Thermo Fisher Scientific GeneAmp® PCR System 9700 Base Module User's manual

GeneAmp

®

PCR

System 9700

Base Module

STOP

GeneAmp

PCR System 9700

ENTER

7

F1

F2

0

F3

4

1

8

5

2

9

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CE

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POWER

User’s Manual

P/N N805-0200

GeneAmp ® PCR System 9700

Base Module

User’s Manual

© Copyright 2003, 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.

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.

NOTICE TO PURCHASER: LABEL LICENSE

The GeneAmp ® PCR System 9700 thermal cycler is covered by US p atent

claim s and claims in their non-US counterparts, owned by Appli ed

Biosystems

. No right is conveyed expressly, by implication, or by estoppel under any other patent claim, such as claims to apparatus, reagents, kits or methods such as 5’ nuclease methods.

Further information on purchasing licenses may be obtained by contacting the Director of Licensing, Applied Biosystems, 850 Lincoln Centre Drive, Foster City, CA

94404, USA.

ABI Prism, Applied Biosystems, and BigDye are registered trademarks of Appl ied

Biosystems

or its subsidiaries in the U.S. and/or certain other countries.

AB (Design) is a trademark of Appl ied

Biosystems

or its subsidiaries in the U.S. and/or certain other countries.

AmpliCyle, AmpliTaq, AmpliTaq Gold, and GeneAmp are registered trademarks of Roche Molecular Systems, Inc.

All other trademarks are the sole property of their respective owners.

12/2010

Part Number 4303481 Rev. H

Contents

1 Introduction and Safety

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1

About This Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1

In This Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1

About This Manual. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2

Instrument Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-3

Before Operating the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-3

Documentation User Attention Words. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-3

Symbols on Instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4

Electrical Symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4

Safety Symbols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4

Safety Labels on Instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-5

Chemical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-6

Chemical Hazard Warning. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-6

Chemical Waste Hazard Warning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-6

About MSDSs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-7

Ordering MSDSs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-7

About Waste Disposal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-8

GeneAmp PCR System 9700 Labels and Warnings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-9

Instrument Safety Labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-9

Instrument Warnings Diagram. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-9

Danger of Burns. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-10

Grounding and Electrical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-10

Fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-10

Laboratory Environmental Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-11

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-11

Temperature, Humidity, and Environment. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-11

Pollution. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-11

Emission/Immunity Statement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-11

Routine Maintenance for Safe Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-11

U.S. and Canadian Safety Standards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-12

Canadian EMC Standard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-12

European Safety and EMC Standards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-12

Australian EMC Standards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-12

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2 Product Overview

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1

About This Chapter. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1

In This Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1

About the GeneAmp PCR System 9700 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2

About the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2

Control Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2

Control Panel Diagram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2

Using the Keys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3

Selecting a Field . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3

Entering Numeric Values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3

Transfer or Storage of Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-4

Upgrading the Firmware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-4

How the 9700 Differs from the GeneAmp PCR System 9600 . . . . . . . . . . . . . . . . . . . . 2-5

3 Instrument Setup

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1


In This Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1

Unpacking the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2

Inspecting the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2

Additional Part Numbers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2

Setting Up your Laboratory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3

Choosing a Location . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3

Operating Temperature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3

What to Avoid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3

Do Not Block Air Vents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3

Fuse Service Configuration. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4

Input Voltage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4

Interchangeable Sample Block Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4

Double-Line Fuse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5

Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5

Fuse Part Number . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5

Power Entry Module Diagram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5

Turning On the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6

Turning On the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6

Setting Custom Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-7

Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-7

Displaying the Configuration Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-7

Setting the Time . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-8

Setting the Date. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-8

Enabling or Disabling a Printer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-8

Turning the Run-Time Beeper On or Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-9

Setting the Pause Time Out . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-9

Defining the Idle State Setpoint Temperature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-10

Defining the Baud Rate for Your Printer Port . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-10

Configuring the Contrast and Screen Saver Options . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-11

Setting the IP Address . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-11

Running Instrument Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-13

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-13

Viewing the Diagnostic Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-13

Testing the Electrical Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-14

Testing the Display Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-15

Testing the Keypad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-16

Using the T m

Calculator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-17

How to Use the T m

Calculator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-17

Upgrading the System Firmware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-18

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-18

Upgrading Through the Serial Port . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-18

Downloading Firmware Using Windows 95 or Windows NT. . . . . . . . . . . . . . . . . . . . 3-20

Downloading Firmware Using Windows 3.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-21

Upgrading Firmware from a PCMCIA Flash Memory Card. . . . . . . . . . . . . . . . . . . . . 3-22

Copying Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-24

How to Copy Methods. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-24

Connecting and Configuring a Printer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-26

Connecting a Printer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-26

Configuring the Printer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-26

4 Running PCR Samples

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1


In This Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1

Selecting a Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2

What Is a Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2

Predefined Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2

Selecting a Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-3

Viewing Method Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-4

Searching for Methods. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-4

Sorting Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-5

Running a Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-6

Starting a Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-6

About the Run Time Screen. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-7

Viewing Method Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-8

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Pausing a Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-8

Stopping a Run Before It Completes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-9

Reviewing the History of a Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-10

How to Review the History of a Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-10

History Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-10

History File Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-11

When a Run Completes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-12

End of Run Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-12

Method Not Stored Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-12

5 Creating and Editing Methods

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-1


In This Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-1

Adding or Changing Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2

Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2

Adding a New User Name . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2

Protecting Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-3

Changing a User Name . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-5

Deleting a User Name. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-5

Creating Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-6

About the Default Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-6

Basic Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-6

Displaying the Create Methods Screen. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-7

Entering Temperature Control Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-8

Defining Pre-PCR Holds. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-9

Defining PCR Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-9

Defining Post-PCR Holds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-10

Modifying Cycling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-11

Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-11

Changing Temperature Control Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-11

Modifying Ramp Rates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-12

Inserting Holds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-13

Deleting Holds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-14

Inserting Cycles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-14

Inserting Programmed Pauses. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-14

Editing Programmed Pauses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-16

Naming and Storing Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-16

Printing a Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-17

Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-17

Printing a Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-17

Editing or Deleting Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-18

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-18

Editing a Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-18

Deleting a Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-20

6 Converting Hold Times

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1


In This Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1

About Setting Hold Times . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2

Hold Time Differences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2

Guidelines for Converting Hold Times . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-3

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-3

What to Base the New Hold Times On . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-3

Setting Up Ramps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-3

Table of Conversions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-3

Up Ramp Example. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-4

Setting Down Ramps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-4

Table of Conversions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-5

Down Ramp Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-5

7 Routine Maintenance

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-1


In This Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-1

Changing the External Fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2

Power Entry Module Diagram. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2

Changing Fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-3

8 Troubleshooting

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-1


In This Chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-1

If There Is a Power Failure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-2

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-2

During a Power Failure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-2

Display Screen Error Messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-3

Error Messages Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-3

Troubleshooting Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-6

Troubleshooting Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-6

vii

viii

A Instrument Specifications

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-1

About This Appendix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-1

In This Appendix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-1

System Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-2

Dimensions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-2

Power Configurations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-2

Electrical Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-2

Control Panel Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-4

Display Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-4

Keys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-4

Sample Temperature Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-4

Temperature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-4

Printer Specifications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-4

Serial Interface Board Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-4

Cable Part Number . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-4

B Supplied Methods

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-1

About this Appendix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-1

In This Appendix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-1

About the Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-2

Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-2

AmpliCycle Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-2

AmpliTaq Gold DNA Polymerase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-2

BigDye Terminators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-3

General PCR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-3

LMS2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-4

Time Release PCR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-4

Touchdown PCR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-5

XL PCR. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-5

C Contacting Services and Support

D Limited Warranty Statement

Computer Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . D-1

Limited Product Warranty . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . D-1

Damages, Claims, and Returns. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .D-3

Damages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .D-3

Claims . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .D-3

Returns. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .D-3

Index

ix

Introduction and Safety

1

Overview

About This Chapter

This chapter provides information to help you safely operate the GeneAmp



PCR

System 9700.

In This Chapter

The following topics are covered in this chapter:

Topics

About This Manual

Instrument Safety

Chemical Safety

GeneAmp PCR System 9700 Labels and Warnings

Laboratory Environmental Requirements

See Page

1-2

1-3

1-6

1-9

1-11

1

Introduction and Safety 1-1

About This Manual

Overview

This manual describes how to use the GeneAmp

®

PCR System 9700. It includes the following chapters and appendixes:

♦ Chapter 1, “Introduction and Safety,” contains safety information.

♦ Chapter 2, “Product Overview,” describes the instrument, its components, and requirements for installation.

♦ Chapter 3, “Instrument Setup,” provides information on how to set up the instrument and place it correctly in the laboratory, how to configure the instrument, and how to connect and configure a printer.

♦ Chapter 4, “Running PCR Samples,” provides information on selecting a method, starting and stopping a run, reviewing the history of a run, and what to do when the run is completed.

♦ Chapter 5, “Creating and Editing Methods,” describes how to create and edit PCR methods and how to work with stored methods.

♦ Chapter 6, “Converting Hold Times,” provides information about setting hold times for the GeneAmp

®

PCR System 9700 compared to the DNA Thermal Cycler or

DNA Thermal Cycler 480.

♦ Chapter 7, “Routine Maintenance,” provides procedures for routine maintenance on the instrument.

♦ Chapter 8, “Troubleshooting,” lists error messages and suggestions for dealing with other problems you may encounter.

♦ Appendix A, “Instrument Specifications,” describes the dimensions, power, and electrical specifications of the GeneAmp ® PCR System 9700 system, including the control panel, sample temperature information, and printer specifications.

♦ Appendix B, “Supplied Methods,” contains information about the methods that are supplied with the instrument.

♦ Appendix C, “Contacting Services and Support,” explains how to contact Applied

Biosystems’ Technical Support staff.

♦ Appendix D, “Limited Warranty Statement,” contains the instrument warranty statement.

1-2 Introduction and Safety

Instrument Safety

Before Operating the

Instrument

Ensure that everyone involved with the operation of the instrument has:

♦ Received instruction in general safety practices for laboratories

♦ Received instruction in specific safety practices for the instrument

♦ Read and understood all related MSDSs

Avoid using this instrument in a manner not specified by Applied

Biosystems. Although the instrument has been designed to protect the user, this protection can be impaired if the instrument is used improperly.

Documentation User

Attention Words

Five user attention words appear in the text of all Applied Biosystems user documentation. Each word implies a particular level of observation or action as described below.

Note

Calls attention to useful information.

IMPORTANT

Indicates information that is necessary for proper instrument operation.

Indicates a potentially hazardous situation which, 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 which, if not avoided, could result in death or serious injury.

Indicates an imminently hazardous situation which, if not avoided, will result in death or serious injury. This signal word is to be limited to the most extreme situations.


Symbols on Instruments

Electrical Symbols

The following chart is an illustrated glossary of all electrical symbols that are used on

Applied Biosystems instruments. Whenever such symbols appear on instruments, please observe appropriate safety procedures.

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 an alternating or direct current or voltage.

Safety Symbols

The following is an illustrated glossary of all nonelectrical safety alert symbols found 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 1-5). 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.


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

Material Safety Data Sheets (MSDSs) before handling.

ATTENTION Produits chimiques dangeureux. Lire les fiches techniques de sûreté de matériels avant la manipulation des produits.

CAUTION Hazardous waste. Read the waste profile (if any) in the site preparation guide for this instrument before handling or disposal.

ATTENTION Déchets dangereux. Lire les renseignements sur les déchets avant de les manipuler ou de les éliminer.

CAUTION Hazardous waste. Refer to

MSDS(s) and local regulations for handling and disposal.

ATTENTION Déchets dangereux. Lire les fiches techniques de sûreté de matériels et la régulation locale associées à la manipulation et l'élimination des déchets.

WARNING Hot lamp.

WARNING Hot. Replace lamp with an

Applied Biosystems lamp.

CAUTION Hot surface.

DANGER High voltage.

AVERTISSEMENT Lampe brûlante.

AVERTISSEMENT Composants brûlants.

Remplacer la lampe par une lampe

Applied Biosystems.

ATTENTION Surface brûlante.

DANGER Haute tension.

WARNING To reduce the chance of electrical shock, do not remove covers that require tool access. No user-serviceable parts are inside. Refer servicing to

Applied Biosystems qualified service personnel.

AVERTISSEMENT Pour éviter les risques d'électrocution, ne pas retirer les capots dont l'ouverture nécessite l'utilisation d'outils. L’instrument ne contient aucune pièce réparable par l’utilisateur. Toute intervention doit être effectuée par le personnel de service qualifié de

Applied Biosystems.

CAUTION Moving parts.

ATTENTION Parties mobiles.


Chemical Safety

Chemical Hazard

Warning

CHEMICAL HAZARD

. Some of the chemicals used with Applied

Biosystems instruments and protocols are potentially hazardous and can cause injury, illness, or death.

♦ Read and understand the material safety data sheets (MSDSs) provided by the chemical manufacturer before you store, handle, or work with any chemicals or hazardous materials.

♦ Minimize contact with chemicals. Wear appropriate personal protective equipment when handling chemicals (e.g., 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 (e.g., 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.

Chemical Waste

Hazard Warning

CHEMICAL WASTE HAZARD.

Wastes produced by Applied Biosystems instruments are potentially hazardous and can cause injury, illness, or death.

♦ 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.

♦ Handle chemical wastes in a fume hood.

♦ Minimize contact with chemicals. Wear appropriate personal protective equipment when handling chemicals (e.g., 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 (e.g., fume hood). For additional safety guidelines, consult the MSDS.

♦ 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.


About MSDSs

Some of the chemicals used with this instrument may be listed as hazardous by their manufacturer. When hazards exist, warnings are prominently displayed on the labels of all chemicals.

Chemical manufacturers supply a current MSDS before or with shipments of hazardous chemicals to new customers and with the first shipment of a hazardous chemical after an MSDS update. MSDSs provide you with the safety information you need to store, handle, transport and dispose of the chemicals safely.

We strongly recommend that you replace the appropriate MSDS in your files each time you receive a new MSDS packaged with a hazardous chemical.

CHEMICAL HAZARD

. Be sure to familiarize yourself with the MSDSs before using reagents or solvents.

Ordering MSDSs You can obtain from Applied Biosystems the MSDS for any chemical supplied by

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.

For chemicals not manufactured or distributed by Applied Biosystems, call the chemical manufacturer.


About Waste

Disposal

As the generator of potentially hazardous waste, it is your responsibility to perform the actions listed below.

♦ 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, or national regulations.

Note

Radioactive or biohazardous materials may require special handling, and disposal limitations may apply.


GeneAmp PCR System 9700 Labels and Warnings

Instrument Safety

Labels

Safety labels are located on the instrument. Each safety label has three parts:

♦ A signal word panel, which implies a particular level of observation or action (e.g.,

CAUTION or WARNING). If a safety label encompasses multiple hazards, the signal word corresponding to the greatest hazard is used.

♦ A message panel, which explains the hazard and any user action required.

♦ A safety alert symbol, which indicates a potential personal safety hazard.

Instrument

Warnings Diagram

The following diagram shows the hazards and warnings labels located on the back of the GeneAmp ® PCR System 9700 instrument.


Danger of Burns

PHYSICAL INJURY HAZARD. Hot Surface. Use care when working around this area to avoid being burned by hot components.

Grounding and

Electrical Safety

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

ELECTRICAL HAZARD.

Do not use an adapter to a two-terminal outlet since this does not provide positive ground protection.

Fuses

Improper fuses can damage the wiring system and cause a fire.

FIRE HAZARD. For continued protection against the risk of fire, replace fuses only with fuses of the type and rating specified for the instrument.

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.


Laboratory Environmental Requirements

Introduction

Take the precautions described in this section whenever you operate the system 9700.

Read this section before you install the instrument.

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.

Temperature,

Humidity, and

Environment

IMPORTANT

This instrument is designed for indoor use.

IMPORTANT

Do not operate in a Cold Room or a refrigerated area. The system 9700 will operate safely when the ambient temperature is 5 °C to 40 °C (41 °F to 104 °F) and will meet performance specifications when the ambient temperature is 15 °C to 30 °C and the ambient relative humidity is 20 to 80%. These specifications have been calculated for altitudes between

0 and 2,000 meters.

FIRE HAZARD.

This instrument is not designed for operation in an explosive environment. Do not place the instrument close to potentially explosive materials or objects.

IMPORTANT

The instrument should be stored between –20 °C and 60 °C (–4 °F and 140 °F) at altitudes between 0 and 12,000 meters.

Note

This instrument is able to withstand transient overvoltage according to Installation

Category II as defined in IEC 1010-1.

Pollution

The installation category (overvoltage category) for this instrument is II, and it is classified as portable equipment. The instrument has a pollution degree rating of 2 and may be installed in an environment that has non-conductive pollutants only.

Emission/Immunity

Statement

For our European customers, any product marked with the CE label meets the

European EMC directive 89/336/EEC and the Low Voltage Directive 72/23/EEC. This product meets Class B emission limits.

Routine

Maintenance for

Safe Operation

If you use any cleaning or decontamination method, except those recommended in the manual, you may risk damaging 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.), contact your local sales office for advice.


Safety and Electromagnetic Compatibility (EMC)

Standards

U.S. and Canadian

Safety

Standards

This section provides information on:

• U.S. and Canadian Safety Standards

• Canadian EMC Standard

• European Safety and EMC Standards

• Australian EMC Standards

This instrument has been tested to and complies with standard UL 3101-1, “Safety

Requirements for Electrical Equipment for Laboratory Use, Part 1: General

Requirements.”

Canadian EMC

Standard

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.”

This instrument has been tested to and complies with ICES-001, Issue 3: Industrial,

Scientific, and Medical Radio Frequency Generators.

European Safety and

EMC

Standards

Safety

This instrument meets European requirements for safety (Low Voltage Directive

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

Standards

This instrument has been tested to and complies with standard AS/NZS 2064, “Limits and Methods Measurement of Electromagnetic Disturbance Characteristics of

Industrial, Scientific, and Medical (ISM) Radio-frequency Equipment.”


Product Overview

2

Overview


This chapter describes the GeneAmp

®

PCR System 9700, its components, and requirements for installation.

In This Chapter

The following topics are contained in this chapter:

Topic

About the GeneAmp PCR System 9700

See page

2-2

2

Product Overview 2-1

About the GeneAmp PCR System 9700

About the

Instrument

The GeneAmp PCR System 9700 is an automated instrument, specifically designed for the amplification of nucleic acids using the Polymerase Chain Reaction (PCR) process. The user interface consists of a control panel with a full numeric keypad, soft keys, and a graphical display screen that shows the time and temperature profile for each run.

Control Panel

The instrument control panel consists of a display screen and 22 keys. The display screen shows a graphical representation of PCR events, including pre-PCR holds,

PCR cycling, and post-PCR holds. You use the keys to enter information into fields on the display screen.

Control Panel

Diagram

The following diagram shows the control panel.

Soft keys

(F1–F5)

Numeric keys

STOP

GeneAmp ®

PCR System 9700

F1 F2

1

4

7

ENTER

F3

2

5

8

0

F4

3

6

9

CE

F5

POWER

Power on/off

Stop key Clear Entry key

Enter key Circular Key Pad

2-2 Product Overview

Using the Keys

The following table describes the Control Panel keys in the previous figure.

Key

Soft keys (F1-F5)

Numeric keys

Stop key

Enter key

Clear Entry key (CE)

Circular Key Pad

Use to...

Select the function specified above the key.

The function of each key is defined on the display screen above the key, and is redefined as you view different screens.

Enter numbers from left to right into a field you highlight.

Stop a method while it is running.

Enter information typed into a field and advance the highlight box to the next field on a screen.

Remove information from a field.

Move the highlight box to different fields on the display screen in the direction of the arrow.

Selecting a Field

There are two ways to select a field.

If you want to...

move the highlight box in one of four directions advance the box to the next field

Then....

Use the Circular Key Pad.

Press the Enter key.

Entering Numeric

Values

The following table lists how to enter numeric values for the Temperature and Hold

Time parameters.

Parameter

Temperature parameters

Hold Time parameters

Description

Enter values for temperature in decimal form. It is not necessary to type a decimal point.

For example, to specify 89.0 °C, press 8 9 0, then press Enter.

A hold time is the length of time the samples will be maintained at a specified temperature.

Specify all hold times in minutes and seconds, then press Enter.

For example, to specify one minute and five seconds, press 1 0 5, then press Enter.


Transfer or Storage of Methods

You can transfer or store methods using a Methods Storage Card. The instrument can run a method from its own software or from the methods stored on a Methods Storage card.

Use...

Methods Storage Card,

Centennial 256kb SRAM

(P/N 0940-1064)

To...

transfer methods from the

Methods Storage card to the instrument or from the instrument to the card for storage.

See...

“Copying Methods” on page

3-24.

Upgrading the

Firmware

There are two ways to upgrade the firmware:

♦ With a serial cable connection (PC communication cable P/N N805-1327 or

Macintosh

®

communication cable P/N N805-1328) from the instrument’s

RS485 ports

♦ With a PCMCIA Flash Memory Card

Note

Upgrade firmware can be ordered from the Applied Biosystems web site or by contacting PCR Technical Support.

For more information about upgrading the firmware, see the following.

If you are using...

a serial cable connection (RS485 ports) a PCMCIA Flash Memory Card

Microsoft Windows ® 95 or Windows NT ®

Windows

®

3.1

See...

“Upgrading Through the Serial Port” on page 3-18.

“Upgrading Firmware from a PCMCIA

Flash Memory Card” on page 3-22.

“Downloading Firmware Using

Windows 95 or Windows NT” on page 3-20.

“Downloading Firmware Using Windows

3.1” on page 3-21.

2-4 Product Overview

How the 9700 Differs from the GeneAmp

PCR System 9600

The GeneAmp PCR System 9700 differs from the GeneAmp ® PCR System 9600 in the following ways:

♦ Reaction volumes of up to 50 µL only can be run and in the “9600 Mode”, as opposed to 100 µL in the GeneAmp PCR System 9600.

♦ Methods are stored under a user name, allowing users to keep track of and protect their own methods.

♦ Hold, Cycle, and Auto programs no longer exist as menu items under the Create function. Instead of linking programs together to create a method, you create a single method on the GeneAmp PCR System 9700.

♦ If the allowed pause time elapses during a manual pause of a method, the method will continue running (instead of stopping).

♦ The last method run cannot be re-run or edited unless it is first saved.

♦ The history file no longer includes individual setpoint time and temperature information.

♦ An automated restart or incubate function is available for use after a power outage.


Instrument Setup

3

3

Overview


This chapter provides information on how to set up the GeneAmp

®

PCR System 9700 and place it correctly in the laboratory, how to configure the instrument, and how to connect and configure a printer.

In This Chapter


Topic

Unpacking the Instrument

Setting Up your Laboratory

Double-Line Fuse

Turning On the Instrument

Setting Custom Parameters

Running Instrument Diagnostics

Using the T m

Calculator

Upgrading the System Firmware

Copying Methods

Connecting and Configuring a Printer

See page

3-2

3-3

3-5

3-6

3-7

3-13

3-17

3-18

3-24

3-26

Instrument Setup 3-1

Unpacking the Instrument

Inspecting the

Instrument

Inspect the GeneAmp

®

PCR System 9700, and all other supplied parts, for any damage that may have occurred during shipment. If there has been any damage during transit, notify the carrier and Applied Biosystems immediately.

Note

Save the shipping container and all packing materials in case it becomes necessary to reship the instrument.

To order additional instruments or supplies, contact one of the regional offices listed in

Appendix C, “Contacting Services and Support.”

Additional Part

Numbers

You can order modules, accessories, and disposables from Applied Biosystems.

To order this part...

GeneAmp PCR System 9700 Base Module

60-Well 0.5 mL Sample Block Module

Auto-Lid Sample Block Module

96-Well Gold Sample Block Module

96-Well Aluminum Sample Block Module

Dual 384-Well Sample Block Module

Temperature Verification System

PC (method storage) card

Printer cable

PC communication cable

Macintosh

®

communication cable

Use P/N...

N805-0200

4309131

4312904

4314443

4314445

N805-0400

N801-0435

940-1064

N805-1326

N805-1327

N805-1328

Note

See the Interchangeable Sample Block Module Users Manual for part numbers of disposable items.

3-2 Instrument Setup

Setting Up your Laboratory

Choosing a Location

To prevent vibration, place the GeneAmp PCR System 9700 on a solid, stable, level surface that allows free airflow overhead and around the sides and back. You should keep all ventilation slots in the instrument cover free of obstruction, for example from excess printer paper.

Operating

Temperature

The instrument will meet performance specifications when the ambient temperature is

15 °C to 30 °C (59 ° to 86 °Fahrenheit) and the ambient relative humidity is 20% to 80%.

What to Avoid

When setting up the instrument, avoid:

♦ Placing the instrument under overhanging shelves, especially when there is a wall behind the unit.

♦ Proximity to other instruments on the same bench or other heat-generating equipment.

♦ Locations subject to wide temperature fluctuation, such as direct sunlight, or air drafts.

♦ Damp areas.

♦ Environments where there is an oil mist.

Do Not Block Air

Vents

Do not block the circulation of air to the vents located on the sides and bottom of the instrument air vents

Note

When operating multiple 9700 instruments, provide at least 8 in. of space in-between the instruments.


Fuse Service

Configuration

The instrument is shipped with double-line service configuration.

ELECTRICAL SHOCK HAZARD.

To protect yourself against shock hazards, use a properly wired three-terminal outlet. Do not use an adapter to a two-terminal outlet

.

FIRE HAZARD. Improper fuses can damage the wiring system and cause a fire. Before turning on the instrument, verify that the fuses are properly installed.

Input Voltage

IMPORTANT

You must be able to disconnect the main power supply to the instrument immediately if necessary.

The following table specifies the electrical operating range for the instrument in various parts of the world. Select the appropriate fuse configuration based on the voltage used.

Location

Japan

USA/Canada

EC

Voltage (VAC)

100 ±10%

120 ±10%

230 ±10%

a Frequency

50/60 Hz ±1%

50/60 Hz ±1%

50/60 Hz ±1%

Amperage (A) Nominal

3.16

4.20

3.14

a. Acceptable AC line voltage tolerances: 100, 120, 220, 230 ±10%; 240 VAC +6%/–10%, 50/60 Hz ± 1%.

Note

The Volt-Amp number for this instrument is 725 Volt Amps.

Interchangeable

Sample Block

Modules

The instrument features an interchangeable sample block module allowing portability and versatility in sample configuration.

Sample Block Module

96-Well Gold Sample Block Module

96-Well Aluminum Sample Block Module

60-Well 0.5 mL Sample Block Module

Dual 384-Well Sample Block Module

Auto-Lid Sample Block Module

Part Number

4314443

4314445

4309131

N805-0400

4312904

Note

The GeneAmp PCR System 9700 will not operate without an interchangeable sample block module installed.

For an example, refer to the GeneAmp PCR System 9700 96-Well Sample Block

Module User Guide, for instructions on how to install a block and configure the samples.


Double-Line Fuse

Introduction

FIRE HAZARD. For continued protection against the risk of fire, replace fuses only with listed and certified fuses of the same type and rating as those currently in the instrument.

IMPORTANT

For proper operation, you must know the power source(s) available and determine if the instrument fuse configuration is correct. The instrument is shipped configured for single-line operation.

Fuse Part Number

The correct fuse is an 8 amp Type T 250 V 5x20 mm fuse, P/N 0999-1683

.

Power Entry Module

Diagram

The following is a diagram of the Power Entry Module.

Fuse

Compartment door

Jumper clip

Fuse

Fuse compartment


Turning On the Instrument

Turning On the

Instrument

To turn on the instrument:

Step Action

1

Plug the power cord into the side of the instrument and into an outlet.

2

Press the power switch to the

ON

position.

The cooling fan powers up, and the Start-up screens appear.

APPLIED BIOSYSTEMS www.appliedbiosystems.com

F1 F2 F3 F4

Applied Biosystems

GeneAmp® PCR System 9700

Copyright © 1996

F5

3

F1 F2 F3 F4 F5

After several seconds the

Main

menu appears. You can use any of the functions displayed above the soft keys.

08:00 AM 4/25/01

GeneAmp® PCR System 9700

Name:tc001 User:<<pe>>

25.0°C

Run

F1

Create

F2

Edit

F3

Util

F4

User

F5

Note

The Main menu should appear within a few seconds. If any permanent patterns of lines or bars display on the screen, contact Applied Biosystems

Technical Support.


Setting Custom Parameters

Overview

The instrument is shipped with default configuration values. The following procedure describes how to set customized values as well as how to enable or disable optional features.

Displaying the

Configuration

Screen

To display the Configuration Screen:

Step Action

1

From the

Main

menu, press

Util

.

The Utilities screen appears.

2

Utilities

Diag - Instrument diagnostics

TmCalc - Calculates melting temp

Config - Instrument configuration

Diag

F1

TmCalc

F2

Config

F3

More

F4

Exit

F5

From the Utilities screen, you can take the following action:


Delete a method

Run instrument diagnostics

Review the history of a run

Access the T m

calculator

Copy methods to or from a methods transportability card

Press

Config

.

The first Configuration screen appears.

Instrument Configuration

Time: 11:30 AM

Date: 01/25/00 M/D/Y

Run Time Printer: Off

Run Time Beep: Off

Accept 24Hr PM More Cancel

F1 F2 F3 F4 F5

See page

5-20

3-13

4-10

3-17

3-24


Setting the Time

In the first Configuration screen, you can set the current time and date for file memory maintenance, and run-time displays. You can also enable or disable the run-time printer and the run-time beep.

To set the time:

Step Action

1

2

3

4

Use the Circular Key Pad to select the

Press the

24 Hr

or

PM (AM)

soft keys until the format you want for the current time displays in the Time field.

Use the numeric keys to type in the hours followed by minutes.

Press

Accept

Time

field.

when your entries are complete.

Note CE

clears an entry.

Setting the Date

You must set the instrument to the correct date.

To set the date:

Step Action

1

2

3

Use the circular key to select the

Date

field.

The three fields to set in the

Date

field are the:

♦ Days field

♦ Month field

♦ Year field

Press the

D/M/Y

or

Y/M/D

soft keys until the format you want for the current date displays in the Date field.

4

Use the numeric keys and type in a number for each of the three fields.

The order of these three fields depends on the format you chose in step 3.

Enabling or

Disabling a Printer

Enabling the printer allows you to print method parameters or records of run time events directly from the display screen. The default value for the optional printer is Off.

Note

For connection and configuration see “Connecting and Configuring a Printer” on page 3-26.

To enable or disable the optional printer:

Step Action

1

Select the

Run Time Printer

field. This changes the functions of the soft keys.

2

You can take the following action:

3

4


enable the printer disable the printer

Then...

Press ON.

Press Off.

Press

Enter

to accept your entry.

Press

Cancel

to cancel all entries and return to the previous screen.


Turning the

Run-Time Beeper

On or Off

When turned on, the run-time beeper beeps during a pause and once at the completion of a run. The default value is Off.

To turn the Run Time-Beeper on or off:

Step Action

1

2

Select the

Run Time Beep

field. This changes the value of the soft keys.


3


turn the beeper on turn the beeper off

Press

Enter


Then...

Press ON.

Press Off.

Setting the Pause

Time Out

The Pause Time Out field sets the time in minutes:seconds format for the length of a pause when you use the Pause soft key to pause a run from the Run Time screen. For more information on Pausing a Run, see “Pausing a Run” on page 4-8.

To set the pause time out:

Step Action

1

Select

More

to display the second configuration screen.

2

3


Pause Time Out: 10:00 (00:01-99:59)

Idle State Setpoint: 25.0°C (4.0-99.9)

Baud Rate: 9600

Accept More Cancel

F1 F2 F3 F4 F5

Set the

Pause Time Out

field by using the numeric keys to enter a time in minutes and seconds.

From this screen, you can also define the:

♦ Idle state setpoint temperature.

♦ Baud rate for your printer port.

Press

Accept

when all information on this screen is correct.

Note CE

clears an entry.


Defining the Idle

State Setpoint

Temperature

The Idle State Set Point temperature is the temperature at which the instrument will remain when powered up, but idle.

IMPORTANT

After a run is completed or terminated, there is approximately a 30 second delay before the instrument attains the specified idle state temperature. This allows you to stop one method and start another before the instrument temperature changes.

To define the Idle State Set Point temperature:

Step Action

1

2

Select the

Idle State Set Point

field.

Use the numeric keys and type in a temperature between 4.0° C and 99.9 °C.

3

Note

The default is 25 °C.

Press

Enter


Defining the Baud

Rate for Your

Printer Port

The following section contains a table that lists serial board specifications and a procedure that describes how to define the printer port value in the Baud Rate field.

Serial Board Specifications

You can connect the GeneAmp PCR System 9700 to any printer with a serial interface board and the following specifications.

Baud Rate

Parity

Data Bits

Stop Bits

9600

NONE

8

1

How to Set the Baud Rates

To set baud rates:

Step Action

1

2

Select the

Baud Rate

field.



increase the baud rate

Then...

Press Up.

decrease the baud rate Press Down.

3

Note

Available baud rates are 19200, 9600, 4800, 1200, 600, and 300.

Press

Enter



Configuring the

Contrast and Screen

Saver Options

You can use the third Configuration screen to set:

♦ Screen contrast from 1 to 20 (light to dark)

♦ Screen saver mode

Displaying the Screen

From the second Configuration screen, choose More to display the third Configuration screen.

Screen Saver Options

The following table lists the screen saver options:

Use This Option...

To Activate the Screen Saver...

Smart

Always

Never

After 15 minutes unless a method is running

After 15 minutes

Never

Setting the

IP Address

You can use the fourth Configuration screen to set the IP address for the instrument.

The instrument can be linked to a network via the RS485 ports located on the right-rear side of the instrument (see the figure on page 3-18). Once connected and configured, the instrument will be visible from the network under the IP address and instrument name you select in the following procedure.

Note

See the System 9700 Networking Software User’s Manual (P/N 4309575) for more information about networking GeneAmp PCR System 9700 instruments.

To set the IP Address for an instrument:

Step Action

1

Select

More

to display the second configuration screen.


Set IP: RS485 Name: Cycler 01

IP: 0. 0. 0. 1

2

3

4

Accept

F1 F2

-

F3

Set the

Set IP

field using the + and – keys.

+

F4

The following settings are available:

Cancel

F5

Setting

RS485

Definition

Activates the RS 485 ports.

Must be used with the networking software

Turns off the networking capability and turns on the RS232 ports.

Off

Use the Circular Key Pad to select the

Name

field.

Select

Name

.



To set the IP Address for an instrument:

(continued)

Step Action

5

Using the Circular Key Pad and

Enter

key, enter up to a 16 character name for identifying the instrument on the network.

6

7

8

abcdefghi jklmnopqr

IP Name: Cycler 01 stuvwxyz

.,-+/():=

Press ENTER key to select a character.

Accept Back sp Cancel

F1 F2 F3 F4

Press

Accept

when finished entering a name.

F5

The software returns to the previous screen and displays the new name in the

Name field.

Use the Circular Key Pad to select the last

IP

field.

Set the IP field by using the numeric keys to enter an IP address for the instrument.


Set IP: RS485 Name: Cycler 01

IP: 0. 0. 0. .1

9

Accept More Cancel

F1 F2 F3 F4 F5

Press

Accept

when all information on this screen is correct.

Running Instrument Diagnostics

Overview

The instrument provides a number of internal diagnostic utilities, tests you can run to verify that the instrument hardware and software components meet performance specifications.

Viewing the

Diagnostic Screen

The following procedure describes how to view the Diagnostic screen.

To view the Diagnostic screen:

Step Action

1

From the

Main

menu, press

Util

.

The Utilities screen appears.

Utilities




2

3

Diag TmCalc Config

F1 F2 F3

From the

Utilities

screen, press

Diag

.

The Diagnostics screen appears.

More

F4

Exit

F5

Diagnostics

Hard - Hardware Diagnostics

System - System Performance Tests

TmpVer - Temperature Verification

Upgrad - Firmware Upgrade

Hard System TmpVer Upgrad Exit

F1 F2 F3 F4 F5

Press the soft key that accesses the diagnostic utility you want to run:

Press this soft key...

Hard

System

To...

Access hardware diagnostic utilities that allow you to test hardware and electrical components such as the

Display screen and Keypad.

Access the system performance tests.

TmpVer

Upgrade

You can run these two system tests to test the rate of system heating and cooling, and the performance of

PCR cycling.

Access the temperature verification tests that allow you to verify sample block calibration and uniformity.

These two tests are discussed in the users manual for the interchangeable sample block.

Access a utility that allows you to update the 9700 instrument firmware through the RS485 serial port or using a PCMCIA Flash Memory card.


Testing the

Electrical

Components

Use the hardware diagnostic utilities to test the electrical components of the 9700 instrument.

To test the electrical components:

Step Action

1

From the

Diagnostics

screen, press

Hard

.

The Hardware Diagnostics appears.

2

Hardware Diagnostics

Disp - LCD Display Diagnostic

Keypad - Keypad Diagnostic

Disp Keypad Exit

F1 F2 F3 F4 F5

Use the corresponding soft key to select the hardware component for which you want to perform one of the following tasks:

Press this soft key...

Display

Keypad

To...

Visually determine if the Liquid Crystal Display

(LCD) screen is functioning properly.

Verify the operation of the keypad.


Testing the Display

Screen

The Display diagnostic test allows you to visually determine if the display screen is properly functioning by turning on and off all the LCD pixels.

To test the display screen:

Step Action

1

From the

Hardware Diagnostics

screen, press

Display

.

The Display Diagnostic screen appears.

2

Display Diagnostics

1. Read all instructions first.

2. Press Run to turn ON all pixels.

3. Press STOP to turn OFF all pixels.

4. Press STOP to exit.

Run Exit

F1 F2 F3


F4 F5

Press...

Run

Stop

Stop, again

To...

Turn ON all pixels.

Check display.

Turn OFF all pixels.

Check display.

Exit.


Testing the Keypad

Use the Keypad diagnostic test to verify that all 22 keys on the control panel are functioning properly.

To test the keypad:

Step Action

1

From the

Hardware Diagnostics

screen, press

Keypad

.

The Keypad Diagnostic screen appears.

2

Keypad Diagnostic

After pressing Run, press the blinking key or press STOP twice to exit.

Run

F1

Press

Run

.

F2 F3

The Control Panel screen appears.

F4

Exit

F5

3

STOP

F1 F2

F1 F2 F3 F4 F5

1 2 3

4 5 6

7

ENTER

8 9

0 CE

F4

Press the indicated flashing key.

F3 F5


Using the T

m

Calculator

How to Use the

T

m

Calculator

Use the T m

Calculator to determine the annealing temperature of a primer set of known sequence.

To use the T m

Calculator:

Step Action

1

From the

Main

menu, press

Util

. The Utilities screen opens as shown below.

2

Utilities




Diag

F1

Press

TmCalc

.

TmCalc

F2

The Tm Calculator appears.

Config

F3

More

F4

Exit

F5

3

4

5

6

7

[Salt]: 50 mM

P1: 5’

P2: 5’

Tm of P1=

[Primer] 0.20 uM

Tm of P2=

Press ENTER to calculate Tm’s

Enter the salt concentration.

Note

The default is 50. Enter values 5 to 1000.

Enter the primer concentration.

Note

The default it 0.20. Enter values 0.01 to 10.00.

Enter primer sequence in P1.

Enter primer sequence in P2 and press

Enter

to calculate the T m s.

The melting points are displayed. Use this information to program a run.

For more information, see Chapter 5, “Creating and Editing Methods.”

Press

Return

to display the

Utilities

screen.


Upgrading the System Firmware

Introduction

You can update the GeneAmp PCR System 9700 firmware from a serial connection to the RS485 port or from a PCMCIA Flash Memory Card.

\

Contact your local Applied Biosystems representative to obtain a PCMCIA Flash

Memory Card.

Upgrading Through the Serial Port

The following procedure describes how to upgrade the firmware through the RS485 serial port.

To upgrade the firmware through the RS485 serial port:

Step Action

1

Connect the appropriate communication cable from a computer to the RS485 port on the 9700 instrument Base Module (see the figure below).

You can use the following cables:

Communication cable

PC communication cable

Macintosh

®

communication cable

Part number

N805-1327

N805-1328

For information on connecting the printer cable, see page 3-26.

RS485

Ports


2

From the

Diagnostics

screen, press

Upgrade

.

The Firmware Upgrade screen appears.

Firmware Upgrade

PCcard - Upgrade from PC card

Serial - Upgrade from serial port

PCcard

F1

Serial

F2 F3 F4

Exit

F5

To upgrade the firmware through the RS485 serial port:

(continued)

Step Action

3

From the

Firmware Upgrade

screen, press

Serial

.

4

Serial Port Firmware Upgrade

Attach cable from RS485 port on 9700 to serial port on computer. Press Update, then begin download of file from the computer.

Update Exit

F1 F2 F3 F4 F5

IMPORTANT

Do not remove the cable or turn off the instrument until the upgrade is completed.

From the

Serial Port Firmware Upgrade

screen, press

Update

.

5

DO NOT TURN OFF THE INSTRUMENT

OR REMOVE SERIAL CABLE!

Upgrading over the serial port will take approximately 10 minutes.

Instrument will re-boot when complete.

F1 F2

Take the following action:

F3 F4 F5


Microsoft

™

Windows

®

95, or Microsoft

Windows NT

®

Microsoft Windows ®

3.1

See...

“Downloading Firmware Using Windows 95 or

Windows NT” on page 3-20.

“Downloading Firmware Using Windows 3.1” on page 3-21.


Downloading

Firmware Using

Windows 95 or

Windows NT

To download the system firmware using Windows 95 or Windows NT:

Step Action

1

2

Click

Start

Click the

>

Programs

>

HyperTerminal

Accessories

icon.

>

HyperTerminal

.

3

The Connection Description dialog box appears.

In the

Connection Description

dialog box, enter the following information and click

OK

. The Connect Using dialog box appears.

In this field...

Name

Icon

Take this action...

Enter a name, for example TEC.

Choose one of the icons.

4

5

6

7

In the

Connect Using

dialog box, connect using either

Direct to Com 1

or

Direct to

Com 2

, depending on the port to which the cable is attached.

Note

For Windows NT applications this dialog box is titled

Connect To

, and the fields are

COM1

and

COM2

.

Depending on whether you chose Com 1 or Com 2 in the previous step, in the

Properties

dialog box, enter the following.


Bits Per Second

Data Bits

Enter...

9600

8

Parity None

Stop Bits 1

Flow Control None

When you have competed entering the information, click

OK

.

From the

Transfer

menu, choose

Send file

.

z

The Send File dialog box appears.

In the

Send File

dialog box, enter the following and click

Send

.


Filename

Protocol

Take this action...

Locate the upgrade file with the name under which you saved the file.

Enter Kermit.

8

A dialog box appears that displays the current packet number and the number remaining. When the download is complete, the GeneAmp PCR System 9700 automatically resets.

From the

File

menu, choose

Save

to save the parameters.


Downloading

Firmware Using

Windows 3.1

To download the system firmware using Windows 3.1:

Step Action

1

2

3

From the

From the

Program Manager

Settings

, click the

menu, choose

Terminal

program icon.

Communication

. A dialog box appears.

Enter the following information in the dialog box and click

OK

.

4

5

6

7

8


Baud Rate

Data Bits

Stop Bits

Parity

Flow Control

Connector

Enter...

9600

8

1

None

None

Com1 or Com2 (depending on the port to which the cable is attached).

From the

Binary Transfers

menu, choose

Settings

. A dialog box appears.

Select

Kermit

and click

OK

.

From the

Send Binary File

menu, choose

Transfers

.

A directory dialog box appears.

From the directory dialog box, find and select the

9700 upgrade file

, and click

OK

.

A message at the bottom of the window indicates that the program is sending the file and a progress bar appears.

When the download is complete the GeneAmp PCR System 9700 automatically resets.

When the download is complete, from the

File

menu, choose

Save

to save these parameters.


Upgrading

Firmware from a

PCMCIA Flash

Memory Card

The following procedure describes how to upgrade the firmware using a PCMCIA

Flash Memory Card.

Note

Contact your local Applied Biosystems representative to obtain a PCMCIA

Flash Memory Card.

To upgrade using a PCMCIA Flash Memory Card:

Step Action

1

Insert a PCMCIA Flash Memory Card that contains the updated firmware into the slot at the rear of the right side of the instrument.

Note

The label and arrow on the card face forward and toward the instrument.


2

3

4

5

PCMCIA Flash Memory Card

Press the card firmly to ensure the card is seated in the slot.

IMPORTANT

Do not remove the card or turn off the instrument until the upgrade is completed.

From the

Diagnostics

screen, press

Upgrade

.

From the

Diagnostics

screen, press

PCcard

.

The

Checksum

screen appears while the instrument checks the inserted PCMCIA

Flash Memory Card to ensure that it contains a valid firmware upgrade.

F1

Checking PC card checksums...

F2

Update

F3 F4

Exit

F5

To upgrade using a PCMCIA Flash Memory Card:

(continued)

Step Action

6

If the PCMCIA Flash Memory Card contains a valid firmware upgrade, the screen appears.

Upgrade

7

DO NOT TURN OFF THE INSTRUMENT

OR REMOVE THE PC CARD!

Upgrading the instrument firmware will take approximately 30 seconds.

Instrument will re-boot when complete.

F1 F2 F3 F4 F5

If successful, the

Firmware Upgrade Successful

screen displays the firmware version to which you have upgraded.

Pressing the

Run

key in the lower right corner brings up the

Main

menu with the new revision number of the software listed on the screen.

Remove the PCMCIA Flash Memory Card after you have successfully upgraded the firmware.


Copying Methods

How to Copy

Methods

You can copy methods from a Methods Transportability card to the instrument or from the instrument to a Methods Transportability card (P/N 940-1064). Runs can be made directly from methods on a Methods Transportability card.

To copy a method:

Step Action

1

Insert a Methods Transportability card that contains the updated firmware into the slot at the rear of the right side of the instrument.

Note

The label and arrow on the card face forward and toward the instrument.


2

3

Methods Transportability Card

Press the card firmly to ensure the card is seated in the slot.

IMPORTANT

Do not remove the card or turn off the instrument until the upgrade is completed.

From the

Utilities

screen, press

More

, and from this secondary utility screen, press

Copy

. The

Copy Method

dialog box appears.

Copy Method

ToInst - Copy a method to the instrument

ToInst

F1

ToCard

F2 F3 F4

Cancel

F5

To copy a method:

(continued)

Step Action

4

In the

Copy Method

dialog box, you can take the following action:

5

6

Press...

ToInst

ToCard

To...

Transfer a method from a Methods Transportability card to the instrument.

Transfer a method from the instrument to a Methods

Transportability card.

A screen appears with a list of the methods on the instrument or the Methods

Transportability card, depending on whether you selected ToInst or ToCard.

Methods on Inst

XL PCR

Touchdown PCR

AmpliTaq Gold™

AmpliCycle Seq

Copy

F1

View

F2

User

F3

User

<<pe>>

<<pe>>

<<pe>>

<<pe>>

Sort

F4

Size

11

6

9

8

Stored

9/9/96

9/9/96

9/9/96

9/9/96

Cancel

F5

Use the Circular Key Pad to select a method and press

Copy

.

Confirmation appears when the method has been successfully copied.

Copy Method

Method XXXXX was successfully copied to the PC card.

Copy another method?

Yes No

F1 F2 F3 F4 F5


Connecting and Configuring a Printer

Connecting a Printer

If you connect an optional printer to your 9700 instrument, you can print out a hard copy of the time and temperature parameters for the PCR methods you create.

Connect one end of your printer cable (N805-1326) to the RS-485 serial port on the side panel of the 9700 instrument and connect the other end to the RS-232C interface serial adapter on the rear panel of the printer.

Configuring the

Printer

After you have connected the printer cable to the printer, you must configure the instrument for the printer. You can connect the 9700 instrument to any printer with a serial board and the following specifications:

Baud Rate

Parity

Data Bits

Stop Bits

8

1

9600

NONE

See your printer manual for instructions on how to complete any other necessary installation steps.


Running PCR Samples

4

4

Overview


This chapter provides information on selecting a method, starting and stopping a run, reviewing the history of a run, and what to do when the run is completed.

In This Chapter


Topic

Selecting a Method

Running a Method

Reviewing the History of a Run

When a Run Completes

See page

4-2

4-6

4-10

4-12

Note

For information on loading and unloading samples, see the instructions accompanying your interchangeable sample block module.

Running PCR Samples 4-1

Selecting a Method

Introduction

After you have prepared your samples and loaded them in the sample block, you can run a PCR amplification with a new or a stored method.

What Is a Method

A method is a set of instructions in which you specify how the instrument should heat and cool your samples in a PCR thermal profile.

Methods are stored in the instrument software.

Predefined Methods

The GeneAmp

®

PCR System 9700 supplies eight predefined methods that you can run:

♦ AmpliCycle

® Sequencing

♦ AmpliTaq Gold

®

DNA Polymerase

♦ BigDye

® Terminators

♦ General PCR

♦ LSM2

♦ Time Release PCR

♦ Touchdown PCR

♦ XL PCR

Each of these methods is stored under the user name <<pe>>. You can edit these methods and store them under a different name, a different user name, or select any one and run it.

For a detailed description of each of these pre-coded methods, and how you can use them, see Appendix B, “Supplied Methods.”

4-2 Running PCR Samples

Selecting a Method

If the method you want to run has already been created and stored, you can select it from a list. If the method you want to run has not been created, see Chapter 5,

“Creating and Editing Methods.”

To select a method:

Step Action

1

From the

Main

menu, press

Run

.

Note

If a PC card is inserted, choose whether to run the method from the PC card or the instrument.

The

Stored Methods

screen appears.

2

3

4

5

Methods on Inst User Size Stored exp001 lisa 10 06/23/96 exp002 lisa 15 06/25/96

Start

F1

View

F2

User

F3

Sort

F4

Cancel

F5

Note

Stored

represents the date the method was last saved. In the appropriate case, this column designates the date last used.

The units for the

Size

field are based on a calculation of the complexity and length of a method relative to a maximum size of 1102 size segments for the storage capacity of the instrument.

If you need help deciding which method to select you can:

♦ View method parameters.

♦ Sort methods by different categories.

♦ Search for a method by user name.

Select a method by using the Circular Key Pad to move the highlight box to a method listed on the

Stored Methods

screen.

Note

You can use the up and down keys as repeat keys for quick scrolling.

The top line of the display continuously cycles between the following three lines:

♦ Methods on Inst User Size Stored.

♦ Used Mem: xxx methods xxx segments.

Note

The

Used Mem

field displays the number of size segments used by all stored methods.

♦ Free Mem: xxx methods xxx segments.

Note

The

Free Mem

field displays the number of size segments available to store created methods.

Press

Start

and start running your samples (see “Running a Method” on page 4-6).


Viewing Method

Parameters

To view parameters of a method before running:

Step Action

1

From the

Stored Methods

screen, press

View

.

The

View Method

screen appears. The screen shows all the parameters of the method you selected.

2 Hld

55.0

2:00

94.0

10:00

3 Tmp 25 Cycles

94.0

0:30

55.0

0:30

72.0

0:30

2 Holds

72.0

5:00

4.0

2

Start

F1 F2

Method: exp 001

F3 F4

Return

F5

After reviewing PCR and post-PCR parameters of a stored method, you can:

♦ Press

Start

to start the method.

♦ Press

Return

and return to the

Stored Methods

screen.

Note

You cannot edit parameters from the

View Method

screen.

Searching for

Methods

You can find any method that has been stored under a user name.

To search for a method:

Step Action

1

From the

Stored Methods

screen, press

User

.

Select which user’s methods to view by taking the following action.

2


Then...

list all the methods currently stored on the instrument Press All.

display the methods stored under that user’s name Press Accept.

Note

You cannot add, delete, or modify a user name from this screen.

Making a selection returns you to the

Stored Methods

screen which now displays the methods of the user you selected.


Sorting Methods

If you have a large number of stored methods, you can sort them by name, date last used, date stored and size.

To sort methods:

Step Action

1

From the

Stored Methods

screen, press

Sort

.

The sorting criteria screen appears.

2

3

Sort Methods

By: Method name

Date last used

Date stored

Method size

Accept

F1 F2 F3 F4

Cancel

F5

Use the up and down Circular Key Pad to select the type of sort.

The following table describes the sort methods:

Choose this item...

Method name

Date last used

To sort...

Methods alphabetically.

Methods chronologically in descending order by date of use.

The last method which ran or was stored is listed first.

Methods chronologically by date stored.

The last method stored is listed first.

Date stored

Note

Uses the most recent title and date, between date last used and the data stored.

Method size Methods in increasing order by the amount of memory used to store each method.

The largest size method is listed first.

Press

Accept

to accept a selection.

This returns you to the

Stored Methods

screen where the displayed methods are sorted according to your selection in step 2.


Running a Method

Starting a Run

After choosing a method, follow these steps to start a run.

To start a run:

Step Action

1

From the

Main

menu, press

Run

to display stored methods.

2

3

Use the up and down Circular Key Pad to select the method.

a. Press

Start

.

The

Select Method Options

screen appears.

b. Choose from the following options:

4

96-Well Gold

Sample Block

Module

Select

9600

or

MAX

mode first, and then select

volume

.

Select Method Options

Reaction Volume: 50 µL

Ramp speed: 9600

Enter a value from 5 to 50 µL

Start

9600 MAX

F1 F2 F3 F4

Select

9600

or

STD

mode first, and then select

volume

.

Cancel

F5

96-Well

Aluminum

Sample Block

Module

Select Method Options

Reaction Volume: 50 µL

Ramp speed: 9600

Enter a value from 5 to 50 µL

Start

9600 STD

F1 F2 F3 F4

Cancel

F5

If the displayed reaction volume differs from your reaction volume, enter the volume of your reactions in the

Reaction Volume

field.

The reaction volume range is dependent on the mode selected.

For...

9600 mode

MAX/STD mode

The range is...

5 to 50 µL.

5 to 100 µL.

Note

Each method remembers the reaction volume.

Press the

CE

key to clear an entry.


To start a run:

(continued)

Step Action

5

Press

Start

to start a run.

If the temperature of the heated cover is less than 103 °C, this message, “Cover is heating” appears.

6

Please wait. Cover is heating

Current temperature: 65°C

The run will begin when the heated cover reaches 103°C.

Cancel

F1 F2 F3 F4 F5

When the heated cover reaches 103 °C, the

Run Time

screen displays and the method you selected starts running.

For a description of this screen, see “About the Run Time Screen” on page 4-7.

Sample 56.7

Cycle 1 of 25

55.0

2:00

94.0

10:00

94.0

0:30

55.0

0:30

72.0

0:30

72.0

5:00

Pause

F1 F2 F3

Info

F4

HOT

4.0

F5

About the Run Time

Screen

You can use the Run Time screen to chart progress at any time during the run. The

Run Time screen displays the executing segment, and the next segment to execute.

Horizontal lines flash as hold times decrement

Cycles count up when run is in PCR segment

Sample 56.7

Cycle 1 of 25

55.0

2:00

94.0

10:00

94.0

0:30

55.0

0:30

72.0

0:30

72.0

5:00

Pause

F1 F2 F3

Pre-PCR segment

PCR segment

Calculated sample temperature updated as run progresses

HOT

4.0

Temperature parameters are displayed above the graph

HOT displays when the sample block exceeds 50 °C

Info

F4

Post-PCR segment

F5

Hold times are displayed below the graph

Ramps flash when system is approaching next temperature value

Use the Run Time screen for...

Viewing Method Information

Pausing a Run

Stopping a Run Before It Completes

For more information, see page

4-8

4-8

4-9


Viewing Method

Information

You can view the Method Information screen during a run by pressing Info. Press

Return to return to the Run Time screen.

02:32 PM Information 55.2°C

User: lisa Method: XL PCR

Run started at 01:32:30 PM, 01/01/00.

Run will end at 06:35:30 PM, 01/01/00.

Reaction vol: 50 µL Ramp Speed: 9600

Return

F1 F2 F3 F4 F5

Pausing a Run

You can manually pause a run for a ten minute period of time during a run by pressing

Pause (Figure 4-1). If you want to specify a different period of time for a pause, see

“Setting the Pause Time Out” on page 3-9.

Press Resume to resume running a method before a pause expires.

Note

You can pause a run in order to add a reagent. Do not to touch the sample block or the bottom of the heated cover during a pause.

Sample 56.7

Cycle 1 of 25

55.0

2:00

94.0

10:00

94.0

0:30

55.0

0:30

72.0

0:30

Resume

F1

72.0

5:00

HOT

4.0

Paused. Will resume in mm:ss

F2 F3 F4 F5

Figure 4-1

Pause screen

Your samples remain at the temperature of the instrument when you pause the run.

The time remaining in a pause appears at the bottom of the screen in minutes:seconds format. It decrements to zero, and the paused run resumes at the point where you paused it.


Stopping a Run

Before It Completes

The following procedure describes how to stop a run before it completes.

To stop a run before it completes:

Step Action

1

Press the

Stop

key.

The

Stop confirmation

screen appears.

Sample 50.1

Confirm Stop

HOT

Press STOP to abort.

Press Resume to continue.

2

Resume

F1 F2 F3 F4 F5

The run pauses for a pre-programmed period of time. When the pause time expires, the run aborts.

Press

Resume

to resume.

Note

The stop and pause times are configured by setting the

Pause Time Out

. See

“Setting the Pause Time Out” on page 3-9.

Press the

Stop

key again.

This stops the run and the

End of Run

screen appears.

3

11:30 AM End of Run 25.1°C

Method:exp001

Run aborted at 11:30:05 AM 01/01/00.

Length of run is 01:34:25.

Hist

F1 F2 F3 F4

Exit

F5

If any errors occur during a run the following message appears, “Exception occurred, check history file.” Press

HIST

to review the history file.

Press

Exit

to return to the

Main

menu.


Reviewing the History of a Run

How to Review the

History of a Run

You can read a record of the events and errors that occurred during a run by reviewing the history file. The instrument stores the history file until it is overwritten by the next method used.

To review the history:

Step Action

1

To display the History File screen:

♦ From the

Utilities

screen, press

More

, and then press

Hist

.

♦ From the

End of Run

screen, press

Hist

.

2

3

History of method exp002

User: lisa Reaction volume: 50 µL

Run started at 02:30:45 PM, 01/01/00.

Run aborted at 02:50:42 PM, 01/01/00.

Length of run 00:19:57 Ramp speed: 9600

No exceptions

PageDn Print Return

F1 F2 F3 F4 F5

Press

PageUp

to move up through the record, or

PageDn

to move down.

Press

Print

to print the record.

]

History Formats

The following table lists the history line formats.

Pre-PCR hold

PCR segment

Any other hold

<Exception> in Pre-PCR xx Setpt xx

<Exception> in Cycle xx Setpt xx Repxx

<Exception> in Hold xx Setpt xx


History File Records

The following table lists the history file records.

Record

History of method xxxxxxxxxxxxxxx

User xxxxxx Reaction volume xxx µL

Run started at hh:mm:ss am mm/dd/yy

Run ended at hh:mm:ss am mm/dd/yy

Length of run hh:mm:ss RampSpeed: 9600

Power failure in Cycle xx at Setpt xx.

Power failed at hh:mm:ss am for hh:mm:ss.

Run resumed at hh:mm:ss am

Drift error in Cycle xx Setpt xx Repxx. Temperature drifted x.x°c from setpt

Cover error in Cycle xx Setpt xx Repxx.

Heated cover at xx.x°c

Sensor error in Cycle xx Setpt xx Repxx.

Block sensor failure.

Sensor error in Cycle xx Setpt xx Repxx.

Cover sensor failure.

Setpt error in Cycle xx Setpt xx Repxx.

Could not reach xx.x in hh:mm:ss

Program pause in Cycle xx Setpt xx Rep xxx Method paused at xx °C for hh:mm:ss

Manual pause in Cycle xx Setpt xx Rep xxx Method paused at xx °C for hh:mm:ss

Description

This header record is always created.

Note

If you stopped a method before it completed running, then the message, Run ended at..., will be Run aborted at...

There was a power failure during a specified point in a cycle.

The message, for >18, indicates that the power was off for more than 18 hours.

Block drift error.

The block has drifted ± 2 °C from set point during the hold segment of a run.

Heated cover drift error.

The cover has drifted ± 5 °C from

105 °C anytime during the run.

Block sensor failure.

Type

Report

Report

Report

Report

Heated cover sensor failure.

Fatal error.

Call for service.

Fatal error.

Call for service.

Fatal error.

Call for service.

This setpoint error is only logged for setpoints above 15 °C.

The limit is 5 times the normal ramping time.

A programmed pause was encountered.

You paused the run.

Report

Report


When a Run Completes

End of Run Screen

At completion of a run, the instrument beeps and the End of Run screen appears.

From the End of Run screen you can perform the same functions as you can from the

Stop Run screen.

11:30 AM

Method: XL PCR

Run completed at 11:30:05 AM, 01/01/00.

Length of run is 01:34:25.

Hist

F1 F2 F3 F4

Exit

F5

If you have not yet stored the method, you must store it before exiting, or you will lose the settings. The Store soft key appears if the method has not yet been stored.

Method Not Stored

Screen

If you attempt to exit the End of Run screen before storing the method, the Method Not

Stored screen displays.

Method Not Stored

Press Store to save the method.

Press Exit to delete the method.

F1

Store

F2 F3 F4

Exit

F5

The following table lists the actions you can take.

If you...

Then press...

want to store the method

Store

.

do not want to store the method

Exit

.

Note

The

Method Not Stored

screen appears for a few seconds before the Exit key is recognized. This prevents you from losing a newly created method.

You return to the top level screen and the method you created is not saved.


Creating and Editing

Methods

5

Overview


This chapter provides information about how to create and edit PCR methods and how to work with stored methods.

In This Chapter


Topic

Adding or Changing Users

Creating Methods

Modifying Cycling

Printing a Method

Editing or Deleting Methods

See page

5-2

5-6

5-11

5-17

5-18

5

Creating and Editing Methods 5-1

Adding or Changing Users

Introduction

The GeneAmp

®

PCR System 9700 stores methods by user’s names. You can add up to 19 different user names to the instrument. Once you’ve added your name to a list of users, and stored a method under that name, you can run the method at any time by selecting it from the Stored Methods screen (See “Selecting a Method” on page 4-3).

Use the User function on the Main menu to add new users or edit existing user names.

The name you add or the name you select from a list of existing user names becomes the current user name. All new methods that you create are stored by default under the current user name.

Adding a New User

Name

You add a new user name by entering an alphanumeric name on the User Name screen.

To add a new user name:

Step Action

1

From the

Main

menu, press

User

.

The

Select User Name

screen appears. A list of names of all users who have been added to the instrument displays in a 4 x 5 matrix.

2

Select User Name

<<pe>> adrian doug peter

Accept New Edit Delete

F1 F2 F3 F4

Press

New

to add a new name to the above list.

The

User Name

screen appears.

Cancel

F5

Note

The blank space after the z is used to insert the blank spaces.

User Name abcdefghi jklmnopqrj stuvwxyz

.,-+/():=

Use ENTER key to select a character.

Accept Backsp Cancel

F1 F2 F3 F4 F5

5-2 Creating and Editing Methods

To add a new user name:

(continued)

Step Action

3

In the

User Name

field, enter an alphanumeric name up to six characters in length.


4


select a character in the list shown in the upper right portions of the screen put the alphabetic character in the

User Name field enter the numbers directly into the

User Name field go back one space and remove a single character

Then...

use the Circular Key Pads.

press

Enter

.

use the numeric keys.

hold down the Soft key and go back multiple spaces.

Press

Accept

to accept a name. The

Security Code

screen appears.


If you...

do not want to protect your method want to protect your method

Then...

press

Accept

again.

see the following section titled

“Protecting Methods.” press

Cancel

.

want to return to the Main menu without adding the new user name

Note

An error message appears if you enter a name that already exists.

Protecting Methods

You can protect methods and prevent other users from accidentally overwriting or deleting them by entering a Personal Identification Number (PIN#) on the Security

Code screen.

User Name: hank PIN number: None

Protection: Unlocked

Press PIN # to create a #. Then you set protection to Locked to prevent methods from being overwritten or deleted.

Accept Name PIN# Cancel

F1 F2 F3 F4 F5

The following table lists the two levels of protection.

If a...

user has entered a PIN # method is locked

Then other users cannot...

edit that user’s name without knowing the PIN #.

delete/overwrite the method.


Follow the procedure below to protect a method.

To protect a method:

Step Action

1

Press

PIN #

.

The

New PIN Number

screen appears.

4

5

2

3

6

7

Create a PIN Number

Your PIN number protects the access to your user name and protection level

Enter a PIN number. New PIN #: XXXX

Accept Cancel

F1 F2 F3 F4 F5

In the

New PIN #

field, use the numeric keys and type in a four-digit PIN.

Press

Enter

.

The

PIN Confirmation

screen appears.

Confirm PIN Number

Your PIN number protects the access to your user name and protection level

Enter a PIN number again. PIN #: XXXX

Press Accept to confirm your PIN #.

Accept Cancel

F1 F2 F3 F4 F5

Confirm your PIN by typing your four-digit PIN in the Confirm PIN # field.

Press

Enter

.

The

Protection Status

screen appears.

Username: hank PIN number: XXXX

Protection: Unlocked

Press PIN # to create a #. Then you set protection to Locked to prevent methods from being overwritten or deleted.

Accept Name PIN# Lock Cancel

F1 F2 F3

Press

Lock

to lock your method.

F4 F5

This toggles between a Locked and Unlocked state. The

Protection

field displays the status of the method.

Press

Accept

when you have entered a PIN you want to keep. The

Select User

Name

screen appears.

The new name you entered should now display on the screen.

Press

Cancel

to cancel your entry and return to the previous screen.


Changing a User

Name

If you know the personal identification number for a user name, you can use the

Circular Key Pad to select that name, and change it.

To change a user name:

4

5

6

7

8

Step Action

1

From the

Main

menu, press

User

.

2

3

The


screen appears.

Use the Circular Key Pad to select the name you want to change.

Press

Edit

.

If a PIN has been previously entered, the

Security Check

screen appears.

Type in the four-digit PIN of the user name you selected.

Press

Name

to enter a new user name.

Press the

CE

key to clear the previous name.

Enter a new user name.

Press

Accept

.

The Security Code screen appears again.

Deleting a User

Name

If there aren’t any methods stored under a user name, you can delete that name from the Select User Name screen.

To delete a user name:

Step Action

1

2

Use the Circular Key Pad from the

Press

Delete

to delete the name.


screen to select a user name.

This removes the name from the Select User Name screen and allows you to add a new name to the instrument.


Creating Methods

About the Default

Method

The GeneAmp PCR System 9700 comes with a default PCR thermal profile called a method. The create screen displays this default method. For information on displaying the create screen, see “Displaying the Create Methods Screen” on page 5-7.

You can run the default method shown above, or use it as a template to create a customized method.

Number of temperature control parameters in the

PCR segment

Number of cycles the

PCR segment will run

Number of temperature control parameters in the post-PCR segment

Number of temperature control parameters in the pre-PCR segment

1 Hld

94.0

5:00

Start

F1

3 Tmp

94.0

0:30

Store

F2

25 Cycles 2 Holds

55.0

0:30

72.0

0:30

72.0

7:00

4.0

Print

F3

More

F4

Cancel

F5

Pre-PCR segment PCR segment Post-PCR segment

Basic Parameters

To create a method, you need to define the following four basic parameters:

♦ Temperature Control Parameters

♦ Pre-PCR Holds

♦ PCR Parameters

♦ Post-PCR Holds

For detailed information about these parameters refer to the table below:

For information about...

Entering Temperature Control Parameters

Defining Pre-PCR Holds

Defining PCR Parameters

Defining Post-PCR Holds

See page

5-8

5-9

5-9

5-10


Displaying the

Create Methods

Screen

Follow the steps below to display the Create Methods screen.

To display the Create Methods screen

Step Action

1

From the

Main

menu, press

Create

. The create screen appears.

2

1 Hld

94.0

5:00

3 Tmp

94.0

0:30

25 Cycles 2 Holds

55.0

0:30

72.0

0:30

72.0

7:00

4.0

Start

F1

Store

F2

Print

F3

More

F4

Cancel

F5

From the

Create

screen, you can take the following action:


Then...

start running the default method press

Start

.

store the method under a user’s name press

Store

.

press

Print

.

print a record of the method parameters enter temperature control parameters display more functions for modifying methods enter the information on the create screen and create a new method.

press

More

.

Note

The More function only displays when you select a time or temperature parameter. For detailed information on using the More function to modify cycles, see “Modifying Cycling” on page 5-11.

return to the previous screen press

Cancel

.


Entering

Temperature

Control Parameters

When you enter temperature control parameters, you define values for parameters in each of the three segments of a method: pre-PCR, PCR, and post-PCR.

To enter temperature control parameters:

Step Action

1

On the

Create

screen, select a field.

2

3

When you first display the Create screen, the

Hld

field is highlighted.

Use the numeric keys to enter values.

Press

Enter

to accept a value. The next field is then selected in the order shown in

Figure 5-1.

4 6 8 5 10 12 13 15

1

2

3

1 Hld

94.0

5:00

3 Tmp

94.0

0:30

25 Cycles 2 Holds

55.0

0:30

72.0

0:30

72.0

7:00

4.0

Start

F1

7

Store

F2

9

Print

F3

11

More

F4

14

Cancel

F5

Pre-PCR segment PCR segment Post-PCR segment

16

Figure 5-1

Order of advancement of the highlight box

11

12

13

14

7

8

9

10

15

16

Number Description

1

2

Number of pre- PCR holds

Pre-PCR temperature parameter

5

6

3

4

Pre-PCR hold time parameter

Number of PCR segment temperatures

Number of cycles for the PCR segment

PCR segment temperature parameter

PCR segment time parameter





Number of post-PCR holds

Post-PCR temperature parameter

Post-PCR hold time parameter

Post-PCR temperature parameter

Post-PCR hold time parameter


Defining Pre-PCR

Holds

The Hld field on the Create screen defines the number of holds for the pre-PCR segment of your method. One (1) is the typical setting for most PCR amplifications and is the default value for the Hld field.

Generally, pre-PCR holds define a temperature and hold-time sufficient to denature any endonucleases or exonucleases that may contaminate your prepared samples.

To define pre-PCR holds:

Step Action

1

On the

Create

method.

screen, in the

Hld

field, type in the number of pre-PCR holds for your

2

3

4

Note

You can enter 0 in this field to delete the pre-PCR hold segment from your method.

Create the first temperature parameter: a. Press

Enter

. b. Type in a temperature value between 4.0 °C and 99.9 °C.

Create the first hold-time parameter: a. Press

Enter

.

b. Type in a hold-time value between 00:00 and 98:59 (minutes:seconds).

Enter information for the next pre-PCR hold: a. Press

Enter

.

b. Repeat step 2 and step 3 until you have hold-time and temperature values for each of the pre-PCR hold parameters you defined in step 1.

Defining PCR

Parameters

The Tmp field on the Create screen defines the number of temperature control parameters in the PCR cycling segment of your method. Three temperature PCR is the typical setting for many PCR amplifications:

♦ Template denaturation

♦ Primer annealing

♦ Primer extension

To define the PCR parameters:

Step Action

1

On the

Create

screen, in the

Tmp

field, type in the number of temperature control parameters (2–6) you want for the PCR segment of your method.

2

3

Note

Specifying only the minimum number of PCR cycles required for analysis will minimize the chance that unwanted targets will amplify competitively.

Enter the number of cycles you want the method to run: a. Press

Enter

to select the

Cycles

field.

b. In the

Cycles

field, type in the number of cycles (from 2–99).

Note

Twenty-five cycles is the default setting.

Create the first temperature parameter: a. Press

Enter

. b. Type in a temperature value between 4.0 °C and 99.9 °C.


To define the PCR parameters:

(continued)

Step Action

4

5

Create the first hold-time parameter: a. Press

Enter

.

b. Type in a hold-time value between 00:00 and 98:59 (minutes:seconds).

Repeat step 3 and step 4 until you have time and temperature values for each of the segment temperature control parameters you defined in step 1.

Defining Post-PCR

Holds

On the Create screen, the Holds field defines the number of temperature control parameters in the post-PCR segment of your method.

The post-PCR incubation temperature and hold time parameters define how to hold your samples at a specified temperature until you are ready to analyze them.

Note

If the idle state setpoint, or the last hold of the Method are below 15 °C, then the heated cover will automatically set to 50 °C.

Post-PCR Parameter Settings

Typical Post-PCR parameter settings:

Temperature

72 °C

72 °C

4 °C

Time (min:sec)

7:00

99:59 (×)

99:59 (×)

Use For

Complete extension of all amplicons

AmpErase

™

applications

General storage

Follow the procedure below to define Post-PCR Holds

To define post-PCR holds:

Step Action

1

Select the

Holds

field.

2

3

In the Holds field, type in the number of post-PCR steps for your method.

Press

Enter

to select the first post-PCR temperature parameter.

4

5

6

Type in a temperature value between 4.0 °C and 99.9 °C.

Press

Enter

to select the first post-PCR hold time parameter.

Type in a hold time value between 00:00 and 98:59 (min:sec).

7

8

Note

The hold time × indicates a hold that lasts indefinitely. You can enter an × hold time, by typing a hold time value of 99:00 or greater.

Press

Enter

. This selects the next temperature parameter.

Repeat step 4 through step 7 until you have time and temperature values for each of the post-PCR hold parameters you defined in step 2.


Modifying Cycling

Introduction

In addition to customizing values for PCR temperature control parameters, you can use the More function on the create screen and access cycle modification functions that allow you to:

♦ Auto-increment/decrement time and temperature parameters.

♦ Modify up-ramp and down-ramp rates in the cycling segment of a method.

♦ Insert holds, cycles, and programmed pauses.

♦ Delete temperature control parameters.

The time or temperature parameter you select on the create screen, determines which modification function you can access when you press More. Different modification functions are available depending on whether you select a temperature control parameter in the pre-PCR segment, the PCR segment, or the post-PCR segment of a method.

Changing

Temperature

Control Parameters

Using the AutoX function, you can automatically increase or decrease the value for any PCR segment parameter by a fixed amount every cycle.

Note

This feature is particularly useful towards the end of the amplification process since the amount of PCR product, available to be extended, increases with the number of cycles while the amount of available enzyme remains constant.

To automatically change temperature control parameters:

Step Action

1

From the

Create

screen, use the Circular Key Pad to select a time or temperature parameter in the PCR segment.

2

Press

More

.

3

4

The

Modify

screen appears.

Press

Modify

.

The

Select Modification

screen appears.

Press

AutoX

. The

AutoX

screen appears.

5

2 Pre-PCR 3 Tmp 25 Cycles 2 Holds

Accept +

+0.0

+0:00

*

+1.0

-0:30

*

-

+0.0

+0:00

Cancel

F1 F2 F3 F4 F5

Note

If you have inserted a programmed pause, the AutoX screen displays the pause, but you cannot modify it from the AutoX screen.

Select the PCR time or temperature parameter that you want modified when you run your method.

Note

From the AutoX screen, you cannot modify the number of parameters in each segment or the number of cycles.


To automatically change temperature control parameters:

(continued)

Step Action

6



increase the value every cycle

(a plus sign displays in the current field) decrease the value every cycle

(a minus sign displays in the current field)

Then press...

+ (plus sign).

- (minus sign).

7

An asterisk * appears on method screens for parameters that have been modified.

Press

Accept

to accept all entries on the AutoX screen.

Modifying Ramp

Rates

The ramp time is the time it takes the instrument to change from one temperature to another. Using functions accessible from the Modify screen, you can modify the up-ramp and down-ramp rates of the instrument by defining it as a percentage of the temperature’s maximum rate of increase. The default maximum up-ramp and down-ramp rates is 100%.

To modify ramp rates:

Step Action

1

2

Press

Press

Modify

Ramp

from the Modify screen. The

. The

Ramp Rate Modification

Select Modification

screen appears.

screen appears.

3

4


94.0

100%

55.0

100%

72.0

100%

Accept

F1

Faster

F2

Slower

F3 F4

Cancel

F5

In this example, you can modify the rate at which the instrument ramps up from

72.0 °C to 94.0 °C, down from 94.0 °C to 55.0 °C, or up from 55.0 °C to 72.0 °C.

Use the Circular Key Pad to select a ramp that you want to modify.

Move the highlight box to the third temperature in the cycling segment of the default method to modify the highlighted ramp rate.

The third ramp rate defines the rate at which the instrument increases from 55.0 °C to 72.0 °C each time the method cycles.


94.0

100%

55.0

100%

72.0

100%

Accept

F1

Faster

F2

Slower

F3 F4

Cancel

F5


To modify ramp rates:

(continued)

Step Action

5

Modify the up-ramp and down-ramp rates you selected by defining them as a percentage of the maximum of 100%:

6


increase the ramp rate by 10% up to a maximum of 100% decrease the ramp rate by 10% from 100% to 10%, and by 5% from 10% to 5%

Then press...

the

Faster

key.

the

Slower

key.

Note

You can also use the numeric keys to enter a value that defines the percentage by which you want to decrease the ramp rate for each cycle of the method. You can enter values between 5 and 95, or 100.

For ramp rates less than 100%, an asterisk * appears next to modified ramps. The asterisk remains beneath the modified temperature parameter to remind you that the method has been modified.

Note

The following message appears if you enter a numeric value outside the range of acceptable values, “Valid range is 5 to 95 and 100.”

Press

Accept

to accept all entries, and return to the previous screen.

Inserting Holds

Use the Insert function to insert holds and cycles into your method, and program pauses that the instrument automatically inserts into your method as it runs.

To insert holds:

Step Action

1

From the

Create

screen, use the Circular Key Pad to select a time or temperature parameter to the right of where you want to insert a hold.

2

Press

More

.

3

Depending on the parameter you select in step 1, one of three screens displays from which you can access the insert function.

Press

Insert

. The Insert screen appears.

4

5

6

7


55.0

2:00

94.0

10:00

94.0

0:30

*

55.0

0:30

72.0

0:30

72.0

5:00

4.0

Hold

F1

Cycle

F2

Pause

F3 F4

Cancel

F5

Note

The Pause function will not display on the Insert screen if the highlighted segment already has a pre-programmed pause or if highlight box is not on a PCR segment parameter.

Press Hold to insert a hold of 4.0 °C for 30 seconds to the left of the parameter you selected in step 1.

Type in a value for the hold temperature.

Type in a value for the hold time.

Press More to return to the Create screen. Your modified method now appears.


Deleting Holds

Follow the procedure below to delete holds.

To delete holds:

1

2

From the

Edit

screen, select a hold parameter and press

More

.

Use the Circular Key Pad to a select a time or temperature hold parameter.

3


55.0

2:00

94.0

10:00

94.0

0:30

*

55.0

0:30

72.0

0:30

72.0

5:00

4.0

F1

Press

Delete

.

Insert

F2

Delete

F3

More

F4 F5

Inserting Cycles

Follow the procedure below to insert cycles.

To insert cycles:

Step Action

1

From the

Create

screen, use the Circular Key Pad to select a time or temperature parameter to the right of where you want to insert a cycle.

2

Press

More

.

3

Depending on the parameter you select in step 1, one of three screens displays from which you can access the insert function.

Press

Insert


4


55.0

2:00

94.0

10:00

94.0

0:30

*

55.0

0:30

72.0

0:30

72.0

5:00

4.0

Hold Cycle Pause Cancel

F1 F2 F3 F4 F5

Press

Cycle

to insert a cycle to the left of the segment you selected in step 2.

Note

You can delete a cycle by entering 0 in the

Tmp

field.

Inserting

Programmed Pauses

Follow the procedure below to insert a programmed pause.

To insert a programmed pause:

Step Action

1

From the

Create

screen, use the Circular Key Pad to select a PCR segment time or temperature parameter where you want to insert a programmed pause.

2

3

Press

Press

More

.

Insert



=

To insert a programmed pause:

(continued)

Step Action

4

From the Insert screen, press

Pause

. The

Programmed Pause

screen appears.

5

6

7

8

9

Define Programmed Pause

Start first pause at cycle 1 of 25.

Pause every 25 cycles for 00:30.

Beep during the pause? No

Accept Cancel

F1 F2 F3 F4 F5

In the

Start first Pause at Cycle

field, type in the cycle number where you want the method to first pause.

In the

Pause Every

field, type in the pause frequency in cycles.

The pause frequency specifies the number of cycles that will run between each pause.

In the

Cycles For

field, type in the length of the pause in minutes:seconds

(00:01–98:59) format.

In the

Beep During The Pause?

field, press

Yes

or

No

.

Press

Accept

to accept the pause information on the screen.

The word

Pause

now displays to the right of the incubation step where you programmed the pause.

Note

You can only insert one pause in each cycle.


Editing

Programmed Pauses

If you have inserted a programmed pause in your method, you can edit the parameters for the pause at any time.

To edit programmed pauses:

Step Action

1

2

From the

Create

screen, use the Circular Key Pad to highlight the word

Edit

soft key appears.

Press

Edit

to access the programmed pause screen.

Pause

. The

From this screen, you can

♦ Change any of the pause parameters, or

♦ Use the Circular Key Pad to select the pause time parameter on the screen, and edit it by entering a different time.

After you have entered all modifications to the customized method you are creating, you should store the method before running it (see “Naming and Storing Methods” below).

Naming and Storing

Methods

Naming and storing completes the creation of the method.

To name and store methods:

Step Action

1

From the

Create

screen, press

Store

.

2


3


store the method under the name displayed in the user field and name the method the default name displayed in the method field

The default method name is expxxx where xxx= a number from

0 to 999. rename the method

Then...

press the

Accept

key.

go to step 3.

From the

Store

screen, press

Method

. The Method Name screen appears.

Note

The blank space after the letter Z is used to insert blank spaces.

Method Name exp001 abcdefghi jklmnopqrj stuvwxyz

.,-+/():=

Use ENTER key to select a character.

Accept

F1 F2

Backsp

F3 F4

Cancel

F5


To name and store methods:

(continued)

Step Action

4

In the name.

Method Name

field, follow these steps to enter a 1–16 character alphanumeric

5

6

Step Action

a.

Use the Circular Key Pad to select a character in the list shown in the upper right portion of the screen.

b.

After selecting a character, press

Enter

to place the character in the

Method Name

field.

c.


enter a number go back one space clear the method name

Then...

press the appropriate number key.

press the

Backsp

key.

press the

CE

key.

Press

Accept

after you have entered a method name.

The

Store

screen appears again. The method name you entered should now display in the Method Name field.

From the

Store

screen, press

Accept

.

This stores the method under the name you entered.

Printing a Method

Introduction

If you have configured your instrument for a printer, you can print a record of the parameters in a method. For more information on configuring a printer, see “Setting

Custom Parameters” on page 3-8.

\

Printing a Method

To print a method:

Step Action

1

Access the

Create

or

Edit

screen.

2

From the

Create

or

Edit

screen you can print a copy of the parameters for the method displayed on the screen.

Press

Print

.


Editing or Deleting Methods

Introduction

After you create a method, you can edit its parameters, and store the method by the same name, or change its name. At some time, you may also want to delete a method if you are no longer using it. You can access all editing functions from the Main menu.

The delete screen is accessed through the utility menu.

Editing a Method

The following procedure describes how to edit a method.

To edit a method:

Step Action

1

From the

Main

menu, press

Edit

.

Note

If an (SRAM) PC Card is detected in the Card slot, you will get a choice of editing a method on the PC Card or the instrument.


Methods on Inst User Size Stored [or Last Used]

[or on PC card]

Used Mem: xxx methods xxx segments

Free Mem: xxx methods xxx segments

The following table describes these fields.

2

Field

units for the Size field

Used Mem field

Free Mem field

Description

Based on a calculation of the complexity and length of a method relative to a maximum size of 1102 size segments for the storage capacity of the instrument.

Displays the number of segments used by all stored methods.

Displays the number of segments available to store created methods.

Select one of the methods displayed on the screen, or select another method as follows:


view the parameters of a method before making a selection

(Refer to “Viewing Method Parameters” on page 4-4.) search for a method by user name

(Refer to “Searching for Methods” on page 4-4.) sort methods by different criteria

(Refer to “Sorting Methods” on page 4-5.)

Then press...

the

View

key.

the the

User

Sort

key.

key.


To edit a method:

(continued)

Step Action

3

Press

Edit

after selecting a method. The Edit screen appears.

4

5

6


55.0

2:00

94.0

10:00

94.0

0:30

55.0

0:30

72.0

0:30

72.0

5:00

4.0

Hold Cycle Pause Cancel

F1 F2 F3 F4 F5

.

Choose a temperature or time parameter within a PCR segment.

Edit temperature control or time parameters.

Note

Editing parameters on the Create screen involves the same tasks and uses the same key combinations as you use when creating a method. The same functions for modifying methods are also available.

From the

Edit

screen, press

Store

to store the method.


Deleting a Method

The following procedure describes how to delete a method.

To delete a method:

Step Action

1

From the

Utilities

screen appears.

screen, press

More

and then press

Delete

. The Delete Method

2

3

Delete Method

Methods on Inst exp001

User lisa

Size

15

Stored

01/01/00

Press Yes to delete the method

Yes

F1 F2 F3 F4

Cancel

F5

Note

If a PC Card is detected in the Card slot, you will get a choice of deleting a method on the PC Card or the instrument.


Methods on Inst User Size Stored [or Last Used]

[or on PC card]

Used Mem: xxx methods xxx segments

Free Mem: xxx methods xxx segments

The following table describes these fields.

Field

Units for the Size field

Used Mem Field

Free Mem Field

Description

Based on a calculation of the complexity and length of a method relative to a maximum size of 1102 size segments for the storage capacity of the instrument.

Displays the number of segments used by all stored methods.

Displays the number of segments available to store created methods.

Select one of the methods displayed on the screen, or select another method as follows:


view method parameters

(Refer to “Viewing Method Information” on page 4-8.) sort methods by different criteria (Refer to “Sorting Methods” on page 4-5.)

Then press...

the the

View

Sort

key.

key.

Press

Delete

. The Delete Confirmation screen appears.

If the method is protected, enter a four-digit PIN and press Accept when the number is correct.


To delete a method:

(continued)

Step Action

4

Press

Yes

to confirm the deletion. This deletes the method and returns you to the

Delete screen.

Note

Even after you delete the last method stored under a User name, the name is removed from the instrument. To delete the name, see “Deleting a User Name” on page 5-5.


Converting Hold Times

6

6

Overview


This chapter provides information about setting hold times for the GeneAmp

®

PCR

System 9700 compared to the DNA Thermal Cycler or DNA Thermal Cycler 480. This information is based upon differences in how the instruments heat and cool samples.

Note

Protocols using sample volumes between 5 µL and 50 µL, developed on either the

GeneAmp

®

PCR System 2400 or 9600, may be transported to the GeneAmp PCR System

9700 without change when using the 9600 emulation mode.

In This Chapter


Topic

About Setting Hold Times

Guidelines for Converting Hold Times

See page

6-2

6-3

Converting Hold Times 6-1

About Setting Hold Times

Introduction

The hold times specified for the GeneAmp PCR System 9700 are shorter than those used for the Step-Cycle or ThermoCycle files on the DNA Thermal Cycler and the

DNA Thermal Cycler 480. This is because the DNA Thermal Cycler and the DNA

Thermal Cycler 480 starts counting the hold time when the block reaches a temperature one degree before the target temperature, while the GeneAmp PCR

System 9700 starts counting the hold time when the samples reach a temperature one degree before the target temperature.

Hold Time

Differences

As shown in the figures below, since the block reaches the target temperature before the sample, the programmed hold time on the DNA Thermal Cycler and the DNA

Thermal Cycler 480 must include enough time for the samples to reach the target temperature. A hold time of one minute or greater is required on the DNA Thermal

Cycler and the DNA Thermal Cycler 480 for samples to reach the target temperature.

On the GeneAmp PCR System 9700, hold times of less than one minute are generally used.

DNA Thermal Cycler and DNA Thermal Cycler 480

Hold Time

94

93

Block

Temp

(˚C)

Sample

Time Clock starts when block reaches target temperature

1 minute

GeneAmp PCR System 9700

Hold Time

94

93

Block

Temp

(˚C)

Sample

Time Clock starts when sample reaches target temperature

6-2 Converting Hold Times

Guidelines for Converting Hold Times

Introduction

This section describes guidelines on how to convert hold times for the DNA Thermal

Cycler or the DNA Thermal Cycler 480 to hold times for the GeneAmp PCR

System 9700 when using the 9600 mode.

What to Base the

New Hold Times On

The following table lists what to base the new hold time on if you are using an up ramp or down ramp.


Then base the new hold time...

an up ramp on the change in the temperature required to reach the next target temperature.

a down ramp on the starting temperature of the ramp and the change in temperature required to reach the next temperature.

For more information see...

Table 6-1 on page 6-3.

Table 6-2 on page 6-5.

Setting Up Ramps

The following table lists the process of setting the up ramp temperature.

Step Action

1

Determine the change in temperature required to reach the next target temperature and round this value off to the closest value found in Table 6-1.

2

Subtract the number of seconds indicated from the hold time used for the DNA

Thermal Cycler or the DNA Thermal Cycler 480.

The result is the hold time to use for the GeneAmp PCR System 9700.

Note

The typical hold time is 10 to 15 seconds for denaturation.

Table of Conversions

The following table lists the times for converting up ramp hold times greater than one minute from the DNA Thermal Cycler and the DNA Thermal Cycler 480 to the

GeneAmp PCR System 9700.

Table 6-1

Converting up ramp hold times

∆ Temp (°C)

10

°

15

°

20

°

30

°

40

°

50

°

60

°

Seconds to subtract from DNA Thermal Cycler or

DNA Thermal Cycler 480 hold times (>1 min.)

38 sec.

45 sec.

49 sec.

54 sec.

55 sec,

57 sec.

57 sec.


Up Ramp Example

In this example, the temperature was increased by 17 °C. This value was rounded to

15 °C. According to Table 6-1, subtract 45 seconds from the hold time on the DNA

Thermal Cycler or the DNA Thermal Cycler 480, resulting in a new hold time of

35 seconds (see the figure below).

Note

If methods developed on the GeneAmp PCR System 9700 will be used on the DNA

Thermal Cycler or the DNA Thermal Cycler 480, you can also use Table 6-1 to convert the hold times. Add the indicated times instead of subtracting them.

DNA Thermal Cycler

Temp.

( ˚ C)

72

Hold

Temp.

( ˚ C)

72


Hold

55 55

∆ temp=17

(round to 15

˚

˚

)

80 sec.

Time

35 sec.

Time

Setting Down Ramps

The following table lists the process of setting the down ramp temperature.

Step Action

1

Determine the change in temperature required to reach the next target temperature and round this value off to the closest value found in Table 6-2.

2

Based on the starting temperature of the ramp, determine the number of seconds to subtract from the DNA Thermal Cycler or DNA Thermal Cycler 480 hold time to arrive at the new hold time.

Note

The typical hold time is 10 to 15 seconds for annealing.

6-4 Converting Hold Times

Table of Conversions

The following table lists the times for converting down ramp hold times greater than one minute from the DNA Thermal Cycler or the DNA Thermal Cycler 480 to the

GeneAmp PCR System 9700.

Table 6-2

Converting down ramp hold times

30

°

40

°

50

°

60

°

A Temp (

°C)

10

°

15

°

20

°

Starting temperature of ramp (

°C)

35-55

°

56-75

°

76-96

°

39 sec.

39 sec.

40 sec.

45 sec.

49 sec.

47 sec.

52 sec.

48 sec.

53 sec.

—

—

—

—

56 sec.

57 sec.

—

—

59 sec.

62 sec.

62 sec.

60 sec.

Down Ramp

Example

In the example below, the temperature was decreased by 22 °C. This value was rounded to 20 °C. According to Table 6-2, with a starting temperature of 94 °C, we should subtract 53 seconds from the hold time on the DNA Thermal Cycler or the DNA

Thermal Cycler 480, resulting in a new hold time of 27 seconds.

Note

If the methods developed on the GeneAmp PCR System 9700 will be used on the DNA

Thermal Cycler or the DNA Thermal Cycler 480, use Table 6-2 to convert the hold times. Add the indicated times instead of subtracting them.

Temp.

(

˚

C)

94

DNA Thermal Cycler

Starting Temp=94˚ Temp.

(

˚

C)


Starting Temp=94

˚

94

72

∆ temp=22

(round to 20

˚

˚ )

Hold

72

Hold

80 sec.

Time

27 sec.

Time


Routine Maintenance

7

7

Overview


This chapter describes how to perform routine maintenance on the GeneAmp

®

PCR

System 9700.

ELECTRICAL SHOCK HAZARD. Severe electrical shock can result from operating the GeneAmp PCR System 9700 Base Module without its instrument panels in place.

Do not remove instrument panels. High-voltage contacts are exposed when instrument panels are removed from the instrument.

There are no components inside the GeneAmp PCR System 9700 that you can safely service yourself. If you suspect a problem, contact an Applied Biosystems Technical

Support Representative.

In This Chapter


Topic

Changing the External Fuses

See page

7-2

Routine Maintenance 7-1

Changing the External Fuses

Introduction

FIRE HAZARD. For continued protection against the risk of fire,

replace fuses only with Listed and Certified fuses of the same type and rating as those currently in the instrument.

All instruments have factory installed fuses. However, if you should ever need to change a fuse, follow the instructions in “Changing the External Fuses” on page 7-2.

Power Entry Module

Diagram

The Power Entry Module is located at the rear of the left side of the instrument.

Fuse

Compartment door Fuse

Fuse compartment

7-2 Routine Maintenance

Changing Fuses

Instruments have two 8 amp Type T 250 V 5x20 mm fuses (

P/N 0999-1683).

To change the fuses:

Step Action

1

Turn off the instrument and disconnect the power cord from the side of the instrument.

ELECTRICAL SHOCK HAZARD. Severe electrical shock, which could cause physical injury or death, can result from working on an instrument when the high voltage power supply is operating. To avoid electrical shock, disconnect the power supply to the instrument, unplug the power cord, and wait at least 1 minute before working on the instrument.

2

3

4

5

6

The fuses are located in the Power Entry Module.

Insert a small flat-tip screwdriver into the slot in the upper portion of the power entry module, and open the door.

Pull the fuse compartment out.

There are two fuses in the fuse compartment.

Pull out the fuse from the back of the fuse compartment and replace the blown fuse with one 8 amp Type T 250 V fuse.

Place the fuse compartment back into the Power Entry Module and close the door.

Press the door until it locks in place.

Connect the instrument power cord.

Routine Maintenance 7-3

Troubleshooting

8

Overview


This chapter describes instrument problems you may have, the probable causes of these problems, and any display screen messages you may encounter when using the GeneAmp

®

PCR System 9700.

In This Chapter


Topic

If There Is a Power Failure

Display Screen Error Messages

Troubleshooting Information

See page

8-2

8-3

8-6

8

Troubleshooting 8-1

If There Is a Power Failure

Introduction

An automated restart function allows for power failures and safe continuation of a PCR run after resumption of power.

During a Power

Failure

The following table lists the actions the instrument takes if the power is interrupted and the instrument turns off while you are operating it.

Note

If the power is off for 15 seconds or longer and fails during execution of a cycle then the cycle currently running will restart. If the power fails while executing a hold, or approaching a hold, then that hold temperature will restart from the beginning.

Note

If the power failure lasts longer than 18 hours, the Resume will not occur.

Do the following in a power failure:

Step Action

1

Restart or continue the PCR experiment.

The instrument determines what temperature was being approached, or was holding.

2

3

Upon resumption of power, it will go to that temperature and countdown the time remaining in the hold as soon as the temperature is within the specified clock start limits.

Incubate the samples until you can continue the experiment.

Enter a record for any power outage in the history file.

8-2 Troubleshooting

Display Screen Error Messages

Error Messages

Table

Refer to the following table for a description of error messages, and recommended actions that you should take.

Table 8-1

Error Messages

Message

Battery RAM version number lost

Block Calibration initialized

Block Calibration reset to default

Block isn’t configured

Block initialized

Block version unknown, update firmware

Bus Error

Calibration battery RAM initialized

Can only enter an infinity hold at end

Can’t allocate timer

Delete your methods first

Enter a name or CANCEL

Enter oligo sequence

Enter user and method names or CANCEL

Description

This error is generated when the battery RAM has been lost and re-initialized.

Software or hardware failure.

System error.

Block data reset to defaults.

The instrument has defaulted to a 96-well configuration.

Block module has been re-initialized.

The calibration data in the block is not recognized by the firmware.

System error.

Calibration lost. Instrument may not perform to specification.

A method can only have a HOLD segment with an infinity hold as the last segment in a method.

This message occurs when you try to enter an infinity hold segment in the middle of a method.

System error.

User tried to delete a user name that has methods stored under it.

You did not enter at least one character on the User

Name screen before pressing the Accept key.

Incomplete TmCalc data.

You did not enter a user name and a method name before storing a method.

Recommended Action

Call Technical Support.





Upgrade the firmware.



Assign finite time segments to holds within a method.


Delete or transfer the associated methods before deleting a user name.

Enter the user name to which the desired method is assigned.

Enter a value in the P1P2 fields of the TmCalc.

Specify the method name and choose a user to store a method.


FATAL – Block shut off by hardware

Block thermal runaway.

FATAL – Block thermal runway Fatal error.

Turn off system.



FATAL – Cover shut off by hardware

FATAL – Heat sink is too hot

FATAL – Heat sink sensor failure

FATAL – Heated cover thermal runaway

Heated cover thermal runaway.

Ambient conditions may be too warm.

System error.

Fatal error.



Turn off system.



Table 8-1

Error Messages

(continued)

Message

FATAL – Sample block sensor failure

Description

Fatal error.


Turn off system.



Fatal – Stack Overflow

Field is full

Heated cover sensor failure

Infinity hold not allowed in cycle

Invalid password/pin#

LCD screen timed-out

List of user names is full

A warning or error message that displays which task stack overflowed.

The warning message is issued when the stack has reached within 10% of overflowing.

You tried to enter more data in a field than the field size allows.

The heated cover sensor failed.

A method can have an infinity hold segment as the last segment in the method.

This message occurs when you tried to enter an infinity time in a CYCLE segment.

You entered an incorrect PIN#.

System error.

Display screen and firmware have a faulty connection.

The maximum number of users has been entered into the system.

You tried to insert more than six temperature control parameters into a hold or cycle.

Reenter data within the specifications of the field.


Use finite values for cycle segments within the method.

Enter the correct PIN#.

Call a Technical Support.

Delete unused user names.

Maximum of 6 segments allowed

Method battery RAM initialized Stored methods have been reset due to hardware or software failure.

Not all methods may be lost.

Method requires at least one segment

You deleted all temperature control parameters in a method.

No seconds in time field

A method must have at least one time and temperature parameter.

You did not include seconds in the time field.

Not enough method memory left

Not implemented yet

PC card and Flash do not verify

PC card does not contain valid data

Do not assign more than six hold or cycle parameters to a method.

Check method directory.


Review and correct the method to include the temperature parameter(s).

This error occurs:

♦ When you attempt to exceed the limit of 137 methods.

♦ When you attempt to store or create a new method which is larger than the available storage space.

The feature is not implemented in the current firmware version.

Include seconds when entering the time.

♦ Determine how much storage memory is available on the instrument or PC card.

♦ Delete or store rarely used methods elsewhere.

Upgrade firmware when the new version is available from Applied Biosystems.


The PC (upgrade) card and instrument memory do not match.

Firmware upgrade unsuccessful.

The PC card being used to upgrade the instrument does not contain a valid program.



Table 8-1

Error Messages

(continued)

Message

Preferences battery RAM initialized

Printer not responding

Description

User configuration has been reset due to software error.

The printer has been disconnected or is off line.



Remove infinity hold first A method can have an infinity hold segment as the last segment in the method.

This message occurs when a user tries to add a segment after one which contains an infinity hold.

Setpoint could not be reached

♦ The instrument could not reach a temperature parameter set by the user.

The unit has a Peltier or power amplifier failure.

♦ Ambient conditions may be out of recommended range.

System error.

SYSTEM ERROR invalid pointer

Tm temperature out of range Tm out of range.

User name already defined

WARNING: Block version unknown

You entered a user name that already exists.

Check printer connections and power switch.

Add segments prior to the post-PCR infinity hold.



Check input value and retry.


Do not duplicate user names.

Upgrade firmware.

Watchdog timeout

Write to block failed

Write to default block failed

Write to default Xicor failed

Write to Xicor failed

Valid range is

Some data in the block is unrecognized.

Instrument operation will not be effected.

Software failure.

Information written to the Interchangeable Sample

Block Module has failed.

System error.

Write to memory in block failed.

System error.

Write to memory in the block failed.

Information written to the Interchangeable Sample

Block Module has failed.

You entered a number out of range.

The message include the valid range limits.






Reenter a value within the parameters of the field.


Troubleshooting Information

Troubleshooting

Table

Refer to the following table for a description of potential problems, possible causes, and recommended actions that you should take.

Table 8-2

Troubleshooting Information

Problem

Control panel not responding

Possible Causes

Keypad failure.

Cooling rate too slow

Cycling time too long

Displayed temperature does not match specified temperature

Heated cover not responsive

Heating rate too slow

Instrument can’t reach high or low temperature range

Instrument making too much noise

No beep

No screen display

No response when you turn the instrument on

Printer fails

Instrument cooling fan does not make whirring sound

♦ Ambient temperature is too warm.

♦ Peltier failure.

Peltier failure.

Instrument may require calibration.

Heated cover failure.


♦ Ambient temperature is too warm.


Fan failure.

♦ Run time beeper disabled.

♦ Beeper failure.

♦ Fuse blown.

♦ Not connected to power source.

♦ Interchangeable module not installed correctly.

♦ Incorrect printer configuration.

♦ Incorrect printer cable.

♦ Fuse blown.

♦ Not connected to power source.

♦ Interchangeable module not installed correctly.

Check and/or Remedy

Run keypad diagnostic.


♦ Move instrument to well-ventilated location(15-30°C).

♦ Run rate test diagnostic.


Run cycle test diagnostic

Run the Temperature Verification test.


Run Rate Test diagnostic.

Call Applied Biosystems Technical

Support.

♦ Run Rate Test diagnostic.

♦ Run Cycle Test diagnostic.


Check for sidevent obstructions.

Check Run-Time Beep configuration.


♦ Is power switch ON?

♦ Is power cord connected?

♦ Check fuses.

♦ Check printer settings: baud rate = 9600, no parity, one stop bit, eight data bits.

♦ Purchase Applied Biosystems printer cable.

♦ Is power switch ON?

♦ Is power cord connected?

♦ Check fuses.


Instrument

Specifications

A

A

Overview

About This

Appendix

This appendix describes the dimensions, power, and electrical specifications for the

GeneAmp

®

PCR System 9700 system, including the control panel, sample temperature information, and printer specifications.

In This Appendix

The following topics are covered in this appendix:

Topic

System Specifications

Control Panel Specifications

Sample Temperature Information

Printer Specifications

See page

A-2

A-4

A-4

A-4

Instrument Specifications A-1

System Specifications

Dimensions

The following tables list the footprint and the weight of the instrument with the 96–Well or 60–Well sample block module.

Footprint (With Sample Block Module Installed)

Height

Width

Depth

26 cm (10 in)

28 cm (11 in)

41 cm (16 in)

Note

You must provide sufficient space around the instrument for unrestricted air circulation.

Weight

Base Module

96-Well Gold/Aluminum Sample Block Modules

8.6 kg (19 lbs)

3.2 kg (7 lbs)

Note

See the sample block module user’s manual for physical information on a module.

Power

Configurations

There is one version of the instrument. The power requirements of the instrument under various power configurations are:

VAC ~100/120 8 AMP T (5x20 mm) or

8 AMP Slow Blow (3 AB)

VAC ~220/230/240

8 AMP T (5x20 mm)

50/60 Hz

Use 250 V fuses

Max Power 725 VA

Electrical

Requirements

IMPORTANT

You must be able to disconnect the main power supply to the instrument immediately if necessary.

In areas where the supplied power is subject to voltage fluctuations exceeding +/-10% of the nominal value, a power line regulator may be required. High or low voltages can have adverse effects on the electronic components of the instrument. The following table specifies the electrical operating range for the instrument in various parts of the world. Select appropriate fuse configuration based on the voltage used.

In Japan, the unit must have a dedicated 220-volt outlet! The unit will not operate properly with a 100-volt outlet.

A-2 Instrument Specifications

Location

Japan

USA/Canada

Europe (pre-1992)

EC

UK (pre-1992)

Australia

Voltage (VAC)

220 ±10%

120 ±10%

220 ±10%

230 ±10%

a

240 +6%/–10%

240 +6%/–10%

Frequency

50/60 Hz ±1%

50/60 Hz ±1%

50/60 Hz ±1%

50/60 Hz ±1%

50/60 Hz ±1%

50/60 Hz ±1%

Amperage (A)

Nominal

3.16

4.20

3.16

3.14

3.12

3.12

a. Acceptable AC line voltage tolerances: 100, 120, 220, 230 ±10%; 240 VAC +6%/–10%, 50/60 Hz ± 1%.

Note

The Volt-Amp number for this instrument is 725Volt Amps.

Instrument Specifications A-3

Control Panel Specifications

Display Screen

The display screen is a 7 x 40 character display with a graphics mode of 60 x 240 pixel resolution.

Keys

The instrument control panel consists of a display screen and 22 keys. The keys are:

♦ Function keys

♦ Arrow keys

♦ Stop key

♦ Enter key

♦ 10 number keypad

Sample Temperature Information

Temperature

The following table lists sample temperature information.

Note

Sample temperatures are displayed in degrees Celsius to the nearest 0.1 °C.

Sample Temperature Range

Temperature Calibration

4.0 to 99.9 °C.

Traceable to National Institute of Standards and

Technology (NIST).

Printer Specifications

Serial Interface

Board Specifications

The instrument can use any printer with a serial (RS-232C) interface board with the following parameters.

Baud Rate

Parity

Data Bits

Stop Bits

8

1

9600

NONE

Cable Part Number

Connect the printer to the Instrument port with printer cable part number N805-1326.

A-4 Instrument Specifications

Supplied Methods

B

B

Overview

About this Appendix

This appendix provides information about the methods that are supplied with the

GeneAmp

®

PCR System 9700.

In This Appendix

The following topics are covered in this appendix:

Topic

About the Methods

AmpliCycle Sequencing

AmpliTaq Gold DNA Polymerase

BigDye Terminators

General PCR

LMS2

Time Release PCR

Touchdown PCR

XL PCR

See page

B-2

B-2

B-2

B-3

B-3

B-4

B-4

B-5

B-5

Supplied Methods B-1

About the Methods

Introduction

The instrument supplies you with eight pre-coded methods stored under the user name <<pe>>.

The eight pre-coded methods are:

♦ AmpliCycle

® Sequencing

♦ AmpliTaq

Gold

®

DNA Polymerase

♦ BigDye

® Terminators

♦ General PCR

♦ LSM2

♦ Time Release PCR

♦ Touchdown PCR

♦ XL PCR

See the following sections for detailed information about the methods.

AmpliCycle

Sequencing

Cycle sequencing has revolutionized Sanger sequencing of PCR products and other

DNA templates. The AmpliCycle Sequencing protocol is for 3-temperature cycling and for achieving clean sequence ladders from femtomole amounts of template.

1 Hld 3 Tmp 25 Cycles 1 Hold

95.0

1.00

Start

F1

95.0

0:30

68.0

0:30

72.0

1:00

4.0

45:00

Method: AmpliCycle Seq

F2 F3 F4

Return

F5

This cycle sequencing process and the benefits of AmpliTaq

®

DNA Polymerase, CS, are described in the product insert for the AmpliCycle

®

Sequencing Kit

(P/N N808-0175).

AmpliTaq Gold DNA

Polymerase

The AmpliTaq Gold protocol specifies a 5-minute pre-PCR heat step, required for the activation of AmpliTaq Gold



DNA Polymerase. This additional step provides seamless “hot start” PCR and replaces labor intensive methods such as manual hot start or wax bead-mediated hot start techniques.

1 Hld

95.0

5:00

3 Tmp 35 Cycles

95.0

72.0

0:15

55.0

0:30

0:15

Start

F1

2 Holds

72.0

7:00

4.0

Method: AmpliTaq Gold



F2 F3 F4

Return

F5

B-2 Supplied Methods

Utilizing hot start techniques helps to minimize the formation of primer-dimers or non-specific products, thus increasing specificity and sensitivity of PCR.

You can find further information on AmpliTaq Gold DNA Polymerase in the product insert (P/N N808-0241) or at the Applied Biosystems website.

BigDye Terminators

The BigDye ® method consists of cycle sequencing parameters for dideoxy (Sanger) terminator sequencing using ABI P

RISM®

BigDye ® Terminator Cycle Sequencing

Ready Reaction Kits (available from Applied Biosystems). It consists of 25-cycle, three-temperature cycle sequencing followed by an infinite hold at 4 °C.

3 Tmp 25 Cycles

96.0

0:10 50.0

60.0

1 Hld

0:05

4:00

4.0

Start

F1 F2

Method: BigDye™

F3 F4

Return

F5

The pre-coded conditions in the BigDye

®

method are optimized for AmpliTaq

®

DNA

Polymerase, FS and the cycle sequencing reagents supplied with the BigDye terminator kits. This process is further described in the ABI P

RISM

BigDye Terminator

Cycle Sequencing Ready Reaction Kits Protocol (P/N 4303237).

General PCR

The General PCR method is a basic one and can be easily modified with both pre- and post-PCR holds.

1 Hld 3 Tmp 35 Cycles 2 Holds

95.0

1.00

95.0

0:15

55.0

0:15

72.0

0:30

72.0

7:00

4.0

Start

F1

Method: General PCR

F2 F3 F4

Return

F5


LMS2

The GeneAmp PCR System 9700 software includes a pre-coded LMS2 method for

ABI P

RISM®

Linkage Mapping Set Version 2 (LMS2) thermal cycling. Linkage Mapping

Set 2 employs over 400 fluorescent-labeled PCR primer pairs for analysis of select microsatalite loci from the Généthon human linkage map.

1,2,3 The following figures illustrate the thermal cycling profile for the LMS2 method.

1 Hld

95.0

12:00

Start

F1

3 Tmp 10 Cycles

94.0

0:15

72.0

F2

55.0

0:15

0:30

3 Tmp 20 Cycles

89.0

0:15

55.0

0:15

72.0

0:30

Method: LMS2

F3 F4

Return

F5

3 Tmp x 10

55.0

0:15

Start

F1

3 Tmp 20 Cycles 2 Holds

72.0

0:30

F2

89.0

0:15

72.0

72.0

55.0

0:15

Method: LMS2

F3

0:30 10:00

F4

4.0

×

Return

F5

This supplied method consists of an initial hold at 95.0 °C, two sets of three temperature cycles, followed by two additional holds at 72.0 °C and 4.0 °C.

See the ABI P

RISM

Linkage Mapping Set Version 2 User’s Manual (P/N 904999) for comprehensive information on PCR amplification conditions, electrophoresis conditions, detection, and data analysis.

Time Release PCR

The Time Release PCR method is designed for use with AmpliTaq Gold DNA

Polymerase. The enzyme is activated more slowly than with the AmpliTaq Gold method. Here the pre-PCR hold is only 1 minute, and the number of cycles is increased to 40.

1 Hld 3 Tmp 40 Cycles 2 Holds

95.0

1.00

95.0

0:15

55.0

0:15

72.0

0:30

72.0

7:00

4.0

Start

F1

Method: Time Release PCR

F2 F3 F4

Return

F5

B-4 Supplied Methods

1. Weissenbach, J. et al. 1992. A second-generation linkage map of the human genome. Nature

359:794–801.

2. Gyapay, G., et al. 1994. Généthon Human Genetic Linkage Map. Nature Genet. 7:246–339.

3. Dib, C., et al. 1996. Nature 380: 152–154.

Touchdown PCR

When the optimal annealing temperature is unknown, one strategy, touchdown PCR, incrementally decreases the annealing temperature in early cycles in order to maximize the yield of specific products.

2 Tmp x 20

F1 F2

2 Tmp x 10

94.0

0:15

65.0

Start

94.0

0:15

0:30

*

55.0

0:30

Method: Touchdown PCR

F3 F4

Return

F5

This supplied method has an initial annealing temperature (65 °C) that incrementally decreases by an additional 0.5 °C in each of the first 20 cycles, followed by 10 cycles at 55 °C.

XL PCR

XL PCR is the protocol specified for amplification of 5 kb-40 kb PCR products, using rTth DNA Polymerase, XL, and unique reaction conditions.

1 Hld

94.0

1:00

Start

2 Tmp X 16 2 Tmp X 12

94.0

94.0

0:15

68.0

0:15

68.0

10:00

10.00

*

Method: XL PCR

F1 F2 F3 F4

2 Holds

72.0

10.00

4.0

Return

F5

This protocol uses two-temperature cycling (94 °C for 15 seconds; 68 °C for

10 minutes) and invokes a 15 second AutoX (automatic segment extension) for the anneal/extend step in the last 12 cycles.

By providing longer templates, XL PCR complements technologies for rapid, long-range PCR. More complete genes can be amplified in one reaction from known expressed sequences, thus more introns can be crossed. You can use XL PCR for the amplification of the control target, a 20.8 kb product from Lambda DNA, supplied in the kit.

This process is further described in the product insert for the GeneAmp ® XL PCR Kit

(P/N N808-0192).


Contacting Services and

Support

C

C

How to Obtain Services and Support

To contact Applied Biosystems Technical Support from North America by telephone, call 1.800.899.5858.

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.

Contacting Services and Support C-1

Limited Warranty

Statement

D

D

Computer Configuration

Applied Biosystems supplies or recommends certain configurations of computer hardware, software, and peripherals for use with its instrumentation.

Applied Biosystems reserves the right to decline support for or impose extra charges for supporting nonstandard computer configurations or components that have not been supplied or recommended by Applied Biosystems. Applied Biosystems also reserves the right to require that computer hardware and software be restored to the standard configuration prior to providing service or technical support. For systems that have built-in computers or processing units, installing unauthorized hardware or software may void the Warranty or Service Plan.

Limited Product Warranty

Limited Warranty

Applied Biosystems warrants that all standard components of its GeneAmp ® PCR

System 9700 Base Module will be free of defects in materials and workmanship for a period of one (1) year from the date the warranty period begins. Applied Biosystems will repair or replace, at its discretion, all defective components during this warranty period. After this warranty period, repairs and replacement components may be purchased from Applied Biosystems at its published rates. Applied Biosystems also provides service agreements for post-warranty coverage. Applied Biosystems reserves the right to use new, repaired, or refurbished instruments or components for warranty and post-warranty service agreement replacements. Repair or replacement of products or components that are under warranty does not extend the original warranty period.

Applied Biosystems warrants that all optional accessories supplied with its GeneAmp

PCR System 9700 Base Module, such as peripherals, printers, and special monitors, will be free of defects in materials and workmanship for a period of ninety (90) days from the date the warranty begins. Applied Biosystems will repair or replace, at its discretion, defective accessories during this warranty period. After this warranty period, Applied Biosystems will pass on to the buyer, to the extent that it is permitted to do so, the warranty of the original manufacturer for such accessories.

With the exception of consumable and maintenance items, replaceable products or components used on or in the instrument are themselves warranted to be free of defects in materials and workmanship for a period of ninety (90) days.

Applied Biosystems warrants that chemicals and other consumable products will be free of defects in materials and workmanship when received by the buyer, but not thereafter, unless otherwise specified in documentation accompanying the product.

Limited Warranty Statement D-1

Applied Biosystems warrants that for a period of ninety (90) days from the date the warranty period begins, the tapes, diskettes, or other media bearing the operating software of the product, if any, will be free of defects in materials and workmanship under normal use. If there is a defect in the media covered by the above warranty and the media is returned to Applied Biosystems within the ninety (90) day warranty period, Applied Biosystems will replace the defective media.

Applied Biosystems does not warrant that the operation of the instrument or its operating software will be uninterrupted or error free.

Warranty Period

Effective Date

Any applicable warranty period under these sections begins on the earlier of the date of installation or ninety (90) days from the date of shipment for hardware and software installed by Applied Biosystems personnel. For all hardware and software installed by the buyer or anyone other than Applied Biosystems, and for all other products, the applicable warranty period begins the date the product is delivered to the buyer.

Warranty Claims

Warranty claims must be made within the applicable warranty period, or, for chemicals or other consumable products, within thirty (30) days after receipt by the buyer.

Warranty

Exceptions

The above warranties do not apply to defects resulting from misuse, neglect, or accident, including without limitation: operation with incompatible solvents or samples in the system; operation outside of the environmental or use specifications or not in conformance with the instructions for the instrument system, software, or accessories; improper or inadequate maintenance by the user; installation of software or interfacing, or use in combination with software or products, not supplied or authorized by Applied Biosystems; and modification or repair of the product not authorized by Applied Biosystems.

THE FOREGOING PROVISIONS SET FORTH APPLIED BIOSYSTEMS’

SOLE AND EXCLUSIVE REPRESENTATIONS, WARRANTIES, AND

OBLIGATIONS WITH RESPECT TO ITS PRODUCTS, AND

APPLIED BIOSYSTEMS MAKES NO OTHER WARRANTY OF ANY KIND

WHATSOEVER, EXPRESSED OR IMPLIED, INCLUDING WITHOUT

LIMITATION, WARRANTIES OF MERCHANTABILITY AND FITNESS FOR

A PARTICULAR PURPOSE, WHETHER ARISING FROM A STATUTE OR

OTHERWISE IN LAW OR FROM A COURSE OF DEALING OR USAGE OF

TRADE, ALL OF WHICH ARE EXPRESSLY DISCLAIMED.

Warranty

Limitations

THE REMEDIES PROVIDED HEREIN ARE THE BUYER'S SOLE AND

EXCLUSIVE REMEDIES. WITHOUT LIMITING THE GENERALITY OF

THE FOREGOING, IN NO EVENT SHALL APPLIED BIOSYSTEMS BE

LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY, OR UNDER ANY

STATUTE (INCLUDING WITHOUT LIMITATION, ANY TRADE

PRACTICE, UNFAIR COMPETITION, OR OTHER STATUTE OF SIMILAR

IMPORT) OR ON ANY OTHER BASIS, FOR DIRECT, INDIRECT,

PUNITIVE, INCIDENTAL, MULTIPLE, CONSEQUENTIAL, OR SPECIAL

DAMAGES SUSTAINED BY THE BUYER OR ANY OTHER PERSON OR

ENTITY, WHETHER OR NOT FORESEEABLE AND WHETHER OR NOT

APPLIED BIOSYSTEMS IS ADVISED OF THE POSSIBILITY OF SUCH

DAMAGES, INCLUDING WITHOUT LIMITATION, DAMAGES ARISING

FROM OR RELATED TO LOSS OF USE, LOSS OF DATA, FAILURE OR

INTERRUPTION IN THE OPERATION OF ANY EQUIPMENT OR

SOFTWARE, DELAY IN REPAIR OR REPLACEMENT, OR FOR LOSS OF

REVENUE OR PROFITS, LOSS OF GOOD WILL, LOSS OF BUSINESS, OR

OTHER FINANCIAL LOSS OR PERSONAL INJURY OR PROPERTY

DAMAGE.

NO AGENT, EMPLOYEE, OR REPRESENTATIVE OF

APPLIED BIOSYSTEMS HAS ANY AUTHORITY TO MODIFY THE TERMS

OF THIS LIMITED WARRANTY STATEMENT OR TO BIND

APPLIED BIOSYSTEMS TO ANY AFFIRMATION, REPRESENTATION, OR

WARRANTY CONCERNING THE PRODUCT THAT IS NOT CONTAINED

IN THIS LIMITED WARRANTY STATEMENT, AND ANY SUCH

MODIFICATION, AFFIRMATION, REPRESENTATION, OR WARRANTY

MADE BY ANY AGENT, EMPLOYEE, OR REPRESENTATIVE OF

APPLIED BIOSYSTEMS WILL NOT BE BINDING ON

APPLIED BIOSYSTEMS, UNLESS IN A WRITING SIGNED BY AN

EXECUTIVE OFFICER OF APPLIED BIOSYSTEMS.

THIS WARRANTY IS LIMITED TO THE BUYER OF THE PRODUCT FROM

APPLIED BIOSYSTEMS AND IS NOT TRANSFERABLE.

Some countries or jurisdictions limit the scope of or preclude limitations or exclusion of warranties, of liability, such as liability for gross negligence or wilful misconduct, or of remedies or damages, as or to the extent set forth above. In such countries and jurisdictions, the limitation or exclusion of warranties, liability, remedies or damages set forth above shall apply to the fullest extent permitted by law, and shall not apply to the extent prohibited by law.

Damages, Claims, and Returns

Damages If shipping damage to the product is discovered, contact the shipping carrier and

request inspection by a local agent. Secure a written report of the findings to support any claim. Do not return damaged goods to Applied Biosystems without first securing an inspection report and contacting Applied Biosystems Technical Support for a

Return Authorization (RA) number.

Claims After a damage inspection report is received by Applied Biosystems,

Applied Biosystems will process the claim unless other instructions are provided.

Returns Do not return any material without prior notification and authorization.

If for any reason it becomes necessary to return material to Applied Biosystems, contact Applied Biosystems Technical Support or your nearest Applied Biosystems subsidiary or distributor for a return authorization (RA) number and forwarding address. Place the RA number in a prominent location on the outside of the shipping container, and return the material to the address designated by the Applied Biosystems representative.

Limited Warranty Statement D-3

Index

Numerics

480 DNA Thermal Cycler converting hold times 6-2 to 6-5

A

alphanumeric characters, entering 5-3

AmpliCycle Sequencing 4-2, B-2 about supplied method B-1, B-2, B-3

AmpliTaq Gold 4-2, B-2 about supplied method B-2

AutoX function 5-11 to 5-12

B

baud rate, setting 3-10 beeper, run-time, turning on/off 3-9

BigDye 4-2, B-2 about supplied method B-3

C

calculator, T

M

, how to use 3-17

Changing 7-2 changing temperature control parameters 5-11 to 5-12 chemical hazard warning 1-6 chemical waste hazard warning 1-6

Circular Key Pad, definition of 2-3 claims, processing D-3 computer configuration requirement D-1 technical support for altered configuration D-1

Config, function of 3-7

Configuration Screen, displaying 3-7

Contacting Technical Support C-1

Control Panel diagram 2-2 entering numeric values, how to 2-3 selecting a field, how to 2-3 specifications A-4 using the keys 2-3 counting cycles.See cycles

CPU board testing 3-15

Create Methods screen, displaying 5-7 custom parameters, setting 3-7 to 3-11 baud rate, setting 3-10 date, setting 3-8

Idle State Setpoint temperature, setting 3-10

Pause Time Out, setting 3-9 printer, enabling/disabling 3-8 screen contrast/saver mode, setting 3-11 time, setting 3-8 custom parameters, settings

Configuration Screen, displaying 3-7 run-time beeper, turning on/off 3-9 cycles counting of 4-7 inserting 5-14 cycling, modifying 5-11 to 5-17

AutoX function, using 5-11 to 5-12 cycles, inserting 5-14 deleting holds 5-14 holds inserting 5-13 ramp rates, modifying 5-12 to 5-13

D

damage, reporting D-3 damaged items, returning D-3 data bit, serial board specifications 3-10, 3-26 date last used, sorting methods by 4-5 setting 3-8 deleting methods 5-18 to 5-21 user name 5-5 diagnostic (tests), running 3-13 to 3-16

CPU board, testing 3-15

Diagnostic screen, viewing 3-13

Display screen, testing 3-15 electrical components, testing 3-14 keypad, testing 3-16

Diagnostic screen, viewing 3-13 dimensions, instrument A-2 display screen.See diagnostic (tests), running

Display softkey, function of 3-14

DNA Thermal Cycler, converting hold times 6-2 to 6-5

E

editing methods 5-18 to 5-21 electrical components testing 3-14 electrical safety 1-3 to 1-10

End of Run screen, when a run completes 4-12 environment 1-11 error messages, display screen 8-3 to 8-5

F

fields, selecting 2-3 firmware, upgrading 3-18 to 3-23 through serial port 3-18, 3-21 using PCMCIA card 3-22, 3-23 fuses changing for double-line operation 7-3 converting from single to double-line 3-5 to ??

precautions about 1-10 service configuration 3-4

Index-1

G


Control Panel about 2-2 specifications A-4 copying methods 3-24 to 3-25 custom parameters, setting 3-7 to 3-11 baud rate, setting 3-10

Configuration Screen, displaying 3-7 date, setting 3-8

Idle State Setpoint temperature, setting 3-10

Pause Time Out, setting 3-9 printer, enabling/disabling 3-8 run-time beeper, tuning on/off 3-9 screen contrast/saver mode, setting 3-11 time, setting 3-8 diagnostic (tests), running

CPU board, testing 3-15

Diagnostic screen, viewing 3-13

Display screen, testing 3-15 electrical components, testing 3-14 keypad, testing 3-16 fuses, converting from single to double-line fuse 3-5 to

??

laboratory, setting up 3-3 to 3-4 air vents, air circulation 3-3 choosing a location 3-3 fuse service configuration 3-4 input voltage, table of 3-4 interchangeable block module, about 3-4 operating temperature 3-3 what to avoid 3-3 overview 2-2 to 2-5 about the instrument 2-2 control panel keys, using 2-3 control panel, diagram 2-2 entering numeric values, how to 2-3 how differs from 9600 System 2-5 methods, transferring or storing 2-4 selecting a field, how to 2-3 upgrading the firmware 2-4 printer connecting and configuring 3-26 specifications A-4 system firmware upgrading 3-18 to 3-23 system specifications A-2

T

M

calculator, how to use 3-17 turning on instrument 3-6 unpacking 3-2

General PCR 4-2, B-2

General PCR, about supplied method B-3 grounding 1-10

H

Hard soft key, function of 3-13 hazards and warnings 1-3 to 1-8, 1-9 to ??

burns, danger of 1-10 instrument warnings 1-9 heated cover screen 4-7 heating, of samples 5-8 history of run, reviewing history file records 4-11 history formats 4-10 procedure 4-10 hold time converting from DNA Thermal Cycler 6-2 to 6-5 parameters, defined 2-3 holds deleting 5-14 inserting 5-13 humidity 1-11

I

Idle State Setpoint temperature, setting 3-10 input voltage, table of 3-4 inserting holds 5-13

K

keyboard softkey, function of 3-14 keypad, testing 3-16

L

labels, safety 1-9 laboratory environmental requirements 1-11 laboratory, setting up 3-3 to 3-4 air vents, air circulation 3-3 choosing a location 3-3 fuse service configuration 3-4 input voltage, table of 3-4 interchangeable block module, about 3-4 operating temperature 3-3 what to avoid 3-3

LCD pixels, turning on and off 3-15 locking/unlocking methods, about 5-4

LSM2 4-2, B-2

M

maintenance, routine 1-11

Memory Used field, definition of 4-3, 5-20

Method Not Stored screen, actions if displayed 4-12 methods adding or changing users 5-2 to 5-5 adding users 5-2 to 5-3 changing user name 5-5 deleting user name 5-5 protecting methods 5-3 to 5-4 copying using PCMCIA card 3-24 to 3-25 creating 5-6 to 5-10 basic parameters, to create method 5-6

Create Methods screen, displaying 5-7 default method, about 5-6

PCR holds, defining 5-9 to 5-10 post-PCR holds, defining 5-10 pre-PCR holds, defining 5-9

Index-2

temperature control parameters, entering 5-8 editing or deleting methods 5-18 to 5-21 modifying cycling 5-11 to 5-17

AutoX function, using 5-11 to 5-12 cycles, inserting 5-14 deleting holds 5-14 naming and storing methods 5-16 to 5-17 programmed pauses 5-14, 5-16 ramp rates, modifying 5-12 to 5-13 printing a method 5-17 reviewing history of run 4-10 to 4-11 history file records 4-11 history formats 4-10 procedure 4-10 running 4-6 to 4-9 method information, viewing 4-8 pausing a run 4-8

Run Time screen, about 4-7 starting a run 4-6 to 4-7 stopping run before completion 4-9 selecting 4-2 to 4-4 method defined 4-2 method parameters, viewing 4-4 methods, searching for 4-4 methods, sorting 4-5 predefined methods, list of 4-2 procedure 4-3 supplied B-2 to B-5

AmpliCycle Sequencing B-2

AmpliTaq Gold B-2

BigDye B-1, B-3

BigDye™ B-1

LMS2 B-1

Touchdown PCR B-5

XL PCR B-5 transferring or storing, about 2-4 when a run completes 4-12

MSDSs 1-7

N

naming methods 5-16 to 5-17 numeric keys, definition of 2-3

O

operating precautions 1-11

P

parameters

Hold Time 2-3 temperature control 5-11 temperature parameters 2-3

See Also custom parameters, setting parity bit 3-10, 3-26 part numbers for ordering accessories 3-2 fuse part number 3-5

Pause Time Out, setting 3-9 pauses, programmed editing 5-16 inserting 5-14

PCMCIA card using to copy methods 3-24 to 3-25 using to upgrade firmware 3-22, 3-23

PCR holds, defining 5-9 to 5-10

PCR samples, running methods running 4-6 to 4-9 selecting 4-2 to 4-4

PCR thermal profile, method defined 4-2

PIN#, entering 5-4 pollution 1-11 post-PCR holds, defining 5-10 power configurations A-2 power failure, what to do 8-2 precautions, operating 1-11 pre-PCR holds, defining 5-9 printer baud rate, setting 3-10 connecting and configuring 3-26 enabling/disabling 3-8 printer port, defining. See baud rate printing method 5-17 printer specifications A-4 programmed pauses editing 5-16 inserting 5-14 protecting methods 5-3 to 5-4

R

RA number D-3

RA number. See return authorization number ramp rates, modifying 5-12 to 5-13 reaction volume entering 4-6 reporting, damages D-3 return authorization (RA) number D-3 returning damaged items D-3 returns D-3

RS-232C, serial interface board 3-26

Run softkey, function of 3-15 run-time beeper, turning on/off 3-9

S

safety 1-1 to 1-8 sample temperature range A-4

Sanger sequencing B-2 screen contrast, setting 3-11 screen saver mode, setting 3-11 security code, entering 5-4 selecting fields 2-3 serial interface board specifications 3-10 serial port, upgrading firmware 3-18, 3-21

Size field, definition of 5-20 soft keys definition of 2-3

Index-3

Sort, function of 4-5, 5-20

SRAM card, using to copy methods 3-24 to 3-25 starting instrument 3-6 stop bit 3-10, 3-26

Stop key, definition of 2-3 storing methods 5-16 to 5-17 system firmware, upgrading 3-18 to 3-23 through serial port 3-18, 3-21 using PCMCIA card 3-22, 3-23

System soft key, function of 3-13

T

technical support, for computers with altered configuration D-1 temperature entering values 2-3

Idle State Setpoint, setting 3-10 operating precautions 1-11 operating temperature 3-3 sample temperature information A-4 temperature control parameters entering 5-8 temperature control parameters entering 5-8 using AutoX function 5-11 to 5-12

Temperature Verification test part number 3-2

Time Release PCR 4-2, B-2

Time Release PCR, about supplied method B-4 time, setting 3-8

T

M

calculator, how to use 3-17

Tmp field, using to define temperature control parameters 5-9

TmpVer soft key, function of 3-13

ToCard softkey, function of 3-25

ToInst softkey, function of 3-25

Touchdown PCR 4-2, B-2 about supplied method B-5 troubleshooting 8-1 to 8-6 display screen error messages 8-3 to 8-5 power failure, what to do 8-2 table of information 8-6 turning on instrument 3-6

U

unpacking the instrument 3-2

Upgrade soft key, function of 3-13

User, function of 4-4 users 5-2 to 5-5 adding users 5-2 to 5-3 changing user name 5-5 deleting user name 5-5 protecting methods 5-3 to 5-4

Util, function of 3-7

W

warning

Index-4

chemical hazard 1-6 chemical waste hazard 1-6 warranty damages, claims, returns D-3 exceptions D-2 for computers with altered configuration D-1 limitations D-2 period D-1 warranty claims D-2 warranty exceptions D-2 warranty period, effective date D-2 waste disposal 1-8

Win 3.1, downloading firmware using 3-21

Windows 95/Windows NT downloading firmware using 3-20

X

XL PCR 4-2, B-2 about supplied method B-5

Headquarters

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Foster City, CA 94404 USA

Phone: +1 650.638.5800

Toll Free (In North America): +1 800.345.5224

Fax: +1 650.638.5884

Worldwide Sales and Support

Applied Biosystems vast distribution and service network, composed of highly trained support and applications personnel, reaches 150 countries on six continents. For sales office locations and technical support, please call our local office or refer to our Web site at www.appliedbiosystems.com.

Appl ied Biosysstems is committed to providing the world’s leading technology and information for life scientists.

12/2010

Part Number 4304481 Rev.

H

Thermo Fisher Scientific GeneAmp® PCR System 9700 Base Module User's manual

GeneAmp

®

System 9700

Base Module

User’s Manual

GeneAmp ® PCR System 9700

Base Module

User’s Manual

Contents

1 Introduction and Safety

2 Product Overview

3 Instrument Setup

4 Running PCR Samples

5 Creating and Editing Methods

6 Converting Hold Times

7 Routine Maintenance

8 Troubleshooting

A Instrument Specifications

B Supplied Methods

C Contacting Services and Support

D Limited Warranty Statement

Index

Introduction and Safety

Overview

About This Chapter

In This Chapter

About This Manual

Overview

Instrument Safety

Before Operating the

Instrument

Documentation User

Attention Words

Symbols on Instruments

Electrical Symbols

Safety Symbols

Safety Labels on Instruments

Chemical Safety

Chemical Hazard

Warning

Chemical Waste

Hazard Warning

About MSDSs

Ordering MSDSs You can obtain from Applied Biosystems the MSDS for any chemical supplied by

DOCUMENTS at the end of the document list.

Documents Now.

About Waste

Disposal

GeneAmp PCR System 9700 Labels and Warnings

Instrument Safety

Labels

Instrument

Warnings Diagram

Danger of Burns

Grounding and

Electrical Safety

Fuses

Laboratory Environmental Requirements

Introduction

Temperature,

Humidity, and

Environment

Pollution

Emission/Immunity

Statement

Routine

Maintenance for

Safe Operation

Safety and Electromagnetic Compatibility (EMC)

Standards

U.S. and Canadian

Safety

Standards

Canadian EMC

Standard

European Safety and

EMC

Standards

Australian EMC