Applied Biosystems GeneAmp 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

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

i

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

ii

0.5-mL Sample Block
Module 1

Safety and Regulatory Information

General Symbols

IMPORTANT Read this section before you install the GeneAmp

the 0.5-mL Sample Block Module.

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.

®

PCR System 9700 and

~

~

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.

0.5-mL Sample Block Module 1-1

Non-electrical Symbols

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.

Electrical Safety

Testing

Instrument Labels

Routine safety testing of analytical instruments ( e.g. , high potential voltage testing)
may be required by various safety agencies.

Testing should only be carried out by qualified personnel after seeking
advice from the Applied Biosystems Service Department.

The following instrument labels are on the system 9700 with the 0.5-mL Sample Block
Module installed.

! WARNING !

circuit continuity is vital for safe operation of equipment. Ne ver 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 !

area to avoid being burned by hot components.

Attention. Surface chaude.

Disconnect supply cord before opening. Grounding

Hot Surface. Use care when working around this

1-2 0.5-mL Sample Block Module

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

\

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.

Environment, Humidity, and Temperature

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.

0.5-mL Sample Block Module 1-3

Sample Block Module

! WARNING !

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.

To protect yourself against burns, do not open the

Grounding and

Electrical Safety

Voltage Quality

Input/Output

Connections

Physical

Specifications

The system 9700 must be grounded for protection against electrical shock.

! WARNING !

this does not provide positive ground protection.

Refer to the GeneAmp

®

PCR System 9700 Base Module User’s Manual

Do not use an adapter to a two-terminal outlet since

(P/N 0993-6247) for more information on electrical safety.

Line voltage must be within

±

10% of the nominal value. High or low voltages may hav e
adverse effects on the electronic components of the instrument. In areas where the
supplied power is subject to fluctuations exceeding these limits , a pow er line regulator
may be required.

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.

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.

1-4 0.5-mL Sample Block Module

Pollution Category

Instrument Storage

Communautes

Europeennes (CE)

Compliance

FCC Compliance

(U.S.)

Routine

Maintenance for

Safe Operation

The system 9700 will operate safely in environments that contain nonconductive
foreign matter up to Pollution Degree 2 in IEC 1010-1.

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).

\

All instruments shipped to the European Union (EU; formerly known as the
European Community) have the CE label on the bac k of the instrument. This
label signifies that these instruments comply with the Electromagnetic
Compatibility and Low Voltage Directives.

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).

Before using any cleaning or decontamination method, e xcept 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.

0.5-mL Sample Block Module 1-5

Technical Support

To Reach Us on the

Web

Hours for Telephone

Technical Support

To Reach Us by

Telephone or Fax in

North America

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).

In the United States and Canada, technical support is available at the following times.

Product Hours

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LC/MS 9:00 a.m. to 5:00 p.m. Pacific Time
All Other Products 5:30 a.m. to 5:00 p.m. Pacific Time

See the “Regional Offices Sales and Service” section below for how to contact local
service representatives outside of the United States and Canada.

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.)

For Support On This Product Dial 1-800-831-6844, and...

®

RISM

ABI P

ABI P

3700 DNA Analyzer

®

RISM

3100 Genetic Analyzer

Press FAX
8 650-638-5891

Press FAX
26 650-638-5891

BioInformatics (includes BioLIMS
BioMerge

DNA Synthesis

Fluorescent DNA Sequencing

Fluorescent Fragment Analysis (includes
GeneScan

Integrated Thermal Cyclers

1-6 0.5-mL Sample Block Module

™

, and SQL GT

®

applications)

™

™

applications)

,

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

For Support On This Product Dial 1-800-831-6844, and...

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Press FAX
5, or call

1-800-762-4001,
and press 1 for
PCR, or 2 for
Sequence
Detection

240-453-4613

FMAT

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Telephone FAX

1-800-899-5858,
and press 1, then
press 6

Press FAX
31 650-638-5981

Press FAX
32 650-638-5981

Telephone FAX

1-800-542-2369
(U.S. only), or

1-781-271-0045
(Tropix)

Telephone FAX

1-800-952-4716 650-638-6223

508-383-7855

781-275-8581
(Tropix)

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5:00 p.m. ET

9:00 a.m. to
5:00 p.m. PT

Documents on

Demand

Free 24-hour access to Applied Biosystems technical documents, including MSDSs , is
available by fax or e-mail.

You can access Documents on Demand through the internet or by telephone:

If you want to
order... Then...

through the
internet

by phone from the
United States or
Canada

Use http://www.appliedbiosystems.com/techsupport
You can search for documents to order using keywords.
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a. Call 1-800-487-6809 from a touch-tone phone. Have your fax

number ready.

b. Press 1 to order an index of available documents and have it faxed

to you. Each document in the index has an ID number. (Use this as

your order number in step “d” below.)
c. Call 1-800-487-6809 from a touch-tone phone a second time.
d. Press 2 to order up to five documents and have them faxed to you.

0.5-mL Sample Block Module 1-7

If you want to
order... Then...

by phone from
outside the United
States and
Canada

a. Dial your international access code, then 1-858-712-0317 from a

touch-tone phone.

Have your complete fax number and country code ready (011
precedes the country code).

b. Press 1 to order an index of available documents and have it faxed

to you. Each document in the index has an ID number. (Use this as

your order number in step “d” below.)
c. Call 1-858-712-0317 from a touch-tone phone a second time.
d. Press 2 to order up to five documents and have them faxed to you.

To Reach Us by

E-Mail

Regional Offices

Sales and Service

Contact technical support by e-mail for help in the following product areas.

For this product area Use this e-mail address

Chemiluminescence [e-mail]
Genetic Analysis [e-mail]
LC/MS [e-mail]
PCR and Sequence Detection [e-mail]
Protein Sequencing, Peptide and DNA

Synthesis

[e-mail]

If you are outside the United States and Canada, you should contact your local
Applied Biosystems service representative.

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United States
Applied Biosystems
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Foster City, California 94404

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1-8 0.5-mL Sample Block Module

Europe

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Tel: [phone]

Fax: [phone]
United Kingdom (Warrington, Cheshire)

Tel: [phone]
Fax: [phone]

South East Europe (Zagreb, Croatia)
Tel: [phone]

Fax: [phone]
Africa (English Speaking) and West Asia

(Fairlands, South Africa)
Tel: [phone]

Fax: [phone]

Japan

Japan (Hatchobori, Chuo-Ku, Tokyo)
Tel: [phone]
Fax: [phone]

Eastern Asia, China, Oceania

Australia (Scoresby, Victoria)
Tel: [phone]

Fax: [phone]
China (Beijing)

T el: 86 10 6238 1156
Fax: [phone]

Malaysia (Petaling Jaya)
Tel: [phone]

Fax: [phone]
Singapore

Tel: [phone]
Fax: [phone]

0.5-mL Sample Block Module 1-9

Eastern Asia, China, Oceania

Hong Kong
Tel: [phone]

Fax: [phone]
Korea (Seoul)

Tel: [phone]
Fax: [phone]

Taiwan (Taipei Hsien)
Tel: [phone]

Fax: [phone]
Thailand (Bangkok)

Tel: [phone]
Fax: [phone]

1-10 0.5-mL Sample Block Module

About the 0.5-mL Sample Block Module

Overview

Diagram

The GeneAmp

®

PCR System 9700 amplifies nucleic acids using the polymerase
chain reaction (PCR) process. The 0.5-mL Sample Block Module attaches to the top
of the GeneAmp® PCR System 9700 Base Module and allows you to perf orm up to 60
reactions.

You can remove the 0.5-mL Sample Block Module and replace it with another sample
block module as needed. Interchangeability lets you change sample well formats as
well as throughput capacity.

IMPORTANT Interchanging sample block modules may require a firmware change. If the
sample block module is placed on a base module running an earlier software version, the
instrument will not operate correctly. To upgrade the base module software, use the 3.5” floppy
disk that is shipped with the 0.5-mL Sample Block Module. For instructions on upgrading the
software, see the GeneAmp
or visit our web site (www.appliedbiosystems.com/techsupport).

0.5-mL Sample
Block Module

System 9700
Base Module

®

PCR System 9700 Base Module User’s Manual (P/N 0993-6247)

Heated cover

Sample block

0.5-mL Sample Block Module 1-11