Applied Biosystems StepOne Instructions d'utilisation

Applied Biosystems StepOne™

and StepOnePlus™

Real-Time PCR Systems

Installation, Networking, and Maintenance

Installation, Networking, and Maintenance Guide

DRAFT

September 25, 2007 1:07 am, 4376782_Title-Copyright.fm

Applied Biosystems StepOne™

and StepOnePlus™

Real-Time PCR Systems

Installation, Networking, and Maintenance Guide

Applied Biosystems StepOne™and

StepOnePlus™Real-Time PCR Systems

Installation, Networking, and Maintenance

Guide

Get Started

Set Up the

Instrument

Install the

Colocated Layout

Install the

Standalone Layout

Connect the

System

to a Network

Maintain the

System

Installation, Networking, and Maintenance Guide

DRAFT

September 25, 2007 1:07 am, 4376782_Title-Copyright.fm

CONFIDENTIAL — For AB Internal Use Only. Do Not Distribute.

Information in this document is subject to change without notice. Applied Biosystems assumes no responsibility for any errors that may appear in this

document.

APPLIED BIOSYSTEMS DISCLAIMS ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT, EXPRESSED OR IMPLIED, INCLUDING BUT

NOT LIMITED TO THOSE OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. IN NO EVENT SHALL APPLIED

BIOSYSTEMS BE LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY, OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR

SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM

THIS DOCUMENT, INCLUDING BUT NOT LIMITED TO THE USE THEREOF.

NOTICE TO PURCHASER: Label License

The StepOne™and StepOnePlus™Real-Time PCR Systems are covered by one or more of US Patents Nos. 5,038,852, 5,333,675, 5,656,493, 5,475,610,

5,602,756, 6,703,236, 7,238,517, 6,814,934, and corresponding claims in their non-US counterparts, owned by Applera Corporation. 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, California 94404, USA.

TRADEMARKS:

Applera, Applied Biosystems, AB (Design), Primer Express, and VIC are registered trademarks, and FAM, JOE, MicroAmp, ROX, StepOne, StepOnePlus,

TAMRA, and VeriFlex are trademarks of Applera Corporation or its subsidiaries in the U.S. and/or certain other countries.

AmpErase and TaqMan are registered trademarks of Roche Molecular Systems, Inc.

SYBR is a registered trademark of Molecular Probes, Inc.

Microsoft and Windows are registered trademarks of Microsoft Corporation.

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

Part Number 4376782 Rev. D

09/2007

Contents

iii

Applied Biosystems StepOne™and StepOnePlus™Real-Time PCR Systems

Installation, Networking, and Maintenance Guide

DRAFT

September 25, 2007 1:07 am, 4376782_TOC.fm

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii

Purpose of This Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii

How to Obtain More Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix

How to Obtain Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x

Safety Conventions Used in This Document . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi

Symbols on the Instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xii

Safety Labels on Instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiii

General Instrument Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiv

Chemical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv

Chemical Waste Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii

Electrical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xviii

LED Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xviii

Biological Hazard Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xix

Workstation Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xix

Safety and Electromagnetic Compatibility (EMC) Standards . . . . . . . . . . . . . . . . . . . . xx

Chapter 1 Get Started. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

About the StepOne™and StepOnePlus™Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Before You Begin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Select Protective Hardware and Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Select an Installation Layout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Plan the Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Chapter 2 Set Up the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . 13

About the Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Unpack the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Check the Shipped Materials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Set Up the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Complete the Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Table of Contents

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Applied Biosystems StepOne™and StepOnePlus™Real-Time PCR Systems

Installation, Networking, and Maintenance Guide

Chapter 3 Install the Colocated Layout . . . . . . . . . . . . . . . . . . . . 25

About the Colocated Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Install the Computer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Set Up the Computer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Install the StepOne™Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Connect the System Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Perform the RNase P Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Set Up the Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Run the Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

Analyze the Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

After the Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

Chapter 4 Install the Standalone Layout. . . . . . . . . . . . . . . . . . . . 49

About the Standalone Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

Set Up the Computer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

Install the Computer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

Install the StepOne™Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

Prepare the StepOne™Software for Standalone Use . . . . . . . . . . . . . . . . . . . . . 58

Perform the RNase P Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60

Set Up the Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62

Run the Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63

Analyze the RNase P Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

Unload the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

Transfer the Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

Analyze the Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68

After the Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

Chapter 5 Connect the System to a Network . . . . . . . . . . . . . . . . 73

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

Connect the Instrument to a Network . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78

Set Up a Computer for Remote Monitoring . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80

Monitor the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82

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Applied Biosystems StepOne™and StepOnePlus™Real-Time PCR Systems

Installation, Networking, and Maintenance Guide

Chapter 6 Maintain the System . . . . . . . . . . . . . . . . . . . . . . . . . . 87

Regular Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88

Perform a Spatial Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90

Perform a Background Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94

Perform a Dye Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100

Archive and Back Up Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113

Infrequent Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114

Decontaminate the Sample Block . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115

Move the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118

Replace the External Fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120

Ship the Instrument for Service . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122

Update the Windows Operating System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124

Update the StepOne™Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125

Appendix A How to Troubleshoot the Installation . . . . . . . . . . . . . . . 127

StepOne™Software Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128

Network Connection Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129

Background Calibration Failure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132

Dye Calibration Failure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134

Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153

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Applied Biosystems StepOne™and StepOnePlus™Real-Time PCR Systems

Installation, Networking, and Maintenance Guide

vii

Applied Biosystems StepOne™and StepOnePlus™Real-Time PCR Systems

Installation, Networking, and Maintenance Guide

DRAFT

September 25, 2007 1:07 am, 4376782_Preface.fm

Preface

Purpose of This Guide

About the System

Documentation

The guides listed below are shipped with the Applied Biosystems StepOne™and

StepOnePlus™Real-Time PCR Systems (StepOne™and StepOnePlus™systems).

Guide Purpose and Audience PN

Applied Biosystems StepOne™and StepOnePlus™

Real-Time PCR Systems Getting Started Guide for

Genotyping Experiments

Explains how to perform experiments on the

StepOne™and StepOnePlus™systems. Each Getting

Started Guide functions as both:

• A tutorial, using example experiment data provided

with the Applied Biosystems StepOne™Real-Time

PCR System Software (StepOne™software).

• A guide for your own experiments.

Intended for laboratory staff and principal

investigators who perform experiments using the

StepOne™or StepOnePlus™system.

4376786

Applied Biosystems StepOne™and StepOnePlus™

Real-Time PCR Systems Getting Started Guide for

Presence/Absence Experiments

4376787

Applied Biosystems StepOne™and StepOnePlus™

Real-Time PCR Systems Getting Started Guide for

Relative Standard Curve and Comparative CT

Experiments

4376785

Applied Biosystems StepOne™and StepOnePlus™

Real-Time PCR Systems Getting Started Guide for

Standard Curve Experiments

4376784

Applied Biosystems StepOne™and StepOnePlus™

Real-Time PCR Systems Installation, Networking, and

Maintenance Guide

Explains how to install and maintain the StepOne™

and StepOnePlus™systems.

Intended for laboratory staff responsible for the

installation and maintenance of the StepOne™or

StepOnePlus™system.

4376782

Applied Biosystems StepOne™and StepOnePlus™

Real-Time PCR Systems Installation Quick Reference

Card

4376783

Applied Biosystems StepOne™and StepOnePlus™

Real-Time PCR Systems Reagent Guide

Provides information about the reagents you can use

on the StepOne™and StepOnePlus™systems,

including:

• An introduction to TaqMan®and SYBR®Green

reagents

• Descriptions and design guidelines for the

following experiment types:

– Quantitation experiments

– Genotyping experiments

– Presence/absence experiments

Intended for laboratory staff and principal

investigators who perform experiments using the

StepOne™or StepOnePlus™system.

4379704

Applied Biosystems StepOne™and StepOnePlus™

Real-Time PCR Systems Site Preparation Guide

Explains how to prepare your site to receive and install

the

StepOne™

or StepOnePlus

™

systems.

Intended for personnel who schedule, manage, and

perform the tasks required to prepare your site for

installation of the StepOne

™

or StepOnePlus

™

system.

4376768

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September 25, 2007 1:07 am, 4376782_Preface.fm

Preface

Purpose of This Guide

Applied Biosystems StepOne™and StepOnePlus™Real-Time PCR Systems

Installation, Networking, and Maintenance Guide

viii

Text Conv e n t i on s

This guide uses the following conventions:

•

Bold

text indicates user action. For example:

Type

, then press

Enter

for each of the remaining fields.

•

Italic

text indicates new or important words and is also used for emphasis. For example:

Before analyzing,

always

prepare fresh matrix.

• A right arrow symbol (



) separates successive commands you select from a drop-down

or shortcut menu. For example:

Select

File



Open

User Attention

Words

Two user attention words appear in Applied Biosystems user documentation. Each word

implies a particular level of observation or action as described below:

Note:

– Provides information that may be of interest or help but is not critical to the use of

the product.

IMPORTANT!

– Provides information that is necessary for proper instrument operation,

accurate chemistry kit use, or safe use of a chemical.

Examples of the user attention words appear below:

Note:

The Calibrate function is also available in the Control Console.

IMPORTANT!

To verify your client connection, you need a valid user ID.

Safety Alert Words

Safety alert words also appear in user documentation. For more information, see “Safety

Alert Words” on page xi.

Applied Biosystems StepOne™Real-Time PCR

System Software Help

Explains how to use the StepOne™software to:

• Set up, run, and analyze experiments using the

StepOne™and StepOnePlus™systems.

• Monitor networked StepOne™and StepOnePlus™

instruments.

• Calibrate StepOne™and StepOnePlus™

instruments.

• Verify the performance of StepOne™and

StepOnePlus™instruments with an RNase P run.

Intended for:

• Laboratory staff and principal investigators who

perform experiments using the StepOne™or

StepOnePlus™system.

• Laboratory staff responsible for the installation and

maintenance of the StepOne™or StepOnePlus™

system.

Guide Purpose and Audience PN

Ce manuel convient aux modèles suivants

Table des matières

Autres manuels Applied Biosystems Équipement de laboratoire

Applied Biosystems

Applied Biosystems QuantStudio 3 Mode d'emploi

Applied Biosystems

Applied Biosystems A30207 Manuel utilisateur

Applied Biosystems

Applied Biosystems GeneAmp PCR System 9700 Manuel utilisateur

Applied Biosystems

Applied Biosystems 7900HT Manuel utilisateur

Applied Biosystems

Applied Biosystems QuantStudio 3D Manuel utilisateur

Applied Biosystems

Applied Biosystems 7500 Manuel utilisateur

Applied Biosystems

Applied Biosystems GeneAmp PCR System 9600 Manuel utilisateur

Applied Biosystems

Applied Biosystems 7500 Manuel utilisateur

Applied Biosystems

Applied Biosystems CytoFluor 4000 Series Manuel utilisateur

Applied Biosystems

Applied Biosystems 7300 Manuel du produit

Applied Biosystems

Applied Biosystems 2720 Manuel utilisateur

Applied Biosystems

Applied Biosystems QuantStudio 6 Flex Manuel utilisateur

Applied Biosystems

Applied Biosystems ViiA 7 Real Manuel utilisateur

Applied Biosystems

Applied Biosystems 7300 Manuel utilisateur

Applied Biosystems

Applied Biosystems GeneAmp PCR System 9700 Manuel utilisateur

Applied Biosystems

Applied Biosystems 2720 Manuel utilisateur

Manuels Équipement de laboratoire populaires d'autres marques

Qiagen

Qiagen DML 3000 Manuel utilisateur

Queensgate

Queensgate NANOSCAN OP400 Manuel de programmation

Conviron

Conviron GEN1000-GE Manuel utilisateur

Parr Instrument

Parr Instrument 4560 Mode d’emploi

IKA

IKA IC control Manuel utilisateur

Integra

Integra DOSE IT Manuel utilisateur

Agilent Technologies

Agilent Technologies 5800 ICP-OES Manuel utilisateur

Endress+Hauser

Endress+Hauser Cleanfit CPA875 Manuel utilisateur

NI PXI-5422 Manuel

Collomix

Collomix Aqix Manuel utilisateur

SPEX SamplePrep

SPEX SamplePrep 6875 Freezer/Mill Series Manuel utilisateur

Ocean Insight

Ocean Insight FLAME-NIR+ Manuel utilisateur

Parker

Parker ALIGN-MG-NA Manuel utilisateur

BD 644787 Manuel utilisateur

DENTAURUM

DENTAURUM Compact Megaplus Manuel utilisateur

Biuged Laboratory Instruments

Biuged Laboratory Instruments BGD 626 Manuel utilisateur

VWR

VWR SAS Super IAQ Manuel utilisateur

illumina

illumina MiSeqDx Manuel utilisateur