Sample Block . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-18
Cleaning the Sample Block Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-19
Cleaning: Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-19
Cleaning Position . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-19
Cleaning the Heated Cover. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-19
Cleaning the Sample Block Wells. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-20
Running the Calibration Verification Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-21
Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-21
Equipment Required . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-21
Setting Up the 0.5-mL Probe Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-22
Configuring the System 9700 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-23
Running the Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-24
Evaluating the Results. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-26
Running the Temperature Non-Uniformity Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-27
Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-27
Equipment Required . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-27
Setting Up the 0.5-mL Probe Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-28
Configuring the System 9700 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-29
Running the Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-30
Evaluating the Results. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-33
Running System Performance Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-34
Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-34
Equipment Required . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-34
Running the Rate Test. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-34
Running the Cycle Test. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-36
Data Sheet: Calibration Verification Test. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-38
Instructions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-38
Data Sheet: Temperature Non-Uniformity Test. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-39
Instructions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-39
Index

0.5-mL Sample Block Module 1-1
0.5-mL Sample Block
Module 1
Safety and Regulatory Information
IMPORTANT Read this section before you install the GeneAmp
®
PCR System 9700 and
the 0.5-mL Sample Block Module.
General Symbols
The following symbols are used on Applied Biosystems instruments.Whenever such
symbols appear on instruments, please observe appropriate safety procedures.
Electrical Symbols
This symbol indicates the on position of the main power switch.
This symbol indicates the off position of the main power switch.
This symbol indicates the on/off position of a push-push main power switch.
This symbol indicates that a terminal may be connected to another
instrument’s signal ground reference.
This is not a protected ground terminal.
This symbol indicates that this is a protected ground terminal that must be
connected to earth ground before any other electrical connections are made
to the instrument.
This symbol indicates that this terminal either receives or delivers alternating
current or voltage.
This symbol indicates that this terminal either receives or delivers alternating
and direct current or voltage.
~
~

1-2 0.5-mL Sample Block Module
Non-electrical Symbols
Electrical Safety
Testing
Routine safety testing of analytical instruments ( e.g. , high potential voltage testing)
may be required by various safety agencies.
Instrument Labels
The following instrument labels are on the system 9700 with the 0.5-mL Sample Block
Module installed.
This symbol indicates the presence of high voltage and warns the user to
proceed with caution.
This symbol alerts you to consult the manual for further information and to
proceed with caution.
This symbol illustrates a heater hazard.Proceed with caution when working
around these areas to avoid being burned by hot components.
Testing should only be carried out by qualified personnel after seeking
advice from the Applied Biosystems Service Department.
! WARNING !
Disconnect supply cord before opening. Grounding
circuit continuity is vital for safe operation of equipment. Never operate
equipment with grounding conductor disconnected.
AVERTISSEMENT: Debrancher le cordon d’alimentation avant d’ouvrir la
continuite des masses est essentielle.
Pour un fonctionnement sans danger. Ne jamais utiliser l’equipment si le fil
de terre n’est pas raccorde.
\
! WARNING ! Hot Surface. Use care when working around this
area to avoid being burned by hot components.
Attention. Surface chaude.

0.5-mL Sample Block Module 1-3
Operating Precautions
Precautions
The following precautions should be taken whenever you operate the system 9700
with the 0.5-mL Sample Block Module installed.
Note This instrument is able to withstand transient overvoltage according to Installation
Category II as defined in IEC 1010-1.
General Use
Environment, Humidity, and Temperature
\
CAUTION The instrument should be used according to the
instructions provided in this manual. If used otherwise, the protection
provided by this instrument may be impaired.
CAUTION This instrument is designed for indoor use.
CAUTION Do not operate in a Cold Room or a refrigerated area.
The system 9700 will operate safely when the ambient temperature is
5–40 °C (41–104 °F).The system 9700 will meet performance
specifications when the ambient temperature is 15–30 °C and the
ambient relative humidity is 20–80%.These specifications have been
calculated for altitudes between 0 and 2,000 meters.
CAUTION This instrument is not designed for operation in an
explosive environment. Do not place the instrument close to
potentially explosive materials or objects.
CAUTION This instrument is not designed for operation with the
heated cover retracted when running at 4 °C. If the heated cover is
retracted and the instrument runs at 4 °C, water condensation may
be excessive in the sample block area.

1-4 0.5-mL Sample Block Module
Sample Block Module
Grounding and
Electrical Safety
The system 9700 must be grounded for protection against electrical shock.
Refer to the GeneAmp
®
PCR System 9700 Base Module User’s Manual
(P/N 0993-6247) for more information on electrical safety.
Voltage Quality
Line voltage must be within
±
10% of the nominal value.High or low voltages may have
adverse effects on the electronic components of the instrument. In areas where the
supplied power is subject to fluctuations exceeding these limits, a power line regulator
may be required.
Input/Output
Connections
Refer to the GeneAmp
®
PCR System 9700 Base Module User’s Manual
(P/N 0993-6247) for information on the input and output connections of this
instrument.
Physical
Specifications
Refer to the GeneAmp
®
PCR System 9700 Base Module User’s Manual
(P/N 0993-6247) for information on the physical specifications of this instrument.
! WARNING !
To protect yourself against burns, do not open the
heated cover or touch the sample block module when the word Hot
displays on the screen.This indicates a sample block temperature
above 50 °C.
The hot areas for the 0.5-mL Sample Block Module are shown below.
\
CAUTION To protect your samples and to guarantee the best
temperature uniformity, keep the heated cover closed at all times,
except when loading or unloading samples.
! WARNING !
Do not use an adapter to a two-terminal outlet since
this does not provide positive ground protection.

0.5-mL Sample Block Module 1-5
Pollution Category
The system 9700 will operate safely in environments that contain nonconductive
foreign matter up to Pollution Degree 2 in IEC 1010-1.
Instrument Storage
The system 9700 must be stored at a temperature between -20 °C and 60 °C
(-4 °F and 140 °F) at altitudes ranging from 0–12,000 meters above sea level.
IMPORTANT The system 9700 is guaranteed to meet performance specifications only
when the ambient temperature is 15–30 °C and the ambient relative humidity is 20–80%
(between altitudes of 0 and 2,000 meters).
Communautes
Europeennes (CE)
Compliance
FCC Compliance
(U.S.)
This product is classified as a digital device used exclusively as industrial,
commercial, or medical test equipment. It is exempt from the technical standards
specified in Part 15 of the FCC Rules and Regulations, based on Section 15.103(c).
Routine
Maintenance for
Safe Operation
Before using any cleaning or decontamination method, except those recommended in
the manual, the user should check with Applied Biosystems to ensure that the
proposed method will not damage the equipment.
Maintain your instrument in good working order.In the event that the instrument has
been subjected to adverse environmental conditions (such as fire, flood, earthquake,
etc.), a service inspection of the instrument should be made to ensure safe operation.
\
All instruments shipped to the European Union (EU; formerly known as the
European Community) have the CE label on the back of the instrument.This
label signifies that these instruments comply with the Electromagnetic
Compatibility and Low Voltage Directives.

1-6 0.5-mL Sample Block Module
Technical Support
To Reach Us on the
Web
Applied Biosystems web site address is:
http://www.appliedbiosystems.com/techsupport
We strongly encourage you to visit our web site for answers to frequently asked
questions, and to learn more about our products.You can also order technical
documents and/or an index of available documents and have them faxed or e-mailed
to you through our site (see the “Documents on Demand” section below).
Hours for Telephone
Technical Support
In the United States and Canada, technical support is available at the following times.
See the “Regional Offices Sales and Service” section below for how to contact local
service representatives outside of the United States and Canada.
To Reach Us by
Telephone or Fax in
North America
Call Technical Support at 1-800-831-6844, and select the appropriate option (below)
for support on the product of your choice at any time during the call. (To open a
service call for other support needs, or in case of an emergency, press 1 after dialing
1-800-831-6844.)
Product Hours
Chemiluminescence 9:00 a.m. to 5:00 p.m. Eastern Time
LC/MS 9:00 a.m. to 5:00 p.m. PacificTime
All Other Products 5:30 a.m. to 5:00 p.m. PacificTime
For Support OnThis Product Dial 1-800-831-6844, and...
ABI P
RISM
®
3700 DNA Analyzer
ABI P
RISM
®
3100 Genetic Analyzer
BioInformatics (includes BioLIMS
™
,
BioMerge
™
, and SQL GT
™
applications)
DNA Synthesis
Fluorescent DNA Sequencing
Fluorescent Fragment Analysis (includes
GeneScan
®
applications)
Integrated Thermal Cyclers
Press FAX
8650-638-5891
Press FAX
26 650-638-5891
Press FAX
25 505-982-7690
Press FAX
21 650-638-5981
Press FAX
22 650-638-5891
Press FAX
23 650-638-5891
Press FAX
24 650-638-5891