Thermo Fisher Scientific Gene Amp In Situ PCR System 1000 User manual

Gene Amp In Situ

PCR System 1000

User’s Manual

For Research Use Only. Not for use in diagnostic procedures.

Printed in the United States of America. Software programs are protected by copyright. It is unlawful to duplicate these

programs in any manner other than for the user’s personal use. Specifically, it is unlawful to use or duplicate these programs

other than for use with the purchaser’s original computer.

Notice

The information contained in this document is subject to change without notice.

Applied Biosystems MAKES NO WARRANTY OF ANY KIND WITH REGARD TO THIS MATERIAL, INCLUDING,

BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A

PARTICULAR PURPOSE. Applied Biosystems shall not be liable for errors contained herein or for incidental

consequential damages in connection with the furnishing, performance, or use of this material.

Copyright Information

Reproduction or publication of this document in any form or format is prohibited without written permission of Applied

Biosystems.

Part No. 0993-6006 Rev. C

Trademarks

ABI PRISM and its design, Applied Biosystems, AmpliCover and MicroAmp are registered trademarks of Applera

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

AmpliTaq and GeneAmp are registered trademarks of Roche Molecular Systems, Inc. and E. Hoffmann-La Roche AG.

The GeneAmp PCR Process, Taq DNA Polymerase, and AmpliTaq DNA Polymerase are covered by U.S patents owned by

Roche Molecular Systems, Inc., and issued and pending patents owned by E. Hoffmann-La Roche AG.

Epson is a trademark of Seiko Epson Corporation.

Registered trademarks, etc. used in this document even when not specifically marked as such, are protected by law.

AUTHORIZED THERMAL CYCLER NOTICE

This instrument, Serial No. ,________ is an Authorized Thermal Cycler. Its purchase price includes the up-front fee

component of a license under the patents of the Polymerase Chain Reaction (PCR) process, which are owned by Roche

Molecular Systems, Inc. and F. Hoffmann-La Roche Ltd., to practice the PCR process for internal research and development

using this instrument. The running royalty component of that license may be purchased from Applied Biosystems or

obtained by purchasing Authorized Reagents. This instrument is also an Authorized Thermal Cycler for use with

applications licenses available from Applied Biosystems. Its use with Authorized Reagents also provides a limited PCR

license in accordance with the label rights accompanying such reagents. Purchase of this product does not itself convey to

the purchaser a complete license or right to perform the PCR process. Further information on purchasing licenses to practice

the PCR process may be obtained by contacting the Director of Licensing at Applied Biosystems, 850 Lincoln Centre Drive,

Foster City, California 94404.

Contents

Preface: Using the Manual

Using the Manual P-1

Conventions P-3

Software Conventions P-3

Users Manual Summary P-4

Difference Between the DNA Thermal Cyclers and the GeneAmp

In Situ

PCR System 1000 P-6

Setting Cycle Hold Times and Temperatures P-6

Technical Support P-8

Chapter 1. The In Situ PCR Reagent Containment System

The Polymerase Chain Reaction (PCR) 1-2

In Situ

PCR 1-4

Requirements for

In Situ

PCR 1-4

The Applied Biosystems

In Situ

PCR Reagent Containment

System 1-6

AmpliCover Discs, AmpliCover Clips, and

In Situ

PCR Glass

Slides 1-6

The Assembly Tool 1-9

Chapter 2. Introducing GeneAmp In Situ PCR System 1000

Instrument Description 2-2

GeneAmp

In Situ

PCR System 1000 Software 2-5

Contents-2

Contents

System Files 2-5

Soak File (# 1) 2-6

Time Delay File (#2) 2-7

Step-Cycle File (#4) 2-8

Thermo-Cycle File (#3) 2-9

Configuration and Diagnostic Files 2-11

Creating User Files 2-12

Linking User Files – Creating Methods 2-12

System File Directory 2-12

Accessing the System Software 2-13

Chapter 3. Installing the GeneAmp In Situ PCR System 1000

Unpacking 3-2

Laboratory Requirements 3-3

Sample Block Cover 3-3

Grounding and Electrical Safety 3-3

Temperature, Humidity, and Environment 3-4

Connecting Electrical Power 3-4

Checking the Cooling and Heating Systems 3-5

Checking the Cooling System 3-5

Checking the Heating System 3-6

Installing a Printer 3-9

Installing the 120 V Printer 3-9

Installing the 240 V Printer 3-13

Configuring the GeneAmp In situ PCR System 1000 3-15

Contents-3

Contents

Chapter 4. Tutorial: Customizing In Situ PCR Files and Creating a

PCR Method

Goals of this Tutorial 4-2

Starting the Instrument 4-4

Overview of the Tutorial 4-5

Customizing the Soak Files 4-7

Customizing the Step-Cycle Files 4-10

Review of what you have learned so far 4-18

File Numbers 4-18

Summary of the Tutorial 4-19

Starting the Optional Hot Start Soak File and

In Situ

PCR

Method 4-21

Starting the optional Hot Start Soak File 4-21

Chapter 5. Preparing the Slides for In Situ PCR

Checking the Location of Samples on the Slide 5-2

Before You Begin Preparing the Slides 5-7

Processing the Slides 5-12

Loading the Slides 5-20

Starting the Run 5-22

Removing the AmpliCover Clips and Discs 5-26

Chapter 6. Running Samples for In Situ PCR: Run-Time Displays

Beginning a Run 6-2

Using the Start Key 6-2

Selecting the RUN Option 6-3

The Run-Time Displays 6-5

Soak File Run-Time Display 6-5

Time Delay File Run-Time Displays 6-6

Cycle Files Run-Time Displays 6-7

Sample Temperature Display 6-8

Contents-4

Contents

Pausing a Run 6-9

Aborting a Run 6-10

Run-Time Print Options 6-12

Chapter 7. Maintenance

Cleaning the Slide Sample Block 7-2

Cleaning Exterior Surfaces 7-2

Temperature Calibration Verification Test 7-2

Equipment Required 7-2

Test Results 7-6

Temperature Uniformity Test 7-8

Equipment Required 7-8

Test Results 7-12

Chapter 8. Troubleshooting

Instrument Troubleshooting Information 8-2

If the Instrument Turns Off 8-3

Chapter 9. Specifications

Part 1: GeneAmp

In Situ

PCR System 1000 Thermal Cycler

Specifications 9-1

Dimensions and Weight 9-1

The Sample Block 9-2

Slides 9-2

Power Requirements 9-3

Fuses 9-3

Control Panel 9-3

Display 9-3

Keypad 9-4

Indicator Lights 9-4

Block Temperature Range 9-4

Static Block Temperature Uniformity 9-4

Contents-5

Contents

Dynamic Block Temperature Uniformity 9-4

Ramp Time Reproducibility 9-5

Block Temperature Accuracy 9-5

Block Temperature Overshoot and Undershoot 9-6

Ramp Rate 9-6

Printer Interface 9-7

Software 9-7

Temperature Calibration 9-7

Part 2: Assembly Tool Specifications 9-8

Dimensions and Weight 9-8

Assembly Tool Platform Surface 9-8

Assembly Tool Power Requirements 9-9

Indicator Lights 9-9

Time Required to Reach Preset Temperature 9-9

Temperature Accuracy 9-9

Temperature Calibration 9-9

Appendix A: The Time-Delay and Thermo-Cycle Files

The Time Delay File #2 A-2

Customizing the Time-Delay File A-3

The Thermo-Cycle File #3 A-6

Customizing the Thermo-Cycle File A-8

Appendix B: The Demonstration File Parameters

Demonstration Files B-2

Appendix C: The Configuration and Diagnostic Files

Accessing the Configuration and Diagnostic Files C-2

Editing the Configuration File C-3

The Diagnostic File C-7

Accessing the Diagnostic Tests C-7

The Display/Keypad Test (Test #1) C-8

Contents-6

Contents

Delete User Files (Test #2) C-9

Heater Test (Test #3) C-10

The Chiller Test (Test #4) C-12

The Overshoot Test (Test #5) C-14

The Undershoot Test (Test #6) C-16

Appendix D: The File Directory

Using the File Directory D-3

Viewing a Directory of All Files D-4

Viewing a Directory Grouped by File Type D-5

Printing the Parameters of a File D-6

Deleting a File D-7

Using the FILE and CLEAR Keys D-7

Overwriting a File D-8

Appendix E: Using the Keyboard

Using the Keypad E-2

The START Key E-2

The STEP Key E-2

The HELP Key E-3

The STOP Key E-4

The FILE Key E-4

The YES Key E-5

The NO Key E-6

The ENTER Key E-6

The CLEAR Key E-6

The Numeric Keys E-7

Entering Negative Temperatures E-7

Contents-7

Contents

Illustrations

Figure P-1 Heating ramps on the DNA Thermal Cycler and

DNA Thermal Cycler 480 and the GeneAmp

In

Situ

PCR System 1000. P-7

Figure 1-1 PCR Process. 1-3

Figure 1-2

In Situ

PCR Reagent Containment System

Components. 1-7

Figure 1-3 The Assembly Tool. 1-10

Figure 2-1 Components of the GeneAmp

In Situ

PCR Sys-

tem 1000 (120V Model). 2-3

Figure 2-2 Slide, with AmpliCover Disc and Clip attached, in

one of the slots of the GeneAmp

In Situ

PCR Sys-

tem 1000. 2-4

Figure 2-3 Diagram of a Soak File. 2-6

Figure 2-4 Diagram of a Time Delay File. 2-7

Figure 2-5 Diagram of a Three-Temperature Step-Cycle

File. 2-8

Figure 2-6 Diagram of a Three-Temperature Thermo-Cycle

File. 2-10

Figure 2-7 Control Panel Keypad and Display. 2-13

Figure 2-8 Accessing the Main Software Functions. 2-14

Figure 2-9 Summary of Keyboard Functions. 2-15

Figure 3-1 DIP switch settings on the Epson 082302 serial

interface card. 3-10

Figure 3-2 Side panel of the GeneAmp

In Situ

PCR System

1000 and rear panel of the printer showing the

DIP switch settings and cable connections. 3-12

Figure 4-1 Linking Files to create a Method. 4-3

Figure 5-1 Slide Template and Tissue/Cell Spot Areas (To

Scale). 5-3

Figure 5-2 Area that is amplified when samples are off-

center. 5-4

Figure 5-3 Area between adjacent samples that will not be

amplified. 5-5

Contents-8

Contents

Figure 5-4 Area where AmpliCover Clips and Discs can be attached when

there are fewer than three samples. 5-6

Figure 5-5 The Assembly Tool and top-down view of the platform

surface. 5-13

Figure 5-6 Attaching the AmpliCover Clip and Disc to the slide. 5-17

Figure 5-7 Loading the slide Assemblies. 5-20

Figure 5-8 Positioning the slide on the Disassembly Tool. 5-27

Figure 5-9 Removing the AmpliCover Clip from the slide. 5-28

Figure 6-1 A run-time print-out of an incubation file. 6-13

Figure 6-2 A run-time cycle printout. 6-14

Figure 6-3 A run-time segment printout. 6-14

Figure 7-1 Inserting the RTD probe in the vertical slot. 7-4

Figure 7-2 Temperature measurements in the temperature calibration

verification test. 7-5

Figure 7-3 Calibration Label. 7-6

Figure 7-4 Positionlng of the RTD probe in toward the front of slot 1. 7-9

Figure 7-5 Temperature measurements in the temperature uniformity

test. 7-10

Figure 7-6 Positioning the RTD probe toward the back of slot 1. 7-11

Figure 7-7 Location of slots to be used in the Temperature Uniformity

Test. 7-12

Figure 9-1 Static and Dynamic block temperature uniformity while ramp-

ing up. 9-5

Figure 9-2 Block temperature overshoot after ramping up. 9-6

Safety and Regulatory

Information N

Symbols and Conventions Used in this Manual S

In this manual, the following graphic symbols and special text

formats are used to set apart important safety information.

! WARNING ! A warning indicates an operation that could

cause

personal injury

if precautions are not

followed.

CAUTION: A caution indicates an operation that could

cause

instrument damage

if precautions are not

followed.

S-2

Safety and Regulatory Information

Symbols and Conventions Used on the Instrument

There are three different types of symbols that appear on the

instrument.

This symbol indicates an operation (or condition on the

instrument) that could cause personal injury if precautions

are not followed. This can be any type of hazard.

When you see this symbol, refer to the safety pages in the

manual for further information.

Consulter les documents d’accompagnement.

If there is a hazard of heat or electric shock, the following caution

symbols will appear on the instrument:

This symbol indicates the danger of burns, if precautions are

not followed, due to the presence of heat in this area of the

instrument. There may also be hot surfaces that can be

easily touched.

Attention. Surface chaude.

This symbol indicates the danger of electric shock, if

precautions are not followed, due to the presence of high

voltage.

Attention. Risque de choc électrique.

S-3

Symbols and Conventions Used on the Instrument

Additional graphic symbols used on the instrument are the

following:

Indicates alternating current or voltage.

Indicates the primary protective grounding terminal.

Indicates the

off

position of the main power switch.

Indicates the

on

position of the main power switch.

S-4

Safety and Regulatory Information

Warnings on the

Assembly Tool

This section shows the label that is affixed to the Assembly Tool.

CAUTION: Hot Surface. Use care when working around this

area to avoid being burned by hot components

ATTENTION:Surface chaude.

S-5

Symbols and Conventions Used on the Instrument

Warnings on the

Instrument

The following sections present the labels affixed to the

instrument.

100/120/240 Volt Models The following labels are affixed to the front and side of the

instrument as shown in the figure below for all three voltage

models (100/120/240).

! WARNING ! DO NOT OPEN. See Instruction Manual.

! AVERTISSEMENT ! NE PAS OUVRIR. Consulter les documents

d’accompagnement.

CAUTION: Hot Surface. Use care when working around this area to avoid being

burned by hot components.

ATTENTION:Surface chaude.

S-6

Safety and Regulatory Information

100 Volt Model The following warning labels are affixed to the instrument for the

100 volt models as shown in the figure below.

! WARNING ! DISCONNECT SUPPLY CORD BEFORE OPENING.

GROUNDING CIRCUIT CONTINUITY IS VITAL FOR SAFE

OPERATION OF EQUIPMENT. NEVER OPERATE EQUIPMENT

WITH GROUNDING CONDUCTOR DISCONNECTED.

! AVERTISSEMENT ! DÉBRANCHER LE CORDON D’ALIMENTATION AVANT

D’OUVRIR. LA CONTINUITÉE DES MASSES EST

ESSENTIELLE POUR UN FONCTIONNEMENT SANS

DANGER. NE JAMAIS UTILISER L’ÉQUIPMENT SI LE

FIL DE TERRE N’EST PAS RACCORDÉ.

! WARNING ! FOR PROTECTION AGAINST FIRE HAZARD, REPLACE ONLY

WITH SAME TYPE AND RATING OF FUSE.

! AVERTISSEMENT ! AFIN D’ASSURER LA PROTECTION CONTRE LES

RISQUES D’INCENDIE, REMPLACER UNIQUEMENT

PAR UN FUSIBLE DE MÊME TYPE ET DE MÊME

COURANT NOMINAL.

S-7

Symbols and Conventions Used on the Instrument

120 Volt Model The following warning labels are affixed to the instrument for the

120 volt models as shown in the figure below.

! WARNING ! DISCONNECT SUPPLY CORD BEFORE OPENING. GROUNDIN

G

CIRCUIT CONTINUITY IS VITAL FOR SAFE OPERATION OF

EQUIPMENT. NEVER OPERATE EQUIPMENT WITH

GROUNDING CONDUCTOR DISCONNECTED.

! AVERTISSEMENT ! DÉBRANCHER LE CORDON D’ALIMENTATION AVANT

D’OUVRIR. LA CONTINUITÉE DES MASSES EST

ESSENTIELLE POUR UN FONCTIONNEMENT SANS

DANGER. NE JAMAIS UTILISER L’ÉQUIPMENT SI LE FI

L

DE TERRE N’EST PAS RACCORDÉ.

! WARNING ! FOR PROTECTION AGAINST FIRE HAZARD, REPLACE ONLY

WITH SAME TYPE AND RATING OF FUSE.

! AVERTISSEMENT ! AFIN D’ASSURER LA PROTECTION CONTRE LES

RISQUES D’INCENDIE, REMPLACER UNIQUEMENT

PAR UN FUSIBLE DE MÊME TYPE ET DE MÊME

COURANT NOMINAL.

S-8

Safety and Regulatory Information

220–240 Volt Model The following warning labels are affixed to the instrument for the

220–240 volt models as shown in the figure below.

! WARNING ! DISCONNECT SUPPLY CORD BEFORE OPENING.

GROUNDING CIRCUIT CONTINUITY IS VITAL FOR SAFE

OPERATION OF EQUIPMENT. NEVER OPERATE EQUIPMENT

WITH GROUNDING CONDUCTOR DISCONNECTED.

! AVERTISSEMENT ! DÉBRANCHER LE CORDON D’ALIMENTATION AVANT

D’OUVRIR. LA CONTINUITÉE DES MASSES EST

ESSENTIELLE POUR UN FONCTIONNEMENT SANS

DANGER. NE JAMAIS UTILISER L’ÉQUIPMENT SI LE

FIL DE TERRE N’EST PAS RACCORDÉ.

! WARNING ! FOR PROTECTION AGAINST FIRE HAZARD, REPLACE ONLY

WITH SAME TYPE AND RATING OF FUSE.

! AVERTISSEMENT ! AFIN D’ASSURER LA PROTECTION CONTRE LES

RISQUES D’INCENDIE, REMPLACER UNIQUEMENT

PAR UN FUSIBLE DE MÊME TYPE ET DE MÊME

COURANT NOMINAL.

S-9

Electromagnetic Compatibility (EMC)

Electrical Safety Testing

! WARNING ! Routine safety testing of analytical

instruments (e.g., high potential voltage

testing) may be required by various safety

agencies.

Testing should only be carried out by

qualified personnel after seeking advice

from Applied Biosystems.

Internal AC line surge suppressors may

need to be disconnected before a test is

performed. On completion of the tests, it is

essential to reconnect the surge

components.

Electromagnetic Compatibility (EMC) S

United States (FCC)

This product is classified as a digital device used exclusively as

industrial, commercial, or medical test equipment. It is exempt

from the technical standards specified in Part 15 of the FCC

Rules and Regulations, based on Section 15.103 (c).

Japan (FCC)

This equipment has been tested and found to comply with the

Ilimits for a Class A digital device, pursuant to Part 15 of the FCC

Rules. These limits are designed to provide reasonable protection

against harmful interference when the equipment is operated in a

commercial environment. This equipment generates, uses, and

can radiate radio frequency energy and, if not installed and used

in accordance with the instruction manual, may cause harmful

interference to radio communications. Operation of this

equipment in a residential area is likely to cause harmful

interference in which case the user will be required to correct the

interference at his own expense. Changes or modifications not

S-10

Safety and Regulatory Information

expressly approved by the manufacturer could void the user’s

authority to operate the equipment.

European Union (EMC Directive)

This product has passed the following EMC tests:

VDE 0871B

EN 55011 : 91

IEC 801–2 : 84

lEC 801–4 : 84

lEC 801–4 : 88

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Thermo Fisher Scientific Gene Amp In Situ PCR System 1000 User manual

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