Applied Biosystems

GeneAmp® PCR System 9700

Auto-Lid Dual 96 Sample Block Module and
Dual 96 Sample Block Module

User Guide
© Copyright 2003, Applied Biosystems. All rights reserved.
For Research Use Only. Not for use in diagnostic procedures.
Information in this document is subject to change without notice. Applied Biosystems assumes no responsibility for any errors that may appear in this document. This
document is believed to be complete and accurate at the time of publication. In no event shall Applied Biosystems be liable for incidental, special, multiple, or
consequential damages in connection with or arising from the use of this document.
The combination of the Dual 96 and Auto-Lid Dual 96 Interchangeable Sample Block Modules with a GeneAmp® PCR System 9700 Base Unit is licensed under the
thermal cycler apparatus claims of U.S. Patent No. 5,333,675 and counterpart patent claims in other countries.
Patents are pending on the Auto-Lid mechanism.
TRADEMARKS:
ABI PRISM, Applied Biosystems, and MicroAmp are registered trademarks of Applera Corporation or its subsidiaries in the U.S. and/or certain other countries.
AB (Design) and Applera 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 4343363 Rev. B

06/2003

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Contents

Preface
How to Use This Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
How to Obtain More Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vi
How to Obtain Services and Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vi

Safety and EMC Compliance Information

Safety Conventions Used in This Document . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . viii
Symbols on Instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
Safety Labels on Instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
General Instrument Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi
Chemical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi
Chemical Waste Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiii
Electrical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiv
Physical Hazard Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiv
Workstation Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
Safety and Electromagnetic Compatibility (EMC) Standards . . . . . . . . . . . . . . . . . . . . . xvi

Chapter 1 Dual 96 Sample Block Module Overview

About the Dual 96 Sample Block Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
Installing the Dual 96 Sample Block Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-8
Sample Tray and Plate Configurations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-10
Loading Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-12

Chapter 2 Maintaining the Sample Block Module

Cleaning the Sample Block Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
Fixing an Auto-Lid Jam . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-4

Chapter 3 Testing the Dual 96 Sample Block Module

Performing the Calibration Verification Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Performing the Temperature Non-Uniformity Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-8
Performing System Performance Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-15

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Index

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Preface

How to Use This Guide

Purpose of This The Applied Biosystems GeneAmp® PCR System 9700 Auto-Lid Dual 96 Sample
Guide Block Module and Dual 96 Sample Block Module User Guide provides the
information you need to operate the Dual 96 Sample Block Module with the
automatic or manual lid.

Audience This guide is intended for novice and experienced GeneAmp® PCR System 9700
users who incorporate either the Auto-Lid Dual 96 Sample Block Module or the
manual Dual 96 Sample Block module.

Text Conventions This guide uses the following conventions:

• Bold indicates user action. For example:
Type 0, then press Enter for each of the remaining fields.
• Italic text indicates new or important words and is also used for emphasis. For
example:
Before analyzing, always prepare fresh matrix.
• A right arrow bracket (>) separates successive commands you select from a
drop-down or shortcut menu. For example:
Select File > Open > Spot Set.
Right-click the sample row, then select View Filter > View All Runs.

User Attention Two user attention words appear in Applied Biosystems user documentation. Each
Words word implies a particular level of observation or action as described below:
Note: Provides information that may be of interest or help but is not critical to the
use of the product.
IMPORTANT! Provides information that is necessary for proper instrument
operation, accurate chemistry kit use, or safe use of a chemical.
Examples of the user attention words appear below:
Note: The size of the column affects the run time.
Note: The Calibrate function is also available in the Control Console.
IMPORTANT! To verify your client connection to the database, you need a valid
Oracle user ID and password.
IMPORTANT! You must create a separate Sample Entry Spreadsheet for each 96-well
microtiter plate.

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 Preface

Safety Alert Safety alert words also appear in user documentation. For more information, see
Words “Safety Alert Words” on page viii.

How to Obtain More Information

Related The following related documents are shipped with the system:
Documentation • GeneAmp® PCR System 9700 Base Module User's Manual – Describes the
GeneAmp PCR System 9700 hardware and software and provides information
on preparing, maintaining, and troubleshooting the system.
• GeneAmp® PCR System 9700 Quick Reference Guide Set – The Quick
Reference Guide provides the fundamentals of preparing and starting a run and
working with methods.
Portable document format (PDF) versions of supporting documents are also available
on the CD shipped with the system.
Note: For additional documentation, see “How to Obtain Services and Support” on
page vi.

Send Us Your Applied Biosystems welcomes your comments and suggestions for improving its
Comments user documents. You can e-mail your comments to:
[email protected]

How to Obtain Services and Support

For the latest services and support information for all locations, go to
http://www.appliedbiosystems.com, then click the link for Services and Support.
At the Services and Support page, you can:
• Search through frequently asked questions (FAQs)
• Submit a question directly to Technical Support
• Order Applied Biosystems user documents, MSDSs, certificates of analysis,
and other related documents
• Download PDF documents
• Obtain information about customer training
• Download software updates and patches
In addition, the Services and Support page provides access to worldwide telephone
and fax numbers to contact Applied Biosystems Technical Support and Sales
facilities.

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Safety and EMC Compliance Information

This section includes the following topics:

Safety Conventions Used in This Document . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Symbols on Instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . viii
Safety Labels on Instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
General Instrument Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Chemical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
Chemical Waste Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xii
Electrical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiii
Physical Hazard Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiii
Workstation Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiv
Safety and Electromagnetic Compatibility (EMC) Standards . . . . . . . . . . . . . . . . xv

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Safety and EMC Compliance Information

Safety Conventions Used in This Document

Safety Alert Four safety alert words appear in Applied Biosystems user documentation at points
Words in the document where you need to be aware of relevant hazards. Each alert
word–IMPORTANT, CAUTION, WARNING, DANGER–implies a particular
level of observation or action, as defined below:

Definitions
IMPORTANT! – Indicates information that is necessary for proper instrument
operation, accurate chemistry kit use, or safe use of a chemical.

– Indicates a potentially hazardous situation that, if not avoided,

may result in minor or moderate injury. It may also be used to alert against unsafe
practices.

– Indicates a potentially hazardous situation that, if not avoided,

could result in death or serious injury.

– Indicates an imminently hazardous situation that, if not avoided,

will result in death or serious injury. This signal word is to be limited to the most
extreme situations.
Except for IMPORTANTs, each safety alert word in an Applied Biosystems
document appears with an open triangle figure that contains a hazard symbol. These
hazard symbols are identical to the hazard icons that are affixed to Applied
Biosystems instruments (see “Safety Symbols” on page ix).

Examples
The following examples show the use of safety alert words:
IMPORTANT! You must create a separate a Sample Entry Spreadsheet for each
96-well microtiter plate.

The lamp is extremely hot. Do not touch the lamp until it has
cooled to room temperature.

CHEMICAL HAZARD. Formamide. Exposure causes eye,

skin, and respiratory tract irritation. It is a possible developmental and birth defect
hazard. Read the MSDS, and follow the handling instructions. Wear appropriate
protective eyewear, clothing, and gloves.

ELECTRICAL HAZARD. Failure to ground the instrument

properly can lead to an electrical shock. Ground the instrument according to the
provided instructions.

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 Symbols on Instruments

Symbols on Instruments
Electrical The following table describes the electrical symbols that may be displayed on
Symbols on Applied Biosystems instruments.
Instruments
Symbol Description

Indicates the On position of the main power switch.

Indicates the Off position of the main power switch.

Indicates the On/Off position of a push-push main power switch.

Indicates a terminal that may be connected to the signal ground reference

of another instrument. This is not a protected ground terminal.

Indicates a protective grounding terminal that must be connected to earth

ground before any other electrical connections are made to the
instrument.

Indicates a terminal that can receive or supply alternating current or

voltage.

Indicates a terminal that can receive or supply alternating or direct current

or voltage.

Safety Symbols The following table describes the safety symbols that may be displayed on
Applied Biosystems instruments. Each symbol may appear by itself or in
combination with text that explains the relevant hazard (see “Safety Labels on
Instruments” on page x). These safety symbols may also appear next to DANGERS,
WARNINGS, and CAUTIONS that occur in the text of this and other
product-support documents.

Symbol Description

Indicates that you should consult the manual for further information and to
proceed with appropriate caution.

Indicates the presence of an electrical shock hazard and to proceed with

appropriate caution.

Indicates the presence of a hot surface or other high-temperature hazard and

to proceed with appropriate caution.

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Safety and EMC Compliance Information

Symbol Description

Indicates the presence of a laser inside the instrument and to proceed with
appropriate caution.

Indicates the presence of moving parts and to proceed with appropriate

caution.

Safety Labels on Instruments

The following CAUTION, WARNING, and DANGER statements may be displayed
on Applied Biosystems instruments in combination with the safety symbols
described in the preceding section.

English Francais

CAUTION Hazardous chemicals. Read the ATTENTION Produits chimiques

Material Safety Data Sheets (MSDSs) dangeureux. Lire les fiches techniques de
before handling. sûreté de matériels avant la manipulation
des produits.

CAUTION Hazardous waste. Read the ATTENTION Déchets dangereux. Lire les
waste profile (if any) in the site preparation renseignements sur les déchets avant de
guide for this instrument before handling or les manipuler ou de les éliminer.
disposal.

CAUTION Hazardous waste. Refer to ATTENTION Déchets dangereux. Lire les

MSDS(s) and local regulations for handling fiches techniques de sûreté de matériels et
and disposal. la régulation locale associées à la
manipulation et l'élimination des déchets.

WARNING Hot lamp. AVERTISSEMENT Lampe brûlante.

WARNING Hot. Replace lamp with an AVERTISSEMENT Composants brûlants.

Applied Biosystems lamp. Remplacer la lampe par une lampe
Applied Biosystems.

CAUTION Hot surface. ATTENTION Surface brûlante.

DANGER High voltage. DANGER Haute tension.

WARNING To reduce the chance of AVERTISSEMENT Pour éviter les risques

electrical shock, do not remove covers that d'électrocution, ne pas retirer les capots
require tool access. No user-serviceable dont l'ouverture nécessite l'utilisation
parts are inside. Refer servicing to d'outils. L’instrument ne contient aucune
Applied Biosystems qualified service pièce réparable par l’utilisateur. Toute
personnel. intervention doit être effectuée par le
personnel de service qualifié de
Applied Biosystems.

CAUTION Moving parts. ATTENTION Parties mobiles.

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 General Instrument Safety

General Instrument Safety

PHYSICAL INJURY HAZARD. Use this product only as
specified in this document. Using this instrument in a manner not specified by
Applied Biosystems may result in personal injury or damage to the instrument.

Moving and PHYSICAL INJURY HAZARD. The instrument is to be moved

Lifting the and positioned only by the personnel or vendor specified in the applicable site
Instrument preparation guide. If you decide to lift or move the instrument after it has been
installed, do not attempt to lift or move the instrument without the assistance of
others, the use of appropriate moving equipment, and proper lifting techniques.
Improper lifting can cause painful and permanent back injury. Depending on the
weight, moving or lifting an instrument may require two or more persons.

Operating the Ensure that anyone who operates the instrument has:
Instrument • Received instructions in both general safety practices for laboratories and
specific safety practices for the instrument.
• Read and understood all applicable Material Safety Data Sheets (MSDSs). See
“About MSDSs” on page xi.

Chemical Safety
Chemical Hazard CHEMICAL HAZARD. Before handling any chemicals, refer
Warning to the Material Safety Data Sheet (MSDS) provided by the manufacturer, and
observe all relevant precautions.

CHEMICAL HAZARD. All chemicals in the instrument,

including liquid in the lines, are potentially hazardous. Always determine what
chemicals have been used in the instrument before changing reagents or instrument
components. Wear appropriate eyewear, protective clothing, and gloves when
working on the instrument.

About MSDSs Chemical manufacturers supply current Material Safety Data Sheets (MSDSs) with
shipments of hazardous chemicals to new customers. They also provide MSDSs with
the first shipment of a hazardous chemical to a customer after an MSDS has been
updated. MSDSs provide the safety information you need to store, handle, transport,
and dispose of the chemicals safely.
Each time you receive a new MSDS packaged with a hazardous chemical, be sure to
replace the appropriate MSDS in your files.

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Safety and EMC Compliance Information

Obtaining You can obtain from Applied Biosystems the MSDS for any chemical supplied by
MSDSs Applied Biosystems. This service is free and available 24 hours a day.
To obtain MSDSs:
1. Go to https://docs.appliedbiosystems.com/msdssearch.html
2. In the Search field, type in the chemical name, part number, or other
information that appears in the MSDS of interest. Select the language of your
choice, then click Search.
3. Find the document of interest, right-click the document title, then select any of
the following:
• Open – To view the document
• Print Target – To print the document
• Save Target As – To download a PDF version of the document to a
destination that you choose
4. To have a copy of a document sent by fax or e-mail, select Fax or Email to the
left of the document title in the Search Results page, then click RETRIEVE
DOCUMENTS at the end of the document list.
5. After you enter the required information, click View/Deliver Selected
Documents Now.

Chemical Safety To minimize the hazards of chemicals:

Guidelines • Read and understand the Material Safety Data Sheets (MSDS) provided by the
chemical manufacturer before you store, handle, or work with any chemicals or
hazardous materials. (See “About MSDSs” on page xi.)
• Minimize contact with chemicals. Wear appropriate personal protective
equipment when handling chemicals (for example, safety glasses, gloves, or
protective clothing). For additional safety guidelines, consult the MSDS.
• Minimize the inhalation of chemicals. Do not leave chemical containers open.
Use only with adequate ventilation (for example, fume hood). For additional
safety guidelines, consult the MSDS.
• Check regularly for chemical leaks or spills. If a leak or spill occurs, follow the
manufacturer’s cleanup procedures as recommended on the MSDS.
• Comply with all local, state/provincial, or national laws and regulations related
to chemical storage, handling, and disposal.

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 Chemical Waste Safety

Chemical Waste Safety

Chemical Waste HAZARDOUS WASTE. Refer to Material Safety Data Sheets
Hazard and local regulations for handling and disposal.

Chemical Waste To minimize the hazards of chemical waste:

Safety Guidelines • Read and understand the Material Safety Data Sheets (MSDSs) provided by the
manufacturers of the chemicals in the waste container before you store, handle,
or dispose of chemical waste.
• Provide primary and secondary waste containers. (A primary waste container
holds the immediate waste. A secondary container contains spills or leaks from
the primary container. Both containers must be compatible with the waste
material and meet federal, state, and local requirements for container storage.)
• Minimize contact with chemicals. Wear appropriate personal protective
equipment when handling chemicals (for example, safety glasses, gloves, or
protective clothing). For additional safety guidelines, consult the MSDS.
• Minimize the inhalation of chemicals. Do not leave chemical containers open.
Use only with adequate ventilation (for example, fume hood).For additional
safety guidelines, consult the MSDS.
• Handle chemical wastes in a fume hood.
• After emptying the waste container, seal it with the cap provided.
• Dispose of the contents of the waste tray and waste bottle in accordance with
good laboratory practices and local, state/provincial, or national environmental
and health regulations.

Waste Disposal If potentially hazardous waste is generated when you operate the instrument, you
must:
• Characterize (by analysis if necessary) the waste generated by the particular
applications, reagents, and substrates used in your laboratory.
• Ensure the health and safety of all personnel in your laboratory.
• Ensure that the instrument waste is stored, transferred, transported, and disposed
of according to all local, state/provincial, and/or national regulations.
IMPORTANT! Radioactive or biohazardous materials may require special handling,
and disposal limitations may apply.

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Safety and EMC Compliance Information

Electrical Safety
Fuses ELECTRICAL SHOCK HAZARD. Improper fuses or high-
voltage supply can damage the instrument wiring system and cause a fire. Before
turning on the instrument, verify that the fuses are properly installed and that the
instrument voltage matches the power supply in your laboratory.

FIRE HAZARD. For continued protection against the risk of

fire, replace fuses only with fuses of the type and rating specified for the instrument.

Power ELECTRICAL HAZARD. Grounding circuit continuity is vital

for the safe operation of equipment. Never operate equipment with the grounding
conductor disconnected.

ELECTRICAL HAZARD. Use properly configured and

approved line cords for the voltage supply in your facility.

ELECTRICAL HAZARD. Plug the system into a properly

grounded receptacle with adequate current capacity.

Overvoltage The GeneAmp PCR System® 9700 system has an installation (overvoltage) category
Rating of II, and is classified as portable equipment

Physical Hazard Safety

Moving Parts PHYSICAL INJURY HAZARD. Moving parts can crush and
cut. Keep hands clear of moving parts while operating the instrument. Disconnect
power before servicing the instrument.

PHYSICAL INJURY HAZARD. Do not operate the instrument

without the arm shield in place. Keep hands out of the deck area when the instrument
is spotting.

Hot Surface PHYSICAL INJURY HAZARD. During instrument operation,

the temperature of the heated cover can be as high as 108 °C, and the temperature of
the sample block can e as high as 100 °C. Before performing the procedure, keep
hands away until the heated cover and sample block reach room temperature.

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 Workstation Safety

Workstation Safety
Correct ergonomic configuration of your workstation can reduce or prevent effects
such as fatigue, pain, and strain. Minimize or eliminate these effects by configuring
your workstation to promote neutral or relaxed working positions.

MUSCULOSKELETAL AND REPETITIVE MOTION

HAZARD. These hazards are caused by potential risk factors that include but are not
limited to repetitive motion, awkward posture, forceful exertion, holding static
unhealthy positions, contact pressure, and other workstation environmental factors.
To minimize musculoskeletal and repetitive motion risks:
• Use equipment that comfortably supports you in neutral working positions and
allows adequate accessibility to the keyboard, monitor, and mouse.
• Position the keyboard, mouse, and monitor to promote relaxed body and head
postures.

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Safety and EMC Compliance Information

Safety and Electromagnetic Compatibility (EMC)

Standards
This section provides information on:
• U.S. and Canadian Safety Standards
• Canadian EMC Standard
• European Safety and EMC Standards
• Australian EMC Standards

U.S. and This instrument has been tested to and complies with standard UL 3101-1, “Safety
Canadian Safety Requirements for Electrical Equipment for Laboratory Use, Part 1: General
Standards Requirements.”
This instrument has been tested to and complies with standard CSA 1010.1, “Safety
Requirements for Electrical Equipment for Measurement, Control, and Laboratory
Use, Part 1: General Requirements.”

Canadian EMC This instrument has been tested to and complies with ICES-001, Issue 3: Industrial,
Standard Scientific, and Medical Radio Frequency Generators.

European Safety Safety

and EMC This instrument meets European requirements for safety (Low Voltage Directive
Standards 73/23/EEC). This instrument has been tested to and complies with standards
EN 61010-1:2001, “Safety Requirements for Electrical Equipment for Measurement,
Control and Laboratory Use, Part 1: General Requirements” and EN 61010-2-010,
“Particular Requirements for Laboratory Equipment for the Heating of Materials.”

EMC
This instrument meets European requirements for emission and immunity (EMC
Directive 89/336/EEC). This instrument has been tested to and complies with
standard EN 61326 (Group 1, Class B), “Electrical Equipment for Measurement,
Control and Laboratory Use – EMC Requirements.”

Australian EMC This instrument has been tested to and complies with standard AS/NZS 2064,
Standards “Limits and Methods Measurement of Electromagnetic Disturbance Characteristics
of Industrial, Scientific, and Medical (ISM) Radio-frequency Equipment.”

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Dual 96 Sample Block
Module Overview 1 1
This chapter covers:
About the Dual 96 Sample Block Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
Installing the Dual 96 Sample Block Module . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-8
Sample Tray and Plate Configurations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-10
Loading Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-12

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 Chapter 1 Dual 96 Sample Block Module Overview

About the Dual 96 Sample Block Module

What It Does The GeneAmp® PCR System 9700 amplifies nucleic acids using the polymerase
chain reaction (PCR) process.
Sample block modules are interchangeable. You can, for example, remove the Auto-
Lid Sample Block Module and replace it with the manual lid Dual 96 Sample Block
Module. This interchangeable module design allows you to change sample well
formats as well as throughput capacity.

Compatible Interchanging sample block modules may require a firmware change. If the sample
Software 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
floppy disk that is shipped with the Dual 96 Sample Block Module. For instructions
on upgrading the software, see the GeneAmp PCR System 9700 Base Module User’s
Manual (P/N 4303481) or see “How to Obtain Services and Support”on page vi.

Lid Choices The Dual 96 Sample Block Module comes with one of the following:
• An automatic lid
• A manual lid
The major difference between the two lids is that with the manual lid, you must
physically slide the lid back and forth into position; with the Auto-Lid, you simply
press the red button to move the lid.
Both lids are heated.

Heated Cover The heated cover slides over the sample blocks and performs two functions:
• It raises the temperature of the upper part of the tube (the part above the sample
blocks) above the temperature of the reaction mixture. This reduces
condensation, which may have a negative effect on your chemistry.
• It puts pressure on the reaction plates to seat them firmly and precisely in the
sample blocks. This enhances heat transfer.

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 About the Dual 96 Sample Block Module

Auto-Lid The heated Auto-Lid automatically moves over to cover the reaction plates at the
start of a PCR run, and then moves to the back of the module and opens when the run
is complete.
IMPORTANT! If you do not want the lid to open after a run, you need to apply a 4 ° C
hold at the end of the program.
The Auto-Lid Sample Block Module (Figure 1-1) attaches to the top of the
GeneAmp® PCR System 9700 Base Module and allows you to perform up to 192
reactions, 0.2 mL each. The Auto-Lid Sample Block Module also adds automation to
the System 9700, which can increase throughput.

Auto-Lid Dual 96 Sample Block Module

Heated Auto-Lid
(open)

GR1759b
GeneAmp® PCR
System 9700
Dual 96 sample blocks
Base Module
Move the Auto-Lid by pressing the red button

Figure 1-1 Auto-Lid Dual 96 Sample Block Module on the GeneAmp® PCR
System 9700 Base Module

Manual Lid The manual lid Dual 96 Sample Block Module (Figure 1-2) is used throughout this
manual as the primary example.

Manual Lid Dual 96 Sample Block Module

Lever used to manually

move the lid

Heated manual cover

Dual 96 sample blocks
F1
GR2255

STOP F2
F3
1 F4
Gene 2
PCR Sy Amp ®
F5
4
stem 97 3
00 5
7 POWER
6
8
ENTER
9
0
CE

GeneAmp® PCR System 9700

Base Module

Figure 1-2 Manual Lid Dual 96 Sample Block Module on the GeneAmp® PCR
System 9700 Base Module

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 Chapter 1 Dual 96 Sample Block Module Overview

Sample Blocks There are two sample blocks in the Dual 96 Sample Block Module. Each holds one
96-well reaction plate.
IMPORTANT! The right sample block is the primary control block. If you are using
only one reaction plate:
• Place the reaction plate you are using in the right sample block.
• Place an empty reaction plate in the left sample block.

GR2249
GR2249

Using reaction plates on both sides If you use just one reaction plate, place it on
the right. Place an empty plate on the left.

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 About the Dual 96 Sample Block Module

Placing the To place the reaction plates in the sample blocks:

Reaction Plates 1. Place a 96-well reaction plate into the right sample block.

GR2249
2. Place a second reaction plate in the left sample block.
IMPORTANT! You must insert two plates into the sample block for the
instrument to run properly.
3. Close the heated lid:
• For an Auto-Lid, press the red button located near the right sample block.
• For a manual lid, use the handle on top of the lid.
4. Process the samples.

Peltier Heating/ The internal Peltier heating/cooling unit is housed in the sample block module. The
Cooling Unit sample block module is made of aluminum to provide the optimal thermal transfer
rate.
• Platinum sensors in the sample block module provide:
• Wide temperature range: 4 to 99.9 ° C
• Accuracy: ±0.25 ° C from 35 to 100 ° C
• Uniformity of each sample block: ±0.5 ° C (measured after 30 sec at 95 ° C)
• Uniformity of combined sample blocks: ±0.75 ° C (measured after 30 sec at
95 ° C)
• Long-term stability and high reliability

Modules, The modules listed below are available for the GeneAmp PCR System 9700 Base
Accessories, and Module. The accessories and disposables are for use with the Dual 96 Sample Block
Disposables Module.

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 Chapter 1 Dual 96 Sample Block Module Overview

Ordering Order modules, accessories, and disposables from Applied Biosystems by part
number. See Tables 1-1 through 1-3.

Table 1-1 Modules for the 9700 Base Module

Modules Part Number

96-Well Sample Block Module N805-0251

96-Well Gold Sample Block Module 4314443

96-Well Aluminum Sample Block Module 4314445

0.5-mL 60-Well Sample Block Module 4309131

Auto-Lid Dual 384-Well Sample Block Module 4312904

Dual 96-Well GeneAmp PCR System 9700 4343176

Auto-Lid Dual 96-Well GeneAmp PCR System 9700 4343178

Dual 384-Well Sample Block Module N805-0400

Table 1-2 Accessories for the 9700 Base Module

Accessories Part Number

Dual 96-Well Sample Block Module Temperature Verification Kit. 4317939

Dual 384-Well Sample Block Module Temperature Verification Kit 4308354

Note: This kit is also used for the Auto-Lid Sample Block Module.

Tool, 384-Well Plate Extraction T-6273

Table 1-3 Disposables for the 9700 Base Module

Disposable Part Number

ABI PRISM® 96-Well Optical Reaction Plate 4329989

Adhesive Covers 4311971

MicroAmp® Clear Adhesive Covers 4306311

MicroAmp® Optical 96-Well Reaction Plate N801-0560

MicroAmp® Full Plate Cover N8010550

MicroAmp® Cap Installing Tool N801-0438

MicroAmp® 96-Well Tray/Retainer Sets 403081

MicroAmp® Cap Installing Tool N801-0438

MicroAmp® 96-Well Support Base 4312063

MicroAmp® Reaction Tubes N801-0533

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 About the Dual 96 Sample Block Module

Table 1-3 Disposables for the 9700 Base Module (continued)

Disposable Part Number

MicroAmp® Caps, Twelve Caps/Strip N801-0534

MicroAmp® Caps, Eight Caps/Strip N801-0535

MicroAmp® Reaction Tubes with Caps N801-0540

MicroAmp® 96-Well Tray for Tubes with Caps N801-0541

MicroAmp® Centrifuge Adapter N801-3822

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 Chapter 1 Dual 96 Sample Block Module Overview

Installing the Dual 96 Sample Block Module

Release Lever A lever behind the sample block module releases it from the GeneAmp® PCR
System 9700 Base Module. The top and bottom of the Dual 96 Sample Block
Module are shown below.

GR2249

Figure 1-3 Top view, Auto-Lid Dual 96 Sample Block Module

Lever
GR1762

Figure 1-4 Bottom view, Auto-Lid Dual 96 Sample Block Module

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 Installing the Dual 96 Sample Block Module

Installing the To install the sample block module (Auto-Lid and manual lid) into the GeneAmp
Sample Block PCR System 9700 Base Module:
Module 1. Pull out the lever from the sample block module.
2. Place the sample block module onto the base module, then push the sample
block module back to seat the electrical connections.
3. Push the lever into the base module to secure the sample block module.
Note: If the sample block module is not seated correctly, the instrument cannot
be turned on.

Installing the To install the communication card and cable into the GeneAmp PCR System 9700
Auto-Lid Module Base Module:
Communication 1. Insert the communication card into the slot at the rear of the right side of the
Card and Cable instrument (the label on the card face should be facing you).
2. Insert the connector end of the communication cable (very short cable) into the
communication card.
3. Insert the other end of the cable (plug type) into the receptacle on the sample
block module labeled “I/O Port.”

Installing the To install the power line cords into the sample block module and the GeneAmp
Auto-Lid Module PCR System 9700 Base Module:
Power Line Cords 1. Plug one end of the power line cord into the sample block module receptacle and
and Powering Up the other end into an outlet.
2. Plug the very short jumper cable into the sample block module and the other
into the base module.
3. Flip the power switch located on the sample block module near the plug
receptacle and press the power button located on the front of the instrument.

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 Chapter 1 Dual 96 Sample Block Module Overview

Sample Tray and Plate Configurations

The following section describes the possible sample tray and plate configurations.
IMPORTANT! The Tray or the Tray Retainer Set are essential for the operation of the
GeneAmp PCR System 9700.Sample Tray and Plate Configurations
Table 1-4 illustrates the possible sample tray and plate configurations.

Table 1-4 Sample tray and plate configurations

With this
Use... As Shown
vessel...

MicroAmp Adhesive cover

Optical 96-Well
Reaction Plate Adhesive cover

MicroAmp Optical 96-

Well Reaction Plate

MicroAmp 96-Well
Support Base

MicroAmp 96-Well
MicroAmp 96-Well
Full Plate Cover
Full Plate Cover

MicroAmp
Optical 96-Well
Reaction Plate

MicroAmp 96-Well
Support Base
GR2250

MicroAmp 8-Strip Caps MicroAmp Caps,

8-Strip

MicroAmp Optical
96-Well Reaction
Plate
GR2251

MicroAmp 96-Well
Support Base

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 Sample Tray and Plate Configurations

Table 1-4 Sample tray and plate configurations (continued)

With this
Use... As Shown
vessel...

MicroAmp MicroAmp 96-Well Tray for MicroAmp

Reaction Tubes Tubes with Caps Reaction Tubes
with Caps with Caps

MicroAmp 96-Well
Tray for
Tubes with Caps

GR2252
MicroAmp 96-Well
Support Base

MicroAmp MicroAmp MicroAmp MicroAmp Caps,

8-Strip Tubes 96-Well 8-Strip Caps 8-Strip
or Single Tubes Tray Retainer Set
MicroAmp 96-Well
Retainer
MicroAmp
8-Strip Tubes or
Single Tubes

MicroAmp
96-Well Tray
MicroAmp 96-Well

GR2253
Support Base

MicroAmp
96-Well
Full Plate MicroAmp 96-Well
Cover Full Plate Cover

MicroAmp
96-Well Retainer
MicroAmp
8-Strip Tubes or
Single Tubes

MicroAmp
96-Well Tray

MicroAmp 96-Well
Support Base
GR2254

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 Chapter 1 Dual 96 Sample Block Module Overview

Loading Samples
The following procedures describe how to load samples for:
• Tubes with attached caps
• 96-Well reaction plate
• 96-Well Tray Retainer Assembly
• Sample volume range: 5 to 100 µL in “D96” mode
IMPORTANT! Do not use mineral oil or glycerine in the sample block or as a vapor
barrier over the PCR reaction mixture in the tubes. The MicroAmp Reaction Tubes
fit tightly in the wells and a heated cover exerts even pressure on all tubes, reducing
condensation on the tubes when you are using a tray or tray/retainer set.

Loading Tubes To load tubes with attached caps:

with 1. Set the 96-well tray on a 96-well support base.
Attached Caps
2. Place the reaction tubes in the tray.
3. Pipette the samples into the reaction tubes.
4. Cap the tubes.

Loading the To load the 96-well reaction plate:

96-Well 1. Place the reaction plate on the 96-well support base.
Reaction Plate
2. Pipette the samples into the sample wells.
3. Apply the adhesive cover with a compression pad or cap the tubes using either
the MicroAmp 96-Well Full Plate Cover or the MicroAmp 8-Strip Caps.

Loading the To load the 96-Well Tray Retainer Assembly:

96-Well Tray 1. Place the tray on the 96-well support base.
Retainer
Assembly 2. Load tubes onto the tray, either using single tubes or using the 8-well tubes.
3. Place retainer over the tubes.
4. Pipette the samples into the tubes.
5. Cap the tubes using either the MicroAmp 96-Well Full Plate Cover or the
MicroAmp 8-Strip Caps.

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 Loading Samples

Placing the To place a sample tray or plate onto the block:

Sample Tray or 1. Lift the sample tray from the 96-well base and place it in the sample block.
Plate onto
the Block Place the MicroAmp tray or plate so that well H12 is located at the upper right
corner of the tray.

H12

A
1
2
3
4
5
6
7
8
9
10
11
12
GR1070

Figure 1-5 Align well H12 with upper right corner of the tray

IMPORTANT! Do not place the base into the sample block.

2. Slide the heated cover forward (press the red button for an Auto-Lid).
Note: Ensure that the cover is pulled completely forward for a proper seal.
3. Pull the heated cover lever down to engage the heated cover with the reaction
plate.
4. Process the samples
IMPORTANT! Do not open the cover when the block temperature is above 27 °C
because sample caps may pop off or jam.

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 Chapter 1 Dual 96 Sample Block Module Overview

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Maintaining the
Sample Block Module 2 2
This chapter covers:
Cleaning the Sample Block Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
Fixing an Auto-Lid Jam . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-4

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 Chapter 2 Maintaining the Sample Block Module

Cleaning the Sample Block Module

Overview The following procedures describe how to:
• Put the heated cover into the cleaning position
• Clean the heated cover
• Clean the sample block wells

Before using any cleaning or decontamination method, except

those recommended in this manual, check with Applied Biosystems to ensure that
the proposed method will not damage the equipment.

Required To clean the system, you need:

Materials • Bleach, 10%
• Isopropanol, pure
• Cotton swabs
• Clean cloth

CHEMICAL HAZARD. Sodium hypochlorite (bleach) is a

liquid disinfectant that can be corrosive to the skin and can cause skin
depigmentation. Please read the MSDS, and follow the handling instructions. Wear
appropriate protective eyewear, clothing, and gloves.

CHEMICAL HAZARD. Isopropanol is a flammable liquid and

vapor. It may cause eye, skin, and upper respiratory tract irritation. Prolonged or
repeated contact may dry skin and cause irritation. It may cause central nervous
system effects such as drowsiness, dizziness, and headache, etc. Please read the
MSDS, and follow the handling instructions. Wear appropriate protective eyewear,
clothing, and gloves.

Cleaning the Clean the heated cover at least once a month or more frequently, if needed.
Heated Cover
During instrument operation, the temperature of the heated cover
can be as high as 108 ° C, and the temperature of the sample block module can be as
high as 100 ° C. Before performing this procedure, wait until the heated cover and
sample block module reach room temperature.

To clean the heated cover:

1. Power off the instrument.
2. Unplug the instrument.
3. Wait 20–30 minutes for the heated cover to cool down.
4. Put the cover into the cleaning position by raising the front of the lid through the
slots on each side of the module as shown in Figure 2-1.

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 Cleaning the Sample Block Module

Raise front of the lid up through the slots

Slot

Slot

F1

GR2255
STOP F2
F3
1 F4
Gene 2
PCR Sy Amp ®
F5
4
stem 97 3
00 5
7 POWE
6 R
8
ENTE
R 9
0
CE

Figure 2-1 Heated cover in cleaning position (manual lid shown)

5. Soak a cotton swab or clean cloth with pure isopropanol and gently wipe the
bottom of the heated cover.

CHEMICAL HAZARD. Isopropanol is a flammable

liquid and vapor. It may cause eye, skin, and upper respiratory tract irritation.
Prolonged or repeated contact may dry skin and cause irritation. It may cause
central nervous system effects such as drowsiness, dizziness, and headache, etc.
Please read the MSDS, and follow the handling instructions. Wear appropriate
protective eyewear, clothing, and gloves.
6. If the heated cover becomes contaminated with amplified DNA:
a. Wipe the heated cover with a clean cloth or cotton swab soaked in
10% bleach.
b. Wipe with a clean, damp cloth.
7. Remove any remaining isopropanol from the heated cover with a clean cloth and
return the cover to its normal position.

Cleaning the Clean the sample block wells once a month or more frequently, if needed.
Sample Block
Wells To clean the sample block wells:
1. Let the system 9700 cool to the idle setpoint (25 °C).
2. Put the heated cover into the cleaning position. See step 4 on page 2-2 and
Figure 2-1 above.
3. Power off the instrument.
4. Unplug the instrument.
5. Remove the reaction plates from the sample block module and set them aside.

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 Chapter 2 Maintaining the Sample Block Module

6. Soak a cotton swab in pure isopropanol and clean the sample block wells
thoroughly.
7. Remove any remaining isopropanol from the sample block before reloading the
reaction plates.
8. If the sample block wells become contaminated with amplified DNA:
a. Clean the wells thoroughly with a cotton swab soaked in 10% bleach.
b. Wipe with a clean, damp cloth.
c.
CHEMICAL HAZARD. Sodium hypochlorite (bleach) is
a liquid disinfectant that can be corrosive to the skin and can cause skin
depigmentation. Please read the MSDS, and follow the handling instructions.
Wear appropriate protective eyewear, clothing, and gloves.

Fixing an Auto-Lid Jam

The following table describes how to fix a jam that is causing the Auto-Lid to stop.

If the Auto-Lid jams

Then...
while …
Closing The Auto-Lid automatically retracts to the open position.
• Find the jam and clear it.
• Press the red button and hold for 1 sec. The heated cover
returns to the open position and the instrument is reset.
Opening The Auto-Lid stops moving and remains in place.
• Try to find the jam and clear it.
• Press the red button and hold for 1 sec. The heated cover
returns to the open position and the instrument is reset.

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Testing the Dual 96 Sample Block
Module 3 3
This chapter covers:
Performing the Calibration Verification Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Performing the Temperature Non-Uniformity Test . . . . . . . . . . . . . . . . . . . . . . . 3-8
Performing System Performance Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . 3-15

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 Chapter 3 Testing the Dual 96 Sample Block Module

Performing the Calibration Verification Test

Overview Use this test to verify the temperature calibration of the GeneAmp® PCR
System 9700 Dual 96 Sample Block Module.
To complete the Calibration Verification Test, you perform the following tasks, in
order:

Tasks See Page

Setting Up the 0.2-mL Probe Assembly 3-3

Configuring the System 9700 3-3

Performing the Calibration Verification Test 3-4

Evaluating the Results 3-6

Ending the Test 3-6

In this procedure, you use the digital thermometer to take temperature readings of
one sample well connected to the 0.2-mL Probe Assembly. You take a reading at two
setpoint temperatures, 85 °C and 45 °C.

PHYSICAL INJURY HAZARD. Hot Surface. Use care when

working around the heated cover and sample block to avoid being burned by hot
components.
Note: To exit the test at any time, press F5 (Cancel).

Required This test requires the Temperature Verification System, Dual 0.2 mL (P/N 4346117),
Materials which includes:
• Light mineral oil
• Cotton swabs
• Temperature Verification Plates
• 0.2-mL Probe Assembly
• Digital thermometer with 9 V battery installed
Note: This system is also used for the Auto-Lid Sample Block Module.

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 Performing the Calibration Verification Test

Setting Up the To set up the 0.2-mL Probe Assembly:

0.2-mL Probe 1. If the heated cover is in the forward position, lift the lever, then slide the heated
Assembly cover back.
2. Position the 9700 Temperature Verification Plates on the appropriate sample
blocks:
• Right sample block – Plate labeled with R1 to R6
• Left sample block – Plate labeled with L1 to L6
Position the plate with the notch facing the back of the instrument.
Note: The plates are used as a guide to help you locate the probes within the
sample blocks.
3. Using a cotton swab, coat well R3 with mineral oil.
4. Place the 0.2-mL Probe Assembly into well R3.
5. Thread the probe wire through the channel in the Temperature Verification Plate
to prevent damage to the probe and lead wires.
6. Make sure the probe is connected to the digital thermometer.
7. Slide the heated cover forward and pull the lever down.
IMPORTANT! Seat the probe properly and close the heated cover carefully. If
the probe wire is crushed when the heated cover is closed, the probe may be
damaged.
8. Power on the digital thermometer.
Note: Refer to the instructions included with the Temperature Verification
System for a detailed description on operating the digital thermometer.
9. Continue with “Configuring the System 9700” on page 3-3.

Configuring the Before you begin configuring the System 9700, perform the procedure described in
System 9700 “Setting Up the 0.2-mL Probe Assembly” on page 3-3.

To configure the System 9700 for the Calibration Verification Test:

1. Power on the System 9700. The Main menu is displayed.
2. Press F4 (Util). The Utilities screen is displayed.
3. Press F1 (Diag). The Diagnostics screen is displayed.
4. Press F3 (TmpVer).
The Temperature Verification screen is displayed.

Temperature Verification

Temp - Calibration Verification

TNU - Temperature Non-Uniformity

Temp TNU Exit

F1 F2 F3 F4 F5

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 Chapter 3 Testing the Dual 96 Sample Block Module

5. Press F1 (Temp). The Calibration Verification screen is displayed and the

System 9700 is automatically configured for the Calibration Verification Test.

Calibration Verification
Block temp = xx.x°C Cover temp = xxx°C
Place probe in well R3
Press Run
Run Cancel
F1 F2 F3 F4 F5

6. Continue with “Performing the Calibration Verification Test” on page 3-4.

Performing the Before you begin calibrating the System 9700,

Calibration • Perform the procedures in:
Verification Test
– “Setting Up the 0.2-mL Probe Assembly” on page 3-3
– “Configuring the System 9700” on page 3-3
• Obtain the current Calibration Verification Data Sheet for your system, or copy
the form on page 3-7.

To perform the Calibration Verification Test:

1. Press F1 (Run). The Calibration Verification screen is displayed for the first
setpoint, 85 °C.

Calibration Verification
Block temp = xx.x°C Cover temp = xxx°C

Setpoint is 85°C
Cover must be within 1°C of 105°C
Cancel
F1 F2 F3 F4 F5

The System 9700 ramps up the lid temperature (cover temp) to 105 ° C (±1 ° C).
It may take several minutes for the System 9700 to ramp up.
When the lid temperature is reached, the “Stabilizing at setpoint” screen is
displayed. The “Stabilizing at setpoint” value begins to count down.

Calibration Verification
Block temp = xx.x°C Cover temp = xxx°C

Stabilizing at setpoint x:xx

Cancel
.
F1 F2 F3 F4 F5

2. When the “Stabilizing at setpoint” value decrements to zero, read the digital
thermometer.
Refer to the instructions included with the Temperature Verification System for
a detailed description on operating the digital thermometer.

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 Performing the Calibration Verification Test

3. Using the numeric keys, type the value displayed on the digital thermometer in
the “Enter actual block temperature” field.

Calibration Verification
Block temp = xx.x°C Cover temp = xxx°C

Enter actual block temperature xx.x

Cancel
F1 F2 F3 F4 F5

Note: The digital thermometer displays a four-digit value; round off the value
to three digits before typing it in the Calibration Verification screen.
Record the value on the Calibration Verification Test Data Sheet (page 3-7).
4. Press Enter.
The System 9700 automatically begins the second reading. The Calibration
Verification screen is displayed for the second setpoint, 45 °C. If necessary, the
System 9700 ramps up the lid temperature (cover temp) to 105 ° C (±1 ° C)
before initiating the “Stabilizing at setpoint” value countdown.

Calibration Verification
Block temp = xx.x°C Cover temp = xxx°C

Setpoint is 45°C
Cover must be within 1°C of 105°C
Cancel
F1 F2 F3 F4 F5

5. When the “Stabilizing at setpoint” value decrements to zero, read the digital
thermometer and enter the value for the second reading as described in steps 2
and 3. Record the value.
The System 9700 evaluates the calibration of the sample block temperature for
the setpoint values you entered and displays the results. A summary screen is
displayed at the conclusion of the test.

Calibration Verification

Actual temperature at 85 °C xx.x

Actual temperature at 45 °C xx.x

Accept Cancel
F1 F2 F3 F4 F5

Compare the values displayed with the actual test results you recorded. If the
values differ, repeat the procedure to make sure you entered the values
accurately.
6. If the values agree, press F1 (Accept).
7. Continue with “Evaluating the Results” on page 3-6 and “Ending the Test” on
page 3-6.

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 Chapter 3 Testing the Dual 96 Sample Block Module

Evaluating the When the System 9700 completes the Calibration Verification Test, one of two
Results screens is displayed (Table 3-1) to evaluate the results.

Table 3-1 Calibration Verification Test Results

If the screen displays… Then the sample block module...

Is properly calibrated
Calibration Verification

Calibration is good

Exit
F1 F2 F3 F4 F5

Failed the Calibration Verification Test

Calibration Verification
• Repeat the procedure to make sure you
Instrument may require service. accurately read and entered the temperature
readings.
Contact Applied Biosystems
• If the test fails again, contact Applied
Technical Support.
Exit Biosystems Technical Support. For information,
see “How to Obtain Services and Support” on
F1 F2 F3 F4 F5 page vi.

Ending the Test To end the test:

1. Press F5 (Exit). Continue to press F5 (Exit) until the Main Menu screen is
displayed.
2. Remove the 0.2-mL Probe Assembly from the sample block.
3. Power off the digital thermometer and clean off the oil.
4. Wait for the sample block to reach room temperature (~25 °C), then remove the
96-Well Temperature Verification Plates from the sample blocks.
5. Clean the oil from the sample block.

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 Performing the Calibration Verification Test

Data Sheet: When you run the Calibration Verification Test, record the setpoint values for
Calibration well R3 on a copy of the data sheet. At the end of the Calibration Verification Test,
Verification Test check the values displayed on the System 9700 against the values recorded to ensure
accurate test records.
IMPORTANT! Use a photocopy of this page to record values, and keep the original
intact.
.

Setpoint Value: Well R3

Probe Thermometer
Date Tested By
Serial No. Serial No.
85 ° C 45 ° C

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 Chapter 3 Testing the Dual 96 Sample Block Module

Performing the Temperature Non-Uniformity Test

Overview Use this test to find wells within the GeneAmp PCR System 9700 Dual 96-Well
Sample Block Module that exhibit unacceptable temperature variation.
To complete the Temperature Non-Uniformity Test, you perform the following tasks,
in order:

Tasks See Page

Setting Up the 0.2-mL Probe Assembly 3-8
Configuring the System 9700 3-9
Performing the Temperature Non-Uniformity Test 3-9
Evaluating the Results 3-13
Ending the Test 3-13

The Temperature Non-Uniformity Test uses the 0.2-mL Probe Assembly to test the
temperature uniformity of all six wells in the left and right sample blocks. You test
each well at two setpoints, 95 ° C and 55 ° C.

PHYSICAL INJURY HAZARD. Hot Surface. Use care when

working around the heated cover and sample block to avoid being burned by hot
components.
Note: To exit the test at any time, press F5 (Cancel).

Required See “Required Materials” on page 3-2 for information.

Materials

Setting Up the To set up the 0.2-mL Probe Assembly:

0.2-mL Probe 1. If the heated cover is in the forward position, lift the lever, then slide the heated
Assembly cover back.
2. Position the Temperature Verification Plates on the appropriate sample blocks:
• Right sample block – Plate labeled with R1 to R6
• Left sample block – Plate labeled with L1 to L6
Position the plate with the notch facing the back of the instrument.
Note: The plates are used as a guide to help you locate the probes within the
sample blocks.
3. Using a cotton swab, coat wells R1 to R6 and L1 to L6 with mineral oil.
4. Place the 0.2-mL Probe Assembly into the well to be tested. Begin testing with
well L1.
5. Thread the probe wire through the channel in the Temperature Verification Plate
to prevent damage to the probe and lead wires.
6. Make sure the probe is connected to the digital thermometer.

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 Performing the Temperature Non-Uniformity Test

7. Slide the heated cover forward and pull the lever down.
IMPORTANT! Seat the probe properly and close the heated cover carefully. If
the probe wire is crushed when the heated cover is closed, the probe may be
damaged.
8. Power on the digital thermometer.
Note: Refer to the instructions included with the Temperature Verification
System for a detailed description on operating the digital thermometer.
9. Continue with “Configuring the System 9700” on page 3-9.

Configuring the Before you begin configuring the System 9700, perform the procedures described in
System 9700 “Setting Up the 0.2-mL Probe Assembly” on page 3-8.

To configure the System 9700 for the Calibration Verification Test:

1. Power on the System 9700. The Main menu is displayed.
2. Press F4 (Util). The Utilities screen is displayed.
3. Press F1 (Diag). The Diagnostics screen is displayed.
4. Press F3 (TmpVer). The Temperature Verification screen is displayed.

Temperature Verification

Temp - Calibration Verification

TNU - Temperature Non-Uniformity

Temp TNU Exit

F1 F2 F3 F4 F5

5. Press F2 (TNU). The TNU Performance setpoint screen is displayed and the
system is automatically configured for the Temperature Non-Uniformity Test.
When the configuration is complete, the TNU Performance probe position
screen is displayed.

TNU Performance
Sample temp = xx.x°C Cover temp = xxx°C

Place Probe in well L1

Press Run
Run Cancel
F1 F2 F3 F4 F5

6. Continue with “Performing the Temperature Non-Uniformity Test” on page 3-9.

Performing the Before you begin the Temperature Non-Uniformity Test:

Temperature • Perform the procedures in:
Non-Uniformity
– “Setting Up the 0.2-mL Probe Assembly” on page 3-8
Test
– “Configuring the System 9700” on page 3-9
• Obtain the current Temperature Uniformity Data Sheet for your system, or copy
the form on page 3-14.

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 Chapter 3 Testing the Dual 96 Sample Block Module

To perform the Temperature Non-Uniformity Test:

1. Press F1 (Run).
This starts the Temperature Non-Uniformity Test. The TNU Performance screen
is displayed with the first setpoint value, 95 ° C.

TNU Performance
Sample temp = xx.x°C Cover temp = xxx°C

Setpoint is 95°C
Sample must be within 1.0°C of setpoint
Cancel
F1 F2 F3 F4 F5

If necessary, the System 9700 ramps up the sample block (sample temp) and lid
(cover temp) temperatures to the specified values. It may take several minutes
for the System 9700 to stabilize at these temperature.
When the sample block and lid temperatures are reached, the “Stabilizing at
setpoint” screen is displayed. The TNU Performance screen counts down the
time until the setpoint is stabilized.

TNU Performance
Sample temp = xx.x°C Cover temp = xxx°C
Stabilizing at setpoint x:xx

Cancel
F1 F2 F3 F4 F5

2. When the “Stabilizing at setpoint” value decrements to zero, read the digital
thermometer.
Refer to the instructions included with the Temperature Verification System for
a detailed description on operating the digital thermometer.

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 Performing the Temperature Non-Uniformity Test

3. Using the numeric keys, type the value displayed on the digital thermometer in
the “Enter actual block temperature” field.

TNU Performance

Sample temp = xx.x°C Cover temp = xxx°C

Enter actual block temperature 00.0
Cancel
F1 F2 F3 F4 F5

Note: The digital thermometer displays a four-digit value; round off the value
to three digits before typing it in the Calibration Verification screen.
Record the value and well number on the Temperature Non-Uniformity Test
Data Sheet (page 3-14).
4. Press Enter.
The System 9700 automatically begins the second reading.The TNU
Performance screen is displayed for the second setpoint, 55 °C. If necessary, the
System 9700 ramps up the sample and lid (cover temp) temperatures to the
specified values before initiating the “Stabilizing at setpoint” value countdown.

TNU Performance
Sample temp = xx.x°C Cover temp = xxx°C
Setpoint is 55°C
Sample must be within 1.0°C of setpoint
Cancel
F1 F2 F3 F4 F5

5. When the “Stabilizing at setpoint” value decrements to zero, read the digital
thermometer and enter the value for the second reading as described in steps 2
and 3. Record the value.
6. Press Enter.
The TNU Performance screen is displayed with the following message:

TNU Performance
Sample temp = xx.x°C Cover temp = xxx°C
Place probe in well xx
Press Run
Run Cancel
F1 F2 F3 F4 F5

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 Chapter 3 Testing the Dual 96 Sample Block Module

7. Test the next well:

a. Move the probe assembly to the next well – Slide the heated lid back.
Move the probe. Make sure the probe is connected to the digital
thermometer. Seat the probe and close the cover. See “Setting Up the
0.2-mL Probe Assembly” on page 3-8, steps 4 through 6.
b. Initiate and enter the first setpoint reading – Press F1 (Run). Repeat
steps 2 and 3 of this procedure.
c. Initiate and enter the second setpoint reading – Press Enter. Repeat
steps 2 and 3 of this procedure.
8. To initiate testing of the next well, press Enter.
9. Repeat steps 7 and 8 of this procedure until you test all 12 wells (L1 to L6 and
R1 to R6).
10. After the last well is tested, the System 9700 displays the values you entered.

Well 95°C 55°C Well 95°C 55°C

L1 xx.x xx.x L5 xx.x xx.x
L2 xx.x xx.x L6 xx.x xx.x
L3 xx.x xx.x R1 xx.x xx.x
L4 xx.x xx.x R2 xx.x xx.x
Accept More Cancel
F1 F2 F3 F4 F5

Compare the values displayed with the actual test results you recorded on the
Temperature Non-Uniformity Test Data Sheet. If the values differ, repeat the
procedure to make sure the values were accurately entered.
11. If the values agree, press F1 (Accept).
12. Continue with “Evaluating the Results” on page 3-13 and “Ending the Test” on
page 3-13.

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 Performing the Temperature Non-Uniformity Test

Evaluating the When the System 9700 completes the Temperature Non-Uniformity Test, the TNU
Results Performance screen is displayed. See the table below to evaluate the results.

If the performance result displays… Then…

Pass after both setpoint temperatures The temperature of the sample block wells is
uniform.
“Fail” after one or both setpoints The temperature variation of the sample block wells
is unacceptable.
• Repeat the procedure to make sure you
accurately read and entered the temperature
readings.
• If the test fails again, contact Applied
Biosystems Technical Support. See “How to
Obtain Services and Support” on page vi.

Ending the Test To end the test, follow the procedures in “Ending the Test” on page 3-6.

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 Chapter 3 Testing the Dual 96 Sample Block Module

Data Sheet: When you run the Temperature Non-Uniformity Test, record the setpoint values for
Temperature wells L1–L6 and R1–R6 on a copy of this data sheet. At the end of the Temperature
Non-Uniformity Non-Uniformity Test, check the values displayed on the System 9700 against the
Test values recorded to ensure accurate test records.
IMPORTANT! Use a photocopy of this page to record values, and keep the original
intact.

Date

Tested By

Probe Serial No.

Meter Serial No.

Setpoint Value 95 °C 55 °C

L1

L2

L3

L4

L5

L6

R1

R2

R3

R4

R5

R6

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 Performing System Performance Diagnostics

Performing System Performance Diagnostics

After you have configured the GeneAmp PCR System 9700, conduct the system
Rate and Cycle performance tests to verify the integrity of the cooling and heating
system.
IMPORTANT! Before you begin these tests, make sure that you place an empty
96-well plate with full plate lid on the sample block (or use an empty tray and lid the
wells with caps or the full plate cover). Slide the heated lid forward, and pull the lever
down.

Accessing the To access the tests, press System from the Diagnostics screen. The System
Tests Performance screen is displayed.

System Performance

Rate - Cool and Heat Rate Test

Cycle - Cycle Performance Test

Rate Cycle Exit

F1 F2 F3 F4 F5

Performing the Use the Rate Test to verify that the Peltier units are operating correctly. The test takes
Rate Test approximately two minutes to run.

To perform the Rate Test:

1. Press Rate in the System Performance screen. If appropriate, the following
reminder is displayed.

WARNING!!!
Install the appropriate empty
Consumables into the Sample Block.
Refer to System Performance Section
of the Block User Manual.
Cont Cancel
F1 F2 F3 F4 F5

2. After you have installed a plate and lid, press Cont.

The instrument then runs through a series of tests where the sample block is
stabilized at 35 ° C, 94 ° C, and 4 ° C.
At the conclusion of the test, the Cool and Heat Test screen is displayed. The
screen displays the test results and whether the test results passed or failed.

Cool and Heat Rate Test Pass

Heating rate: x.xx °C/s

Cooling rate: x.xx °C/s

Print Cancel
F1 F2 F3 F4 F5

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 Chapter 3 Testing the Dual 96 Sample Block Module

The passing ranges for the Rate Test are:

Block Type Heating Rate Cooling Rate

Dual 96-well > 0.70 ° C/second > 1.4 ° C/second

Performing the Use the Cycle Test to verify that the PCR cycling function operates properly. This
Cycle Test test takes approximately 15 minutes to run.

To perform the Cycle Test:

1. Press Cycle from the System Performance screen. This runs the Cycle Test. If
appropriate, the following reminder is displayed.

WARNING!!!
Install the appropriate empty
Consumables into the Sample Block.
Refer to System Performance Section
of the Block User Manual.
Cont Cancel
F1 F2 F3 F4 F5

2. After you have installed a plate cover, press Cont.

The Cycle Test executes a standard PCR cycling reaction, measures, and reports
the average cycle time, and the cycle to cycle variation.
IMPORTANT! Pressing Pause during the Cycle Test may generate false test results.
Re-run the Cycle Test if Pause is pressed during the test.
3. At the conclusion of the test, the display indicates test results and whether the
test results passed or failed.

Cycle Performance Pass

Average Cycle Time: xxx.x sec

Cycle Time STD: x.x sec
Print Cancel
F1 F2 F3 F4 F5

The following table lists the passing ranges for the Cycle Test.

Average Cycle Time <= 160 sec.

Cycle Time STD < 5 sec.

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Index

Numerics conventions
bold text v
0.2-µL Probe Assembly, setting up IMPORTANTS! v
Temperature Non-Uniformity Test 3-8 in this guide v
96-Well Sample Block Module, part number 1-6 italic text v
96-well sample plate menu commands v
loading 1-12 Notes v
sample tray configurations 1-10, 1-11 user attention words v
conventions, safety viii
A cooling
information 1-5
Accessories, ordering 1-6 verifying cooling system 3-15
Applied Biosystems customer feedback, on Applied Biosystems
contacting vi documents vi
customer feedback on documentation vi
Services and Support vi Cycle Test
Technical Communications vi accessing 3-15
Technical Support vi running 3-16
Australian EMC standards xvi
Auto 1-3 D
Auto-Lid 1-3 DANGER
description viii
example viii
B
data sheet
biohazardous waste, handling xiii Calibration Verification Test 3-7
bold text, when to use v Temperature Non-Uniformity Test 3-14
diagnostics 3-15, 3-16
C accessing the tests 3-15
Cycle Test, running 3-16
Calibration Verification Test 3-2 to 3-6 Rate Test, running 3-15, 3-16
data sheet 3-7
diagrams, sample block module
discontinuing 3-2
cleaning position 2-2
exiting 3-2
top and bottom views 1-8
required materials 3-2
digital thermometer
Canadian safety standards xvi
Calibration Verification Test 3-2
CAUTION
disposables, ordering 1-6
description viii
example viii DNA contamination
heated cover 2-3
chemical safety xi
sample block wells 2-4
chemical safety guidelines xii
documentation
chemical waste feedback vi
hazards xiii related to this guide vi
safety xiii
Dual 384-Well Sample Block Module, part
safety guidelines xiii
number 1-6
chemical waste disposal, guidelines xiii
Dual 96 Sample Block Module Temperature Verification
cleaning the sample block module 2-2, 2-4 Kit, part number 1-6

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E I
electrical hazard symbol ix IMPORTANT
electrical safety xiv description v, viii
electrical symbols, on instruments ix example viii
electromagnetic compatibility standards. See EMC installation category xiv
standards installing the sample block module 1-9
EMC standards xvi instrument operational safety, instructions for xi
Australian xvi interchangeability of sample block modules 1-2
Canadian xvi italic text, when to use v
European xvi
ergonomic safety xv
J
European EMC standards xvi
European safety standards xvi jams, fixing 2-4

G L
labels, instrument safety x
general hazard symbol ix
laser hazard, symbol x
glycerine, warning 1-12
lid types 1-2
guidelines
chemical safety xii loading samples 1-12
chemical waste disposal xiii
chemical waste safety xiii M
waste disposal xiii
manual lid 1-3
menu commands, conventions for describing v
H MicroAmp Caps 1-10
hazard icons MicroAmp Full Plate Cover, part number 1-6
accompanying safety alert words viii
mineral oil, warning 1-12
components viii
described viii modules, ordering 1-6
in documents viii moving and lifting instrument, safety xi
on instruments viii, ix moving parts
See also hazard symbols hazard xiv
See also safety symbols hazard symbol x
hazard symbols safety xiv
electrical ix symbol xiv
general ix MSDSs
hot surface ix description xi
in documents viii obtaining vi, xii
laser hazard x referring to xii, xiii
moving parts x when to review xi
on instruments ix
See also hazard icons
See also safety symbols
N
hazards Notes, description v
chemical waste xiii
moving parts xiv O
moving/lifting instrument xi
physical xiv ordering parts 1-6
repetitive motion xv overvoltage category (rating) xiv
heated cover overvoltage rating xiv
cleaning 2-2
DNA contamination 2-3
heated lid 1-2
heating and cooling, information 1-5

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P sample block
about 1-4
part numbers 1-6 cleaning the wells 2-3
parts, ordering 1-6 DNA contamination in wells 2-4
Peltier unit interchanging modules 1-2
heating/cooling unit 1-5 modules, interchanging 1-2
verifying running correctly 3-15 removing sample block module 1-6
performance tests 3-15, 3-16 verifying temperature uniformity 3-9 to 3-13
accessing the tests 3-15 sample compartment, loading samples 1-12
Cycle test, running 3-16 sample tray, configurations 1-10, 1-11
Rate Test, running 3-15, 3-16 sample tube configurations 1-7, 1-11
physical hazard safety xiv choosing a tube configuration 1-10
physical hazards xiv sample tray configurations 1-10, 1-11
samples, loading 1-12
R Services and Support, obtaining vi
radioactive waste, handling xiii standards
EMC xvi
Rate Test, accessing 3-15
safety xvi
Rate Test, running 3-15, 3-16 symbols
reaction plates hazard ix
placing 1-5 hot surface ix
using with the sample block module 2-2 moving parts xiv
repetitive motion hazard xv symbols on instruments
electrical ix
S safety ix
system performance tests, running 3-15, 3-16
safety
accessing the tests 3-15
before operating the instrument xi
Cycle Test, running 3-16
chemical xi
Rate Test, running 3-15, 3-16
chemical waste xiii
conventions viii
electrical xiv T
ergonomic xv
Technical Communications
instrument xi
contacting vi
instrument operation xi
e-mail address vi
moving and lifting instrument xi
moving parts xiv Technical Support, contacting vi
physical hazard xiv Temperature Non-Uniformity Test 3-8 to 3-13
standards xvi data sheet 3-14
workstation xv discontinuing 3-8
safety alert words evaluating the results 3-13
accompanying hazard icons viii exiting 3-8
CAUTIONS viii required materials 3-8
DANGERS viii running the test 3-9 to 3-13
description viii tests
IMPORTANTS viii accessing system performance 3-15
WARNINGS viii Calibration Verification Test 3-2 to 3-6
safety labels, on instruments x system performance 3-15, 3-16
system performance, Cycle test 3-16
safety standards
system performance, Rate Test 3-16
Canadian xvi
Temperature Non-Uniformity Test 3-8 to 3-13
European xvi
U.S. xvi training, obtaining information about vi
safety symbols tray and retainer set, sample tray configuration 1-10
on instruments ix tube configurations 1-7, 1-11
See also hazard symbols choosing a tube configuration 1-10
sample tray configurations 1-10, 1-11

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tubes with attached caps
loading 1-12
sample tray configuration 1-11

U
unloading samples, procedures for loading
samples 1-12
US safety standards xvi
user attention words, defined v

W
WARNING, description viii
waste disposal, guidelines xiii
workstation safety xv

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Headquarters
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Phone: +1 650.638.5800
Toll Free (In North America): +1 800.345.5224
Fax: +1 650.638.5884
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Printed in USA, 06/2003

Part Number 4343363 Rev. B