Applied Biosystems 3130/3130xl Genetic Analyzers

Preparing the
Instrument
Getting Started Guide
Performing
Spatial
Calibration

Performing
Spectral
Calibration

Autoanalysis
and
Sequencing
Analysis Software

Autoanalysis
and
SeqScape
Software

Autoanalysis
and
Fragment
Analysis

Running the
Instrument
© Copyright 2007, 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:
This instrument is Authorized for use in DNA sequencing and fragment analysis. This authorization is included in the purchase price of this instrument and
corresponds to the up-front fee component of a license under process claims of U.S. patents and under all process claims for DNA sequence and fragment
analysis of U.S. patents now or hereafter owned or licensable by Applied Biosystems for which an Authorization is required, and under corresponding process
claims in foreign counterparts of the foregoing for which an Authorization is required. The running royalty component of licenses may be purchased from
Applied Biosystems or obtained by using Authorized reagents purchased from Authorized suppliers in accordance with the label rights accompanying such
reagents. Purchase of this instrument does not itself convey to the purchaser a complete license or right to perform the above processes. This instrument is
also licensed under U.S. patents and apparatus and system claims in foreign counterparts thereof. No rights are granted expressly, by implication or by
estoppel under composition claims or under other process or system claims owned or licensable by Applied Biosystems. For more information regarding
licenses, please contact the Director of Licensing at Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California 94404, USA.
Applied Biosystems 3130 Genetic Analyzer:
Covered by one or more of U.S. Pats. Nos. RE37,606; RE37,941.
Applied Biosystems 3130xl Genetic Analyzer:
Covered by one or more of U.S. Pats. Nos. RE37,606; RE37,941.
NOTICE TO PURCHASER
The purchase price of this Applied Biosystems 3130/3130xl Genetic Analyzer includes a grant of a limited, non-transferable license under U.S. patent
claims and method claims of its foreign counterparts, and element claims of its foreign counterparts, to use this particular instrument for electrophoresis
methods employing fluorescence as a means of detection. No other licenses or rights are hereby conveyed either expressly, by implication, or estoppel
including, but not limited to, any claims to a composition.
The Applied Biosystems 3130 and 3130xl Genetic Analyzers includes patented technology licensed from Hitachi, Ltd. as part of a strategic partnership
between Applied Biosystems and Hitachi, Ltd., as well as patented technology of Applied Biosystems.
Trademarks
Applied Biosystems, AmpFlSTR, BigDye, Cofiler, GeneMapper, Identifiler, Profiler, Profiler Plus ID, SeqScape, SGM Plus, SNaPshot, and StockMarks are
registered trademarks and AB (Design), Applera, Hi-Di, KB, POP, POP-4, POP-6, POP-7, SEfiler, and Yfiler are trademarks of Applied Biosystems or its
subsidiaries in the U.S. and/or certain other countries.
Dell is a registered trademark of Dell Computer Corporation.
Microsoft, Windows, and Windows XP are registered trademarks of the Microsoft Corporation in the United States and other countries.
Oracle is a registered trademark of the Oracle Corporation.
All other trademarks are the sole property of their respective owners.

January 17, 2007 6:54 pm, 3130_GSGFrntCvr.fm

Part Number 4352715 Rev. D
06/2010

DRAFT
 Applied Biosystems 3130/3130xl Genetic Analyzers
Getting Started Guide Workflow

Check polymer block,

Preparing the Start the Start Data Collection Prepare buffer and
Chapter 1 Instrument system software
select capillary array,
fill reservoirs
and polymer

Performing a Start a spatial Evaluate spatial Accept or reject

Chapter 2 Spatial Calibration calibration run calibration profile spatial calibration

Performing a Prepare spectral Create a spectral Perform a Evaluate the spectral Activate a
Chapter 3 Spectral Calibration calibration chemistry instrument protocol spectral calibration calibration data spectral calibration

Autoanalysis and Create protocols Create a

Chapter 4 Sequencing Analysis for automated Sequencing Analysis
Software sequencing analysis Plate Record

Autoanalysis and Create protocols

Create a
SeqScape® for automated
Chapter 5 SeqScape Software
SeqScape Software Plate
Software
November 5, 2004 1:58 pm, Workflow_Z-fold_ [Link]

Record
analysis

Autoanalysis Create protocols Create a GeneMapper®

Chapter 6 and for automated Software
Fragment Analysis fragment analysis Plate Record
DRAFT

Prepare samples Set up for

Running the Place Plate onto
Chapter 7 Instrument and
Autosampler
Link the Plate Schedule a run Run the instrument continuous
plate assemblies operation

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide iii

 November 1, 2004 9:37 pm, Workflow_Z-fold_ [Link]
DRAFT
iv Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide
 Contents

Preface ix
How to Use This Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
How to Obtain More Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x
How to Obtain Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi

Safety xiii
Safety Conventions Used in This Document . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiv
Symbols on Instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
Safety Labels on Instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvi
General Instrument Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii
Chemical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xviii
Chemical Waste Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xx
Electrical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xxi
Physical Hazard Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xxi
Laser Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xxi
Workstation Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xxii
Safety and Electromagnetic Compatibility (EMC) Standards . . . . . . . . . . . . . . . . xxiii

Chapter 1 Preparing the Instrument 1

Instrument Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Application Summary Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Barcode Readers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Starting the 3130/3130xl Genetic Analyzer System . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Data Collection Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
November 3, 2004 9:51 am, 3130GSGuide_TOC.fm

Preparing the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Preparing Buffer and Filling Reservoirs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
SAMPLE DOCUMENT

Chapter 2 Performing a Spatial Calibration 21

Spatial Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Creating a Spatial Calibration File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Evaluating a Spatial Calibration File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Examples of Spatial Profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide v

Chapter 3 Performing a Spectral Calibration 27
Spectral Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Preparing the Spectral Calibration Chemistry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Loading Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Creating a Spectral Instrument Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Performing a Spectral Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Evaluating the Spectral Calibration Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Activating a Spectral Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Examples of Passing Sequencing Spectral Calibrations . . . . . . . . . . . . . . . . . . . . . 49
Examples of Passing Fragment Analysis Spectral Calibrations . . . . . . . . . . . . . . . . 51

Chapter 4 Autoanalysis and

Sequencing Analysis Software 53
Sequencing Analysis Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
About Plate Records and Sequencing Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Creating Protocols for Automated Sequencing Analysis . . . . . . . . . . . . . . . . . . . . . 59
Analysis Protocol for Sequencing Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Results Group for Sequencing Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Filling Out a Sequencing Analysis Plate Record . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

Chapter 5 Autoanalysis and SeqScape Software 81

SeqScape Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
About Plate Records and Seqscape Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Creating Protocols for Automated SeqScape Software Analysis . . . . . . . . . . . . . . . 88
Filling Out a SeqScape Software Plate Record . . . . . . . . . . . . . . . . . . . . . . . . . . . 101

Chapter 6 Autoanalysis and Fragment Analysis 105

GeneMapper Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
About GeneMapper Software Plate Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108

November 3, 2004 9:51 am, 3130GSGuide_TOC.fm

Creating Protocols for Automated Fragment Analysis . . . . . . . . . . . . . . . . . . . . . . 112
Creating a GeneMapper Software Plate Record . . . . . . . . . . . . . . . . . . . . . . . . . . . 123 SAMPLE DOCUMENT

Chapter 7 Running the Instrument 127

Preparing Samples and Plate Assemblies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
Linking and Unlinking a Plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
Running the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
Controlling the Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
Set Up for Continuous Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
Working with Data in The Run History View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
Viewing Data from a Completed Run in the Data Collection Software . . . . . . . . . . 146

vi Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Viewing Autoextraction Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
Using Autoanalysis Manager Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
Viewing Analyzed Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160

Appendix A Plate Mapping 161

Injection Scheduling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
Capillary Array Map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
96-Well Plate Mapping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
384-Well Plate Mapping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163

Index 3
November 3, 2004 9:51 am, 3130GSGuide_TOC.fm
SAMPLE DOCUMENT

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide vii

 November 3, 2004 9:51 am, 3130GSGuide_TOC.fm
SAMPLE DOCUMENT

viii Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Preface

How to Use This Guide

Purpose of This The Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide provides
Guide step-by-step instructions for preparing and analyzing a sample. It is designed to help you
quickly learn how to use the Applied Biosystems 3130/3130xl Genetic Analyzers.

Audience This manual is written for principle investigators and laboratory staff who are planning
to operate and maintain the Applied Biosystems 3130/3130xl Genetic Analyzers.

Assumptions This guide assumes you have the following background:

• Familiarity with Microsoft® Windows® XP operating system.
• Knowledge of general techniques for handling DNA samples and preparing them
for electrophoresis.
• A general understanding of hard drives, data storage, file transfers, and copying and
pasting.
If you want to integrate the 3130/3130xl Genetic Analyzers into your existing laboratory
data flow system, you need networking experience.

Text Conventions This guide uses the following conventions:

• Bold indicates user action. For example:
Type 0, then press Enter for each of the remaining fields.
• Italic text indicates new or important words and is also used for emphasis. For
example:
November 3, 2004 9:51 am, [Link]

Before analyzing, always prepare fresh matrix.

• A right arrow bracket (>) separates successive commands you select from a drop-
down or shortcut menu. For example:
Select File > Open > Spot Set.
Right-click the sample row, then select View Filter > View All Runs.

User Attention Two user attention words appear in Applied Biosystems user documentation. Each word
Words implies a particular level of observation or action as described below:
DRAFT

• 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.

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide ix

Preface
How to Obtain More Information

Examples of the user attention words appear below:

Note: The size of the column affects the run time.

IMPORTANT! To verify your client connection to the database, you need a valid Oracle
user ID and password.

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

How to Obtain More Information

Related The following related document is shipped with the system:
Documentation
• Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting,
and Reference Guide (P/N 4352716) - Contains information on maintaining the
instrument and computer system, troubleshooting tables to diagnose performance
failures and advance reference content.
• Applied Biosystems 3130/3130xl Genetic Analyzers Site Preparation Guide
(P/N 4352717) - Contains the space, environmental, and electrical requirements to
support the 3130/3130xl Genetic Analyzer system.
• Applied Biosystems 3730/3730xl DNA Analyzers and Applied Biosystems
3130/3130xl Genetic Analyzers AB Navigator Software Administrator Guide
(P/N 4359472) - Contains information and procedures for the administrator
maintaining the computer system and software files of the Applied Biosystems
3130/3130xl Genetic Analyzers.
• Applied Biosystems 3130/3130xl Genetic Analyzers Quick Reference Card
(P/N 4362825) - Contains a flowchart on how to run your samples and instrument, a
table of maintenance tasks, and a Data Collection software reference guide.

Note: For additional documentation, see “How to Obtain Support” on page xi.

November 3, 2004 9:51 am, [Link]

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

x Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Preface
How to Obtain Support

How to Obtain Support

For the latest services and support information for all locations, go to
[Link] then click the link for Support.
At the 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 Support page provides access to worldwide telephone and fax numbers
to contact Applied Biosystems Technical Support and Sales facilities.
November 3, 2004 9:51 am, [Link]
DRAFT

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide xi

Preface
How to Obtain Support

November 3, 2004 9:51 am, [Link]

DRAFT

xii Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Safety

This safety section describes the following:

Safety Conventions Used in This Document . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiv
Symbols on Instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
Safety Labels on Instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xvi
General Instrument Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii
Chemical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xviii
Chemical Waste Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xx
Electrical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xxi
Physical Hazard Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xxi
Laser Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xxi
Workstation Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xxii
Safety and Electromagnetic Compatibility (EMC) Standards . . . . . . . . . . . . . . . . . . xxiii
November 3, 2004 9:51 am, Safety_fm
DRAFT

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide xiii

Safety
Safety Conventions Used in This Document

Safety Conventions Used in This Document

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

Definitions

IMPORTANT! – Indicates information that is necessary for proper instrument operation,

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

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

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

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

could result in death or serious injury.

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

will result in death or serious injury. This signal word is to be limited to the most extreme
situations.

Except for IMPORTANTs, each safety alert word in an Applied Biosystems document
appears with an open triangle figure that contains a hazard symbol. These hazard
symbols are identical to the hazard icons that are affixed to Applied Biosystems
instruments (see “Safety Symbols” on page xvi).

November 3, 2004 9:51 am, Safety_fm

DRAFT

xiv Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Safety
Symbols on Instruments

Examples
The following examples show the use of safety alert words:

IMPORTANT! You must create a separate a Sample Entry Spreadsheet for each 96-well
microtiter plate.

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

CHEMICAL HAZARD. Formamide. Exposure causes eye, skin,

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

ELECTRICAL HAZARD. Failure to ground the instrument

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

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

Indicates the On position of the main power switch.

Indicates the Off position of the main power switch.

November 3, 2004 9:51 am, Safety_fm

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.
DRAFT

Indicates a terminal that can receive or supply alternating current or voltage.

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

voltage.

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide xv

Safety
Safety Labels on Instruments

Safety Symbols The following table describes the safety symbols that may be displayed on
Applied Biosystems instruments. Each symbol may appear by itself or in combination
with text that explains the relevant hazard (see “Safety Labels on Instruments” on
page xvi). 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.

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

Indicates the presence of moving parts and to proceed with appropriate caution.

Safety Labels on Instruments

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

English Francais

CAUTION Hazardous chemicals. Read the ATTENTION Produits chimiques dangeureux.

November 3, 2004 9:51 am, Safety_fm

Material Safety Data Sheets (MSDSs) before Lire les fiches techniques de sûreté de
handling. matériels avant la manipulation des produits.
CAUTION Hazardous waste. Read the waste ATTENTION Déchets dangereux. Lire les
profile (if any) in the site preparation guide for renseignements sur les déchets avant de les
this instrument before handling or disposal. manipuler ou de les éliminer.
CAUTION Hazardous waste. Refer to ATTENTION Déchets dangereux. Lire les
MSDS(s) and local regulations for handling fiches techniques de sûreté de matériels et la
and disposal. régulation locale associées à la manipulation
et l'élimination des déchets.
DRAFT

WARNING Hot lamp. AVERTISSEMENT Lampe brûlante.

WARNING Hot. Replace lamp with an AVERTISSEMENT Composants brûlants.
Applied Biosystems lamp. Remplacer la lampe par une lampe
Applied Biosystems.
CAUTION Hot surface. ATTENTION Surface brûlante.
DANGER High voltage. DANGER Haute tension.

xvi Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Safety
General Instrument Safety

English Francais

WARNING To reduce the chance of electrical AVERTISSEMENT Pour éviter les risques
shock, do not remove covers that require tool d'électrocution, ne pas retirer les capots dont
access. No user-serviceable parts are inside. l'ouverture nécessite l'utilisation d'outils.
Refer servicing to Applied Biosystems L’instrument ne contient aucune pièce
qualified service personnel. réparable par l’utilisateur. Toute intervention
doit être effectuée par le personnel de service
qualifié de Applied Biosystems.
DANGER Class 3B laser radiation present DANGER Class 3B rayonnement laser en cas
when open and interlock defeated. Avoid d’ouverture et d’une neutralisation des
direct exposure to laser beam. dispositifs de sécurité. Eviter toute exposition
directe avec le faisceau.
DANGER Class 3B laser radiation when DANGER Class 3B rayonnement laser en cas
open. Avoid direct exposure to laser beam. d’ouverture. Eviter toute exposition directe
avec le faisceau.
DANGER Class 2(II) laser radiation present DANGER de Class 2(II) rayonnement laser en
when open and interlock defeated. Do not cas d'ouverture et d'une neutralisation des
stare directly into the beam dispositifs de securite. Eviter toute exposition
directe avec le faisceau.
DANGER Class 2(II) laser radiation present DANGER de Class 2(II) rayonnement laser en
when open. Do not stare directly into the cas d'ouverture. Eviter toute exposition
beam. directe avec le faisceau.
DANGER Class 2(II) LED when open and DANGER de Class 2(II) LED en cas
interlock defeated. Do not stare directly into d'ouverture et d'une neutralisation des
the beam. dispositifs de securite. Eviter toute exposition
directe avec le faisceau.
DANGER Class 2(II) LED when open. Do not DANGER de Class 2(II) LED en cas
stare directly into the beam. d'ouverture. Eviter toute exposition directe
avec le faisceau.
CAUTION Moving parts. ATTENTION Parties mobiles.

General Instrument Safety

November 3, 2004 9:51 am, Safety_fm

PHYSICAL INJURY HAZARD. Use this product only as

specified in this document. Using this instrument in a manner not specified by
Applied Biosystems may result in personal injury or damage to the instrument.

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

Lifting the and positioned only by the personnel or vendor specified in the applicable site
Instrument preparation guide. If you decide to lift or move the instrument after it has been installed,
do not attempt to lift or move the instrument without the assistance of others, the use of
DRAFT

appropriate moving equipment, and proper lifting techniques. Improper lifting can cause
painful and permanent back injury. Depending on the weight, moving or lifting an
instrument may require two or more persons.

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide xvii

Safety
Chemical Safety

Moving and
Lifting Stand-
Alone Computers Do not attempt to lift or move the computer or the monitor without
and Monitors the assistance of others. Depending on the weight of the computer and/or the monitor,
moving them may require two or more people.

Things to consider before lifting the computer and/or the monitor:

• Make sure that you have a secure, comfortable grip on the computer or the monitor
when lifting.
• Make sure that the path from where the object is to where it is being moved is clear
of obstructions.
• Do not lift an object and twist your torso at the same time.
• Keep your spine in a good neutral position while lifting with your legs.
• Participants should coordinate lift and move intentions with each other before
lifting and carrying.
• Instead of lifting the object from the packing box, carefully tilt the box on its side
and hold it stationary while someone slides the contents out of the box.

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

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

November 3, 2004 9:51 am, Safety_fm

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

About MSDSs Chemical manufacturers supply current Material Safety Data Sheets (MSDSs) with
shipments of hazardous chemicals to new customers. They also provide MSDSs with the
DRAFT

first shipment of a hazardous chemical to a customer after an MSDS has been updated.
MSDSs provide the safety information you need to store, handle, transport, and dispose
of the chemicals safely.
Each time you receive a new MSDS packaged with a hazardous chemical, be sure to
replace the appropriate MSDS in your files.

xviii Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Safety
Chemical Safety

Obtaining 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 [Link]

2. In the Search field, type in the chemical name, part number, or other information
that appears in the MSDS of interest. Select the language of your choice, then click
Search.

3. Find the document of interest, right-click the document title, then select any of the
following:
• Open – To view the document
• Print Target – To print the document
• Save Target As – To download a PDF version of the document to a destination
that you choose

4. To have a copy of a document sent by fax or e-mail, select Fax or Email to the left
of the document title in the Search Results page, then click RETRIEVE
DOCUMENTS at the end of the document list.

5. After you enter the required information, click View/Deliver Selected Documents
Now.

Chemical Safety To minimize the hazards of chemicals:

Guidelines
• Read and understand the Material Safety Data Sheets (MSDS) provided by the
chemical manufacturer before you store, handle, or work with any chemicals or
hazardous materials. (See “About MSDSs” on page xviii.)
• Minimize contact with chemicals. Wear appropriate personal protective equipment
when handling chemicals (for example, safety glasses, gloves, or protective
clothing). For additional safety guidelines, consult the MSDS.
• Minimize the inhalation of chemicals. Do not leave chemical containers open. Use
only with adequate ventilation (for example, fume hood). For additional safety
November 3, 2004 9:51 am, Safety_fm

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.
DRAFT

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide xix

Safety
Chemical Waste Safety

Chemical Waste Safety

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

CHEMICAL WASTE HAZARD. Wastes produced by Applied

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

Chemical Waste To minimize the hazards of chemical waste:

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

Waste Disposal If potentially hazardous waste is generated when you operate the instrument, you must:
• Characterize (by analysis if necessary) the waste generated by the particular

November 3, 2004 9:51 am, Safety_fm

applications, reagents, and substrates used in your laboratory.
• Ensure the health and safety of all personnel in your laboratory.
• Ensure that the instrument waste is stored, transferred, transported, and disposed of
according to all local, state/provincial, and/or national regulations.

IMPORTANT! Radioactive or biohazardous materials may require special handling, and

disposal limitations may apply.
DRAFT

xx Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Safety
Electrical Safety

Electrical Safety

ELECTRICAL SHOCK HAZARD. Severe electrical shock can

result from operating the Applied Biosystems 3130/3130xl Genetic Analyzers without
its instrument panels in place. Do not remove instrument panels. High-voltage contacts
are exposed when instrument panels are removed from the instrument.

Power ELECTRICAL HAZARD. Grounding circuit continuity is vital for

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

ELECTRICAL HAZARD. Use properly configured and approved

line cords for the voltage supply in your facility.

ELECTRICAL HAZARD. Plug the system into a properly

grounded receptacle with adequate current capacity.

Overvoltage The Applied Biosystems 3130/3130xl Genetic Analyzers have an installation

Rating (overvoltage) category of II, and is classified as portable equipment.

Physical Hazard Safety

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

Laser Safety
November 3, 2004 9:51 am, Safety_fm

Laser The Applied Biosystems 3130/3130xl Genetic Analyzers use an Argon laser. Under
Classification normal operating conditions, the instrument laser is categorized as a Class I laser. When
safety interlocks are disabled during certain servicing procedures, the laser can cause
permanent eye damage, and, therefore, is classified under those conditions as a Class 3B
laser.
The Applied Biosystems 3130/3130xl Genetic Analyzers has been tested to and
complies with 21 CFR, 1040.10 and 1040.11, as applicable.”
DRAFT

The Applied Biosystems 3130/3130xl Genetic Analyzers have been tested to and
complies with standard EN60825-1, “Radiation Safety of Laser Products, Equipment
Classification, Requirements, and User’s Guide.”

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide xxi

Safety
Workstation Safety

Laser Safety To ensure safe laser operation:

Requirements
• The system must be installed and maintained by an Applied Biosystems Technical
Representative.
• All instrument panels must be in place on the instrument while the instrument is
operating. When all panels are installed, there is no detectable radiation present. If
any panel is removed when the laser is operating (during service with safety
interlocks disabled), you may be exposed to laser emissions in excess of the Class
3B rating.
• Do not remove safety labels or disable safety interlocks.

Additional Laser Refer to the user documentation provided with the laser for additional information on
Safety government and industry safety regulations.
Information
LASER HAZARD. Lasers can burn the retina causing permanent
blind spots. Never look directly into the laser beam. Remove jewelry and other items that
can reflect the beam into your eyes. Do not remove the instrument top or front panels.
Wear proper eye protection and post a laser warning sign at the entrance to the laboratory
if the top or front panels are removed for service.

LASER BURN HAZARD. An overheated laser can cause severe

burns if it comes in contact with the skin. DO NOT operate the laser when it cannot be
cooled by its cooling fan. Always wear appropriate laser safety goggles.

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

MUSCULOSKELETAL AND REPETITIVE MOTION

November 3, 2004 9:51 am, Safety_fm

HAZARD. These hazards are caused by potential risk factors that include but are not
limited to repetitive motion, awkward posture, forceful exertion, holding static unhealthy
positions, contact pressure, and other workstation environmental factors.

To minimize musculoskeletal and repetitive motion risks:

• Use equipment that comfortably supports you in neutral working positions and
allows adequate accessibility to the keyboard, monitor, and mouse.
• Position the keyboard, mouse, and monitor to promote relaxed body and head
DRAFT

postures.

xxii Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Safety
Safety and Electromagnetic Compatibility (EMC) Standards

Safety and Electromagnetic Compatibility (EMC) Standards

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

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

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

European Safety Safety

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

EMC
This instrument meets European requirements for emission and immunity (EMC
Directive 89/336/EEC). This instrument has been tested to and complies with standard
EN 61326 (Class B), “Electrical Equipment for Measurement, Control and Laboratory
Use – EMC Requirements.”
November 3, 2004 9:51 am, Safety_fm

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

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide xxiii

Safety
Safety and Electromagnetic Compatibility (EMC) Standards

November 3, 2004 9:51 am, Safety_fm

DRAFT

xxiv Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 1

Preparing the Instrument 1

Preparing the
Instrument

Start the
See page 7
system

Performing a
Spatial Calibration

Start Data Collection

See page 9
software

Performing a
Spectral Calibration

Check polymer block,

select capillary array, See page 12
and polymer
Autoanalysis
and Sequencing
Analysis
Software

Prepare buffer and

November 3, 2004 9:51 am, 01_PrepInstrument.fm

See page 16
fill reservoirs

Autoanalysis
and
SeqScape Software

See page 2

Autoanalysis
and
Fragment Analysis

See page 2
DRAFT

Running the
Instrument

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 1

 Chapter 1 Preparing the Instrument
Instrument Description

Instrument Description
Instrument Layout A typical laboratory layout is shown below.

Monitor 3130/3130xl
CPU
Genetic Analyzer

Keyboard

Mouse
and
pad

November 3, 2004 9:51 am, 01_PrepInstrument.fm

F15 caps scroll
F13 F14 num lock lock
F11 F12 lock
F10
F4 F5 F6 F7 F8 F9
pageup clear = *
F1 F2 F3 help home page 7 8 9
_ += delete
esc
9 0 - x end down
5 6 +
7 8 [ ] 4
5 6 P
3 4 I O " 2 3
1 2 Y U return 1
esc R T L '
W E J K ? / enter
tab Q G H < > shift 0
D F
caps A S N M control
lock V B option
Z X C
shift
control option
GR2462

DRAFT

Notes

2 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 1 Preparing the Instrument
Application Summary Tables

Application Summary Tables

1
Sequencing Decide what combination of capillary array and polymer from the table below matches
Resolution your resolution and performance specifications.
Performance and
Specifications

24 hr Throughput
(number of
Capillary Run samples) KB
Polymer
Type of Run Length Module Time Basecaller
Type (min) 3130 3130xl QV20 LOR a b
(cm)
Genetic Genetic
Analyzer Analyzer

Ultra rapid 36 POP-4™ UltraSeq36_POP4 40 144 576 400

POP-7™ UltraSeq36_POP7 35 164 656 500
™
Rapid 36 POP-6 RapidSeq36_POP6 60 96 384 500
POP-7 RapidSeq36_POP7 96 384 600
Fast 50 POP-7 FastSeq50_POP7 60 96 384 700
Standard 50 POP-4 StdSeq50_POP4 100 56 224 600
POP-6 StdSeq50_POP6 150 36 144 600
POP-7 StdSeq50_POP7 120 48 192 850
Long read 80 POP-4 LongSeq80_POP4 210 24 96 700
POP-7 LongSeq80_POP7 170 32 128 950
a Length of Read (LOR) is the usable range of high-quality or high-accuracy bases determined by Quality Values (QV) generated
by KB™ Basecaller v1.2. The LOR is determined by using a sliding window of 20 bases, which has an average QV > 20.
b 98.5% basecalling accuracy, less than 2% Ns.
November 3, 2004 9:51 am, 01_PrepInstrument.fm
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 3

 Chapter 1 Preparing the Instrument
Application Summary Tables

Fragment Decide what combination of capillary array and polymer from the table below matches
Analysis your resolution and performance specifications. See “Fragment Analysis Kits and Run
Resolution Modules” on page 5 for information on capillary, polymer, and run module.
Performance and
Specifications

Capillary 24 hr Throughput (GTa)

Polymer Run Resolution
Length Specification
Run Modules Time
Type 3130 3130xl (bp) (SD) b
(cm) (min)
Analyzer Analyzer

High Throughput, Small Size Fragment Analysis

FragmentAnalysis22 22 POP-4 20 5,760 23,040 250 0.15
_POP4
SNP22_POP4 22 20 5,760 23,040 120 0.50
Standard Fragment Analysis
FragmentAnalysis36 36 POP-4 45 2,560 10,240 500 0.15
_POP4
HIDFragmentAnalysis 45 2,560 10,240 500 0.15
36_POP4
SNP36_POP4 30 3,840 15,360 120 0.50
FragmentAnalysis36 POP-7 35 3,290 13,170 500 0.15
_POP7
FragmentAnalysis50 50 POP-4 65 1,760 7,040 500 0.15
_POP4
FragmentAnalysis50 POP-6 90 1,200 4,800 500 0.15
_POP6
FragmentAnalysis50 POP-7 50 2,300 9,220 500 0.15
_POP7

November 3, 2004 9:51 am, 01_PrepInstrument.fm

a 20 GT (Genotypes)/capillary/injection.
b 1bp resolution at 99.99% accuracy.

DRAFT

Notes

4 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 1 Preparing the Instrument
Application Summary Tables

Fragment The table below lists the Applied Biosystem kit types, with the available run module(s)
Analysis Kits and and dye sets.
Run Modules 1

Module

HIDFragmentAnalysis36_POP4
FragmentAnalysis22_POP4

FragmentAnalysis36_POP4

FragmentAnalysis36_POP7

FragmentAnalysis50_POP4

FragmentAnalysis50_POP6

FragmentAnalysis50_POP7
HTSNP36_POP7
SNP22_POP4

SNP36_POP4
Application/Kit

SNaPshot® Multiplex System E5 E5

Custom oligos D, F, D, F, D, F, D, F, D, F, D, F,
G5 G5 G5 G5 G5 G5
Linkage Mapping Set (human) D, G5 D, G5 D, G5 D, G5 D, G5 D, G5
v2.5
ABI PRISM® Mouse Mapping Set D, G5 D, G5 D, G5 D, G5 D, G5 D, G5
v1.0
4-Dye Stockmarks® kits (bovine F
and canine)
5-Dye Stockmarks® kit (equine) G5
AFLP® kits F
4-Dye AmpFlSTR® kits F
5-Dye AmpFlSTR kits G5
November 3, 2004 9:51 am, 01_PrepInstrument.fm

AmpFlSTR Kit Table

HIDFragmentAnalysis
Kits
36_POP4
AmpFlSTR COfiler® Kit F
AmpFlSTR Profiler Plus® Kit
AmpFlSTR Profiler Plus ID Kit
AmpFlSTR SGM Plus® Kit
Other 4-Dye AmpFlSTR Kits
AmpFlSTR SEfiler™ Kit G5
DRAFT

®
AmpFlSTR Identifiler Kit
AmpFlSTR Yfiler™ Kit
Other 5-Dye AmpFlSTR Kits

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 5

 Chapter 1 Preparing the Instrument
Barcode Readers

Barcode Readers

ELECTRICAL HAZARD. Power off the instrument and the

computer before connecting an external barcode reader to the instrument.

External Barcode KEYENCE BL-80VE

Readers

An external barcode reader can be used with the 3130/3130xl instrument. With the
KEYENCE BL-80VE (see photo above), which connects to the instrument computer
keyboard, you can scan barcodes into any text box in the Data Collection software. The
KEYENCE BL-80VE barcode reader uses an LED as a light source.

November 3, 2004 9:51 am, 01_PrepInstrument.fm

DRAFT

Notes

6 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 1 Preparing the Instrument
Starting the 3130/3130xl Genetic Analyzer System

Starting the 3130/3130xl Genetic Analyzer System

1
Starting the Computer Workstation

IMPORTANT! You must start the computer

workstation before starting the instrument.

R2491
1. Power on the monitor. 130
ower button 1

F15 caps scroll

F13 F14 num lock lock
F11 F12 lock
F10
F4 F5 F6 F7 F8 F9
pageup clear = *
F1 F2 F3 help home page 7 8 9
_ += delete
esc
9 0 - x end down
5 6 +
6 7 8 [ ] 4
4 5 O P 3
2 3 U I " return 1 2
esc 1 T Y '
E R K L enter
Q W H J > ? / shift 0
tab F G <
A S D M control
caps B N option
lock C V
Z X
shift
control option

2. Power on the computer.

tton 1

F15 caps scroll

F13 F14 num lock lock
F11 F12 lock
F10
F5 F6 F7 F8 F9
pageup clear = *
help home page 7 8 9
_ += delete
9 0 - x end down
5 6 +
6 7 8 [ ] 4
5 O P 3
I " 2
November 3, 2004 9:51 am, 01_PrepInstrument.fm

T Y U ' return 1
R K L enter
H J > ? / shift 0
F G <
D M control
B N option
C V
X
tion

3. In the Log On to Windows dialog box:

a. Enter the user name.
b. If applicable, enter a password.

Note: If the computer is connected to a

network, you do not need to log on to the
network before starting the instrument.
DRAFT

c. Click .

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 7

 Chapter 1 Preparing the Instrument
Starting the 3130/3130xl Genetic Analyzer System

Starting the 3130/3130xl Genetic Analyzer

1. Ensure that the:
• Oven door is closed and locked
• Instrument doors are closed

Note: If the doors are open during power on, the

yellow light will continue to flash until you close
the doors.

2. Ensure that the computer is powered on.

Note: The computer must be on and running to

allow the instrument to copy the firmware from
the computer.

3. Power on the instrument by pressing the on/off

button on the front of the instrument.

Note: While the instrument is booting up and

performing self-checks, the yellow status light
blinks.

4. Ensure the green status light is on and not

flashing before proceeding.

Note: If the green status light does not come on,

start the Data Collection software and view the
log. The pathway to the log is:
E:\AppliedBiosystems\UDC\DataCollection\
Log\Instrument Name

November 3, 2004 9:51 am, 01_PrepInstrument.fm

Status lights

Press the on/off button to start the instrument

DRAFT

Notes

8 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 1 Preparing the Instrument
Data Collection Software

Data Collection Software

1
IMPORTANT! Do not rename the computer. The
instrument computer was assigned a unique name
before the 3130/3130xl genetic analyzer Data
Collection software was installed. Do not rename the
computer once the Data Collection software has been
installed. Doing so may cause the Data Collection
software to malfunction.

Starting the 3130/3130xl Data Collection

Software
1. Select Start > All Programs > Applied
Biosystems > Data Collection > Run 3130
Data Collection v3.0 or Run 3130xl Data
Collection v3.0 to display the Service Console.
By default, all applications are off, indicated by On
the red circles. They launch automatically with
the 3130/3130xl Data Collection software.

Activating

As each application activates, the red circles (off)

change to yellow triangles (activating), and then
to green squares (on) when they are fully
functional.
November 3, 2004 9:51 am, 01_PrepInstrument.fm

When all the applications are running (displaying

all green squares–this could take several
minutes), the Foundation Data Collection
window displays.
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 9

 Chapter 1 Preparing the Instrument
Data Collection Software

2. Click + to expand subfolders in the left tree pane.

All application folders are now visible.
Select items from this tree pane to open manager,
viewer, and other program windows.

3. Click + to expand subfolders in the left tree pane.

All application folders are now visible.
Select items from this tree pane to open manager,
viewer, and other program windows.

November 3, 2004 9:51 am, 01_PrepInstrument.fm

DRAFT

Notes

10 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 1 Preparing the Instrument
Preparing the Instrument

Preparing the Instrument

1
Instrument Doors
and Interior Pump block Polymer delivery pump (PDP)
Oven

Detection cell block

Capillary array

Buffer and water

reservoirs

GR2460
Autosampler

Lower polymer block

Anode buffer reservoir

Part Function

Anode buffer reservoir Contains 16 mL of 1X running buffer.

Buffer and water Each contain 16 mL of 1X running buffer or water.
reservoirs (four)
November 3, 2004 9:51 am, 01_PrepInstrument.fm

Autosampler Holds the sample plates and reservoirs and moves to align
the samples, water, or buffer with the capillaries.
Capillary array Enables the separation of the fluorescent-labeled DNA
fragments by electrophoresis. It is a replaceable unit
composed of 4 or 16 silica capillaries.
Detection cell block and Holds the capillaries in place for laser detection.
heater
Lower polymer block Contains the buffer valve, anode electrode, and anode
buffer reservoir.
Oven Maintains uniform capillary array temperature.
Polymer delivery pump Pumps polymer into the array and performs maintenance
(PDP) procedures.
DRAFT

Pump block Includes the displacement pump chamber, piston water

seal, array attachment point (array port), and connection to
the lower polymer block through the interconnect tube.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 11

 Chapter 1 Preparing the Instrument
Preparing the Instrument

Inspecting the Instrument

1. Open the instrument doors.

2. Perform the daily maintenance tasks -see

Chapter 1 in the Applied Biosystems 3130/3130xl
Genetic Analyzers Maintenance,
Troubleshooting and Reference Guide.
3. Install clean drip trays.

Polymer Delivery Pump

Mounting pin

PDP motor

Syringe fitting PDP motor cover

Capillary array tip

Water seal
Waste fitting
Water trap Capillary array
Mounting pin
Capillary array knob
Piston
Pump chamber
Pump block

Check valve Double-tapered ferrule

Array port

Interconnect tube

November 3, 2004 9:51 am, 01_PrepInstrument.fm

Polymer supply tube

Buffer valve pin

Mounting Lower polymer block
Polymer supply
pin Mounting pin
bottle cap with
hole O-ring Overflow hole
Buffer fill-line
Polymer
supply bottle Anode buffer reservoir
(16 mL anode reservoir)
Electrode GR2459
DRAFT

Notes

12 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 1 Preparing the Instrument
Preparing the Instrument

Inspecting the Instrument

1. Open the instrument doors. 1

2. Perform the daily maintenance tasks -see the
Applied Biosystems 3130/3130xl Genetic
Analyzers Maintenance, Troubleshooting and
Reference Guide for more detail on maintenance.
3. Install clean drip trays.

Installing or Replacing the Capillary Array

IMPORTANT! The capillary array length defined in

the wizard must match the array length you are using
for correct autoanalysis results.

IMPORTANT! Wear gloves while

handling polymer, the capillary array,
septa, or buffer reservoirs.

CHEMICAL HAZARD. POP

polymer may cause eye, skin, and respiratory tract
irritation. Please read the MSDS, and follow the
handling instructions. Wear appropriate protective
eyewear, clothing, and gloves. Use for research and
development purposes only.

1. Install a capillary array by clicking <instrument

November 3, 2004 9:51 am, 01_PrepInstrument.fm

name>, selecting Install Array Wizard and

following the prompts.

IMPORTANT! To install or replace an array that

is a different length than the one you were using,
reset the active spectral calibration (see page 47)
or create a new spectral calibration for your dye
set and array length combination (see page 37).

2. Optional: Select Update Cap Array Info wizard

to correct any errors or update capillary array and
DRAFT

serial number information.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 13

 Chapter 1 Preparing the Instrument
Preparing the Instrument

When to Replenish or Change Polymer

IMPORTANT! Always replace Su M T W Th F S

polymer that has been on the
instrument longer than one week.

If polymer on the instrument... Then ...

has been on less than one week and is in sufficient quantity Remove all bubbles, and then proceed with instrument
to complete your runs a preparation.
has been on less than one week, and insufficient in quantity Add fresh polymer to the polymer supply by following the
to complete your runs Replenish Polymer Wizard.
has been on longer than one week
is the wrong type (a change between POP-4, POP-6, and/or Replace the installed polymer type with a different type by
POP-7 polymers is required) following the Change Polymer Type Wizard.
a A 3130xl genetic analyzer run uses 50 to 80 µL of polymer and a 3130 genetic analyzer run uses ~25 to 40µL of polymer.

Before Using the Polymer

1. Remove the polymer from 4 °C storage.

2. Loosen the cap and bring the polymer to room

temperature.

3. To dissolve deposits, tighten the cap and gently

swirl the polymer.

Replenishing the Polymer

November 3, 2004 9:51 am, 01_PrepInstrument.fm

IMPORTANT! Wear gloves while
handling polymer, the capillary array,
septa, or buffer reservoirs.

CHEMICAL HAZARD. POP

polymer may cause eye, skin, and respiratory tract
irritation. Please read the MSDS, and follow the
handling instructions. Wear appropriate protective
eyewear, clothing, and gloves. Use for research and
development purposes only.
DRAFT

1. Click < Instrument Name> in the tree pane.

Notes

14 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 1 Preparing the Instrument
Preparing the Instrument

2. Select Wizards > Replenish Polymer Wizard

to replenish polymer.
1
IMPORTANT! The polymer type defined in the
wizard must match the polymer type that you are
using.

Changing Polymer Type

IMPORTANT! Wear gloves while

handling polymer, the capillary array,
septa, or buffer reservoirs.

CHEMICAL HAZARD. POP

polymer may cause eye, skin, and respiratory tract
irritation. Please read the MSDS, and follow the
handling instructions. Wear appropriate protective
eyewear, clothing, and gloves. Use for research and
development purposes only.

1. Click < Instrument Name> in the tree pane.

2. Select Wizards > Change Polymer Type

Wizard to change to a different polymer.
November 3, 2004 9:51 am, 01_PrepInstrument.fm
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 15

 Chapter 1 Preparing the Instrument
Preparing Buffer and Filling Reservoirs

Preparing Buffer and Filling Reservoirs

Required Materials

CHEMICAL HAZARD. 10X

Genetic Analyzer Buffer with EDTA may cause
eye, skin, and respiratory tract irritation. Read the
MSDS, and follow the handling instructions. Wear
appropriate protective eyewear, clothing, and gloves.

Required materials to prepare 1X running buffer:

• 10X Genetic Analyzer Buffer (P/N 402824)
• Purified (distilled or deionized) water
• 50 mL graduated cylinder
Preparing Buffer for a Single Run
1. Add 5 mL of 10X Genetic Analyzer buffer into a
graduated cylinder.

2. Add purified water to bring the total volume up

to 50 mL.
50 mL
3. Mix well. total
45 mL DI H2O

5 mL 10X Genetic
Analyzer buffer
50 mL graduated cylinder

November 3, 2004 9:51 am, 01_PrepInstrument.fm

Storing Buffer
Buffer Storage Conditions
Store 1X running buffer at:
Option A Option B
• 2 to 8 °C for up to 1 month
• Room temperature for 1 week 2 °C to 20 °C to
8 °C 25 °C

Su M T W Th F S Su M T W Th F S
DRAFT

1 month 7 days

Notes

16 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 1 Preparing the Instrument
Preparing Buffer and Filling Reservoirs

Replacing Buffer and Water

Replace the 1X running buffer in the anode and 1
cathode buffer reservoirs daily, or before each batch
of runs.

IMPORTANT! Failing to replace buffer may lead to

loss of resolution and data quality.

IMPORTANT! To clean and refill the reservoirs, the

autosampler is brought to the forward position,
thereby leaving the capillary tips exposed to the air.
Do not leave the autosampler in this position for an
extended time because the capillaries can dry out and
the array may be damaged.

Filling the Water and Cathode Buffer

Reservoirs

IMPORTANT! Wear gloves while

performing the following procedure,
and any other time you handle the
capillary array, septa, or buffer
reservoirs.

CHEMICAL HAZARD. 1✕
Genetic Analyzer Buffer with EDTA may cause eye,
skin, and respiratory tract irritation. Read the MSDS,
November 3, 2004 9:51 am, 01_PrepInstrument.fm

and follow the handling instructions. Wear

appropriate protective eyewear, clothing, and gloves.

1. Verify the oven and instrument doors are closed.

2. Press the Tray button on the outside of the
instrument to bring the autosampler to the
forward position

3. Wait until the autosampler stops at the forward

position, then open the instrument door.
Tray button
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 17

 Chapter 1 Preparing the Instrument
Preparing Buffer and Filling Reservoirs

4. Remove the cathode buffer and water reservoirs

from the instrument.

5. Dispose of remaining fluids and rinse out the

reservoirs with deionized water. Remove

Note: Follow your company’s waste disposal

practices for appropriate disposal procedures.

6. Rinse the cathode reservoir with 1X running

buffer, and then fill to the line with 1X running
buffer (about 16 mL). Fill line

GR1857b
7. Fill the two water reservoirs to the line with
quality deionized water (about 16 mL).

Be sure that the septa fit

securely and flush on the tops of the reservoirs to
prevent damaging the capillary tips.

8. Place a clean reservoir septa on each reservoir,

and dry the outside of the reservoirs using a
lint-free tissue wipe.

9. Place the reservoirs into position on the

autosampler as shown. Water reservoir Water reservoir
(waste) (rinse)

Cathode reservoir Water reservoir

(1X running buffer) (unused)

Home position

10. Close the instrument doors.

Note: Closing the doors returns the autosampler

to the last known position, placing the tips of the
capillaries in water or buffer.
DRAFT

Notes

18 Applied Biosystems 3130/3130 Genetic Analyzers Getting Started Guide

 Chapter 1 Preparing the Instrument
Preparing Buffer and Filling Reservoirs

Filling the Anode Buffer Reservoir

Change the anode buffer: 1
Change the Anode Buffer
• Every 24 hours
• Before each run or batch of runs
• Every time you replenish the polymer or change
polymer type
Every 24 hours Before each run
or batch of runs
CHEMICAL HAZARD. 1X
Genetic Analyzer Buffer with EDTA may cause eye,
skin, and respiratory tract irritation. Read the MSDS,
and follow the handling instructions. Wear
appropriate protective eyewear, clothing, and gloves.

1. Remove the anode buffer reservoir by firmly

pulling down and twisting slowly.

2. Discard the used buffer appropriately.

3. Clean and rinse the reservoir with deionized
water, and then rinse with buffer.

4. Fill the anode buffer reservoir to the fill line with

fresh 1X running buffer (about 16 mL).

Note: The meniscus should line up with the

November 3, 2004 9:51 am, 01_PrepInstrument.fm

fill line.

Fill line
5. Put the anode buffer reservoir on the instrument.

6. If the reservoir fills with fluid, repeat this

GR2461

procedure to discard and replace the running

buffer.

Note: The reservoir could fill during bubble

removal.
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 19

 Chapter 1 Preparing the Instrument
Preparing Buffer and Filling Reservoirs

November 3, 2004 9:51 am, 01_PrepInstrument.fm

DRAFT

Notes

20 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 2

Performing a Spatial Calibration

Preparing the
Instrument
2

Performing a
Spatial Calibration

Start a spatial See page 22

calibration run
Performing a
Spectral Calibration

Autoanalysis Evaluate spatial See page 23

and Sequencing
Analysis
calibration profile
Software
November 3, 2004 9:51 am, 02_SpatialCal.fm

Autoanalysis
and
SeqScape Software Accept or reject See page 24
spatial calibration

Autoanalysis
and
Fragment Analysis
DRAFT

Running the
Instrument

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 21

 Chapter 2 Performing a Spatial Calibration
Spatial Calibration

Spatial Calibration
The 3130/3130xl genetic analyzer Data Collection software uses images collected during
the spatial calibration to establish a relationship between the signal emitted by each
capillary and the position where that signal falls on and is detected by the CCD camera.

When to Perform You are required to perform a spatial calibration when you:
the Calibration
• Install or replace a capillary array
• Temporarily remove the capillary array from the detection block
• Move the instrument

Creating a Spatial Calibration File

1. In the tree pane of the Data Collection software, click
GA Instruments > ga3130 or ga3130xl > instrument
name > Spatial Run Scheduler.

Spatial
profile

November 3, 2004 9:51 am, 02_SpatialCal.fm

Start, Accept
or Reject
Spatial profile
Positions (pixel)
of each capillary
DRAFT

Notes

22 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 2 Performing a Spatial Calibration
Evaluating a Spatial Calibration File

2. In the Spatial Protocols section, select one of the

following:
• If the capillaries contain fresh polymer, Select one
select Protocol > 3130SpatialNoFill_1
• Otherwise, select Protocol
> 3130SpatialFill_1

Note: You do not need to fill the capillaries each

time you perform a spatial calibration.
2

3. Click .
The calibration run lasts approximately:
Start spatial calibration
• 2 min. without filling the capillaries
• 6 min. when filling the capillaries

Note: The spatial profile window turns black

when you start a spatial calibration.

Evaluating a Spatial Calibration File

1. Evaluate the spatial calibration profile using the Spatial calibration profile for 3130xl system
following criteria:

Peak
Acceptable Criteria
Attribute

Height Similar heights for all peaks.

Orange One orange cross marking the top
November 3, 2004 9:51 am, 02_SpatialCal.fm

crosses of every peak. No misplaced

crosses.
Shape Single sharp peak for each
capillary. Spatial calibration profile for 3130 system

Small shoulders are acceptable.

Spacing The difference between adjacent
positions is 13 to 16 pixels.
Theoretical spacing between
capillaries is 15.
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 23

 Chapter 2 Performing a Spatial Calibration
Evaluating a Spatial Calibration File

2. Examine each row in the 16 or 4 Capillary

Positions table and verify that the values in both
the Left spacing and Right spacing columns
range between 13 to 16 pixels.
To move the cross:
a. Type a new value in the Positions (pixels)
box for the capillary of interest.
b. Click outside of that box or press Enter.

Left spacing and

Right spacing
columns

Accepting or Rejecting a Spatial

Calibration
If the calibration:
• Passed, click to write the
calibration data to the database and .ini file.
• Failed, click , then see the Applied Accept and
Reject buttons
Biosystems 3130/3130xl Genetic Analyzers
Maintenance, Troubleshooting and
Reference Guide.

November 3, 2004 9:51 am, 02_SpatialCal.fm

DRAFT

Notes

24 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 2 Performing a Spatial Calibration
Examples of Spatial Profiles

Examples of Spatial Profiles

Passing Profiles 3130 Genetic Analyzer

3130xl Genetic Analyzer

Failing Profile 3130xl Genetic Analyzer

November 3, 2004 9:51 am, 02_SpatialCal.fm
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 25

 Chapter 2 Performing a Spatial Calibration
Examples of Spatial Profiles

November 3, 2004 9:51 am, 02_SpatialCal.fm

DRAFT

Notes

26 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 3

Performing a Spectral Calibration

Preparing the
Instrument

Performing a
Spatial Calibration

Prepare spectral See page 31

calibration chemistry
Performing a
Spectral Calibration

Create a spectral See page 35

instrument protocol

Autoanalysis
and Sequencing
Analysis
Software

Perform a spectral See page 37

calibration
November 16, 2004 2:09 pm, 03_SpectralCal.fm

Autoanalysis
and
SeqScape Software

Evaluate the spectral See page 43

calibration data

Autoanalysis
and
Fragment Analysis

Activate a spectral See page 47

calibration
DRAFT

Running the
Instrument

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 27

 Chapter 3 Performing a Spectral Calibration
Spectral Calibration

Spectral Calibration
A spectral calibration creates a matrix that is used during a run to reduce raw data from
the instrument to the 4-dye or 5-dye data stored in sample files. Performing a spectral
calibration is similar to performing a sample run except that calibration standards are run
in place of samples and a spectral calibration module is used in place of a run module.

When to Perform Perform a spectral calibration:

the Calibration
• When you use a new dye set on the instrument
• When you change capillary array length (or polymer type for fragment analysis)
• After the laser or CCD camera has been realigned/replaced by a service engineer
• If you begin to see a decrease in spectral separation (pull-up and/or pull-down
peaks) in the raw or analyzed data

What Happens? Run the spectral standards in all 16 or 4 capillaries. The Data Collection software then:
• Collects the data and stores it in 16 or 4 separate temporary files
• Analyzes the data and generates a matrix for each capillary
• Stores the spectral calibration data for the dye set run

Changing For each dye set, a unique spectral calibration is used for each different capillary array
Capillary Array length.
Lengths and
• For every sequencing dye set, you must create a separate spectral calibration for
Polymer Type
each capillary array length you use.
• For every fragment analysis dye set, you must create a separate spectral calibration
for each capillary array length and polymer type combination you use.
See “Activating a Spectral Calibration” on page 47, on how to switch calibrations once
calibrations are performed for each dye set on each capillary length.

November 16, 2004 2:09 pm, 03_SpectralCal.fm

Supported New basecaller, mobility files, and run modules will be developed for the 3130/3130xl
Sequencing series instruments solely in support of the ABI PRISM® BigDye® Terminator v1.1 and
Chemistries v3.1chemistry kits. For more information, please contact Applied Biosystems Technical
Support.
ABI PRISM® BigDye® Terminator v1.0, v2.0 and v3.0 chemistry kits have been
discontinued. DRAFT

Notes

28 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 3 Performing a Spectral Calibration
Spectral Calibration

Types of There are two types of spectral calibration standards:

Calibration
• Matrix standards for fragment analysis or sequencing - A tube that contains
Standards
four or five fragments each labeled with a different single dye.
• BigDye® v3.1 or BigDye® v1.1 Terminator Sequencing Standard - A tube of a standard
chemistry reaction that contains multiple labeled fragments in each of the four dyes

Dye Set Tables Determine the correct dye set and matrix standard set for the application you are using
by using the tables below.

Sequencing Chemistry Dye Sets, Calibration Standards, and Chemistry File

Sequencing Chemistry Dye Set Spectral Calibration Standard Chemistry File

• BigDye® Terminator v3.1 Cycle Z_BigDyeV3 BigDye® v3.1 Matrix Standards Matrix Standard
Sequencing Kit
BigDye® v3.1 Terminator Sequence Standard
• ABI PRISM® dGTP BigDye® Sequencing Standard
Terminator v 3.0 Cycle Sequencing 3
Ready Reaction Kit a
• BigDye® Terminator v1.1 Cycle E_BigDyeV1 DS-01 Matrix Standards Matrix Standard
Sequencing Kit
BigDye® v1.1 Terminator Sequence Standard
• ABI PRISM® BigDye® Primer Cycle Sequencing Standard
Sequencing Kits
• ABI PRISM® dGTP BigDye®
Terminator Cycle Sequencing Ready
Reaction Kita
ABI PRISM® dRhodamine Terminator dRhodamine Matrix Standards Kit Matrix Standard
Cycle Sequencing Kit
a dGTP kits are not supported on capillary electrophoresis instruments due to compressions on certain sequence context regions; you can
run the kits if compression is not an issue.
November 16, 2004 2:09 pm, 03_SpectralCal.fm
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 29

 Chapter 3 Performing a Spectral Calibration
Spectral Calibration

Fragment Analysis Dye Sets, Calibration Standards, and Chemistry File

Fragment Analysis Chemistry Dye Set Spectral Calibration Standard Chemistry File

Custom oligos D DS-30 Matrix Standards Matrix Standard

• ABI PRISM® Mouse Mapping Set v1.0 D DS-31 Matrix Standards
• Custom oligos
• AFLP® kits F DS-32 Matrix Standards
®
• Stockmarks Kits 4-dye (bovine and
canine)
• AmpFlSTR® COfiler® Kit
• AmpFlSTR® Profiler Plus® Kit
• AmpFlSTR® Profiler Plus® ID Kit
• AmpFlSTR® SGM Plus® Kit
• Other 4-Dye AmpFlSTR Kits
ABI PRISM® SNaPshot® Multiplex System E5 DS-02 Matrix Standards
• ABI PRISM® Linkage Mapping Set v2.5 G5 DS-33 Matrix Standards
®
• Stockmarks Kit 5-dye (equine)
• Custom Oligos
• AmpFlSTR® Identifiler® Kit
• AmpFlSTR® SEfiler™ Kit
• AmpFlSTR® Yfiler™ Kit
• Other 5-Dye AmpFlSTR Kits

November 16, 2004 2:09 pm, 03_SpectralCal.fm

DRAFT

Notes

30 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 3 Performing a Spectral Calibration
Preparing the Spectral Calibration Chemistry

Preparing the Spectral Calibration Chemistry

Preparing the Calibration Standard

1. Prepare one of the following:

CHEMICAL HAZARD.
Formamide causes eye, skin, and respiratory
tract irritation. It is a possible reproductive and
birth defect hazard. Read the MSDS, and follow
the handling instructions. Wear appropriate
protective eyewear, clothing, and gloves.

• ABI PRISM BigDye Terminator v1.1 or v3.1

Sequencing Standard:
– Remove a tube of the Sequencing 3
Standard from the freezer.
– Add 170 µL of Hi-Di™ formamide to
resuspend the BigDye Terminator v1.1 or
v3.1 Sequencing Standard. Vortex
• Sequencing or fragment analysis matrix
standards:
– Remove a tube of the matrix standard 00:00:05
from the refrigerator.
– Mix thoroughly, then spin briefly in a
microcentrifuge. <1500×g
– Follow the matrix standard insert for
matrix standard and Hi-Di formamide
ratios. 00:00:05
November 16, 2004 2:09 pm, 03_SpectralCal.fm

2. Vortex thoroughly.
Briefly centrifuge the mixture.
95 °C

3. Heat the standard tube at 95 °C for 5 minutes to

denature the DNA. 00:05:00

0 °C

4. Cool the tubes on ice for 2 minutes.

DRAFT

00:02:00

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 31

 Chapter 3 Performing a Spectral Calibration
Loading Samples

Loading Samples
Prepared standard
(from step 4 on page 31)
CHEMICAL HAZARD. All
chemicals on the instrument, including liquid in the 96-Well
lines, are potentially hazardous. Please read the Plate
MSDS, and follow the handling instructions. Wear
appropriate eyewear, protective clothing, and gloves
when working on the instrument. 3130xl
instrument
layout

1 2 3 4 5 6 7 8 9 10 11 12
Do not use warped A

or damaged plates. B

3130 D

instrument E

layout F

GR1315c

Note: The efficient way to lay out samples in a plate Add 10 µL prepared standard
is illustrated here. See Appendix A, “Plate Mapping,”
for the relationship between sample position and
priority in scheduled injections.
384-Well
Plate
To load samples:
3130xl
1. Add the denatured samples to the wells of a 96- instrument
layout
or 384-well reaction plate:
• If using a 3130xl genetic analyzer: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
A

– 96-well plate – Add 10 µL of denatured B

C
D

standard to wells A1 through H2. 3130 E

November 16, 2004 2:09 pm, 03_SpectralCal.fm

F
instrument
– 384-well plate – Add 5 µL of denatured
G

layout H
I
J
standard into alternating wells of the K
L

plate: M
N
O

Row 1: A1, C1, E1, …K1, M1, O1

P

GR1316c

Row 2: Empty Add 5 µL prepared standard

into alternating wells
Row 3: A3, C3, E3, …K3, M3, O3
• If using 3130 genetic analyzer:
– 96-well plate – Add 10 µL of denatured
standard to wells A1, B1, C1 and D1.
– 384-well plate – Add 5 µL of denatured
standard into alternating wells of the
DRAFT

plate:
Row 1: A1, C1, E1 and G1

Notes

32 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 3 Performing a Spectral Calibration
Loading Samples

2. Seal the plate:

a. Place the plate on a clean, level surface. Plate septa

b. Lay the septa flat on the plate.

c. Align the holes in the septa strip with the
wells of the plate, then firmly press Sample plate
downward onto the plate.

IMPORTANT!: Do not heat plates that are

sealed with septa.

3. To prevent damage to the capillary array, inspect

the plate and septa to verify the septa fits snugly Septa and well
not aligned
and flush on the plate.

3
Septa and well
not aligned

4. Briefly centrifuge the plate. Prepared standard

<1500 × g 0:05
November 16, 2004 2:09 pm, 03_SpectralCal.fm

5. Remove the plate from the centrifuge and verify

that each sample is positioned correctly in the
bottom of its well.
If the reagents of any well contain bubbles or are
not located at the bottom of the well, repeat
steps 4 and 5.
Sample is at the
bottom of the well
6. Leave the plate on ice until you are ready to
prepare the plate assembly and place the
assembly on the autosampler.
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 33

 Chapter 3 Performing a Spectral Calibration
Loading Samples

7. Assemble the plate assembly: Plate retainer

a. Place the sample plate into the plate base.

b. Snap the plate retainer onto the plate and
plate base.

6b
6a

GR2050 b
Plate base

Assembled
components

8. Verify that the holes of the plate retainer and the

septa strip are aligned. If not, re-assemble the Plate retainer
plate assembly (see step 7). holes and septa
holes are not
aligned
IMPORTANT! Damage to the array tips will
occur if the plate retainer and septa strip holes do
not align correctly.

November 16, 2004 2:09 pm, 03_SpectralCal.fm

DRAFT

Notes

34 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 3 Performing a Spectral Calibration
Creating a Spectral Instrument Protocol

Creating a Spectral Instrument Protocol

1. In the tree pane of the Data Collection software,
click GA Instruments > ga3130xl or
ga3130 > Protocol Manager to open the
Protocol Manager window.
Create instrument
protocols here

Create analysis
protocols here

2. In the Instrument Protocols pane, click . 3

The Protocol Editor dialog box opens.

3. Complete the Protocol Editor dialog box.

a. Type a name for the protocol. 3a
b. Type a description for the protocol 3b
(optional).
November 16, 2004 2:09 pm, 03_SpectralCal.fm

c. Select Spectral in the Type drop-down list. 3c

d. Select the correct dye set for your run. See 3d
“Dye Set Tables” on page 29.
3e

3f
3g
DRAFT

3h

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 35

 Chapter 3 Performing a Spectral Calibration
Creating a Spectral Instrument Protocol

e. Select the Polymer and Array Length from Polymer, Array Length and Spectral Run Modules
the appropriate drop-down list. See table,
“Polymer, Array Length and Spectral Run Polymer Array
Run Module
Type Length (cm)
Modules.”
POP-4 22 Spect22_POP4
f. Select your chemistry file in the Chemistry
drop-down list. Failure to select the correct 36 Spect36_POP4
chemistry file for your spectral calibration SpectSQ36_POP4
samples results in a failing spectral run. See
50 Spect50_POP4
“Dye Set Tables” on page 29 for matching
chemistry files. 80 Spect80_POP4
POP-6 36 Spect36_POP6
Note: The chemistry file for fragment 50 Spect50_POP6
analysis dye sets defaults to the Matrix
Standard. POP-7 36 Spect36_POP7
50 Spect50_POP7
g. In the Run Module drop-down list, select 80 Spect80_POP7
the run module. See the table “Polymer,
Array Length and Spectral Run Modules.”

Note: The modules list is filtered based on

the polymer type, then the array length you
selected in step e. You may have only one
run module option available.

h. Click .

November 16, 2004 2:09 pm, 03_SpectralCal.fm

DRAFT

Notes

36 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 3 Performing a Spectral Calibration
Performing a Spectral Calibration

Performing a Spectral Calibration

Creating the Plate Record
1. In the tree pane of the Data Collection software,
click GA Instruments > ga3130xl or
3130 > instrument name > Plate Plate Manager
Manager.

2. Click to open the New Plate dialog

box.

3. Complete the New Plate dialog box:

a. Enter a name for the plate. 3a

b. Optional: Enter a description for the plate

3b 3
record.
c. In the Application drop-down list, select
3c
Spectral Calibration.
3d
d. In the Plate Type drop-down list, select 96-
3e
Well or 384-Well
3f
e. Enter a name for the owner.
f. Enter a name for the operator. 3g

g. Click .

4. In the Spectral Calibration Plate Editor dialog 4a 4b 4c

box:
a. In the Sample Name column, enter a sample
November 16, 2004 2:09 pm, 03_SpectralCal.fm

name, then click the next cell. The value

100 automatically displays in the Priority
column.
b. Optional: In the Comments column, enter
any additional comments or notations for
the sample at the corresponding position of
the plate.
c. In the Instrument Protocol 1 column, select
a protocol from the list or create a new
protocol (see step 2 on page 35)

5. Highlight the entire row.

DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 37

 Chapter 3 Performing a Spectral Calibration
Performing a Spectral Calibration

6. Select Edit > Fill Down Special.

Based on your plate type (96- or 384-well) and
capillary array (16 or 4 capillaries), the software
automatically fills in the appropriate well
numbers for a single run.

7. Click .
You have successfully created the plate record
for the spectral calibration plate.

November 16, 2004 2:09 pm, 03_SpectralCal.fm

DRAFT

Notes

38 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 3 Performing a Spectral Calibration
Performing a Spectral Calibration

Placing the Plate Assembly into the

Instrument

1. Verify the oven and front doors are closed.

2. Press the Tray button and wait for the

autosampler to stop at the forward position.

3. Open the front doors.

4. Place the plate assembly on the autosampler in
position A or B for the 3130xl genetic analyzer
and position B for the 3130 genetic analyzer.

Note: There is only one orientation for the plate, A B

with the notched end of the plate base away
from you.

GR2142
3

3130xl genetic analyzer

GR2142
November 16, 2004 2:09 pm, 03_SpectralCal.fm

3130 genetic analyzer

5. Ensure the plate assembly fits flat in the

autosampler. Failure to do so may allow the
capillary tips to lift the plate assembly off of the
autosampler.

6. Close the instrument doors.

Note: Closing the doors returns the autosampler

to the home position, placing the tips of the
capillaries in buffer.
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 39

 Chapter 3 Performing a Spectral Calibration
Performing a Spectral Calibration

Running the Spectral Calibration Plate

1. In the tree pane of the Data Collection software,
click GA Instruments > ga3130xl or
3130 > instrument name > Run
Scheduler > Plate View.

2. Search for your plate record. There are two

options:
• Select Barcode in the Type of Search drop-
down list.
– In the Scan or Type Plate ID text box,
type in the plate name and click Search
to find the plate.
– Or if you have a limited number of plates
in the database, click .

All plates in the database display in plate

record section.
• Perform an advanced search by selecting
Advanced in the Type of Search drop-down
list.
– Use the drop-down list to define search
conditions for a category or multiple

November 16, 2004 2:09 pm, 03_SpectralCal.fm

categories (Run Name, Results Group
Name, Plate Name, etc.)

Note: Your entry for Plate Name will also

be set as the Plate ID.

– For each category with a condition

selected, type a value (primary search
string) in the Value 1 column.
– Click . All plates in the database
that match the search criteria display in
the plate record section.
DRAFT

Notes

40 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 3 Performing a Spectral Calibration
Performing a Spectral Calibration

3. Link the plate. .

3a
a. Select the plate record you want to run.
3b
b. Click the plate position indicator that
matches the plate you want linked.
The plate map color will change from
yellow to green when it is successfully
linked.

Note: The 3130 genetic analyzer has only

one plate position (Bay B) to link a plate
record.

4. In the toolbar of the Data Collection software

window, click to begin the run.
5. The Processing Plates dialog box opens. Click
.
3

Note: The instrument may pause before running

the plate to raise the oven temperature.

Spectral Calibration Approximate Run

Times

Capillary Length Ramp Time Approximate Total Run

Run Type
(cm) (min) Time (min)

22 Spec22_POP4 3 21
36 Spec36_POP4 10 35
SpecSQ36_POP4 10 48
November 16, 2004 2:09 pm, 03_SpectralCal.fm

Spec36_POP6 10 54
Spec36_POP7 5 30
50 Spec50_POP4 7.5 110
Spec50_POP6 10 95
Spec50_POP7 7.5 52
80 Spec80_POP4 10 140
Spec80_POP7 10 120
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 41

 Chapter 3 Performing a Spectral Calibration
Performing a Spectral Calibration

Viewing the Pass/Fail Status After the Run

After the spectral calibration run, the pass or fail
status of each capillary is recorded in the Event Log
section of the Instrument Status window.
1. In the tree pane of the Data Collection software,
click GA Instruments > ga3130xl or
ga3130 > instrument name >
Instrument Status > Event Log.

2. In the Event Messages section of the window,

view the status of each capillary.

Note: The window below shows the dye set G5

status results.

Cap # Pass/fail status Q-value Condition Number

Each capillary should have a Q-value above 0.95

Acceptable
and a Condition number range shown in the Dye Set Condition Q-Value
table. Number Range

November 16, 2004 2:09 pm, 03_SpectralCal.fm

Note: If the entire spectral calibration failed, see Sequencing Analysis 0.95
the Applied Biosystems 3130/3130xl Genetic Z_BigDyeV3 3 to 5
Analyzers Maintenance, Troubleshooting and
E_BigDyeV1
Reference Guide for troubleshooting
information. Fragment Analysis
D 4 to 8.5
F 6 to 12
E5 2.5 to 4
G5 8.5 to 14.5
Any 4- or 5-Dye 1 to 20 0.80
DRAFT

set

Notes

42 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 3 Performing a Spectral Calibration
Evaluating the Spectral Calibration Data

Evaluating the Spectral Calibration Data

IMPORTANT! Evaluate the spectral calibration profile
for each capillary, even if the Spectral Calibration
Results box indicates that they passed.

Note: Pages 49 to 50 for examples of passing

sequencing spectral calibration profiles. See pages 51
to 52 for examples of passing fragment analysis
spectral calibration profiles.

Evaluating the Spectral Profile and Raw

Data

1. In the tree pane of the Data Collection software, 3

click GA Instruments > ga3130xl or
ga3130 > instrument name > Spectral
Viewer.

Spectral
profile
November 16, 2004 2:09 pm, 03_SpectralCal.fm

Raw data
(matrix
standards)

View, rename,
Plate diagram
or set the
Click each cell active
to verify the spectral
spectral profile calibration for
and raw data the selected
DRAFT

dye set

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 43

 Chapter 3 Performing a Spectral Calibration
Evaluating the Spectral Calibration Data

2. In the Dye Set drop-down list, select the dye set

you just created.

Note: If the spectral calibration failed (no

spectral profiles are created), see the Applied
Biosystems 3130/3130xl Genetic Analyzers
Maintenance, Troubleshooting and Reference
Guide for more information.

3. In the plate diagram, select a well on the plate

diagram to view the capillary spectral results. Well A1

Note: A failing capillary is automatically

assigned the spectral profile of its nearest passing
capillary.
Capillary status:
Passed (dark green)
Passed well elected (light green)
Failed (tan)
Failed well selected (light tan)

4. Evaluate the spectral profile and raw data for the

selected capillary:
a. Verify that the order of the peaks in the Blue Green Yellow Red
spectral profile from left to right are:
– 4-dye: blue-green-yellow-red
– 5-dye: blue-green-yellow-red-orange

November 16, 2004 2:09 pm, 03_SpectralCal.fm

Do the peaks in
the profile appear
Then
in the correct
order? Example of a 4-dye spectral profile

Yes Go to step b.
Blue Green Yellow Red Orange
No The calibration run
has failed. See the
Applied
Biosystems
3130/3130xl
Genetic Analyzers
Maintenance,
Troubleshooting,
and Reference
DRAFT

Example of a 5-dye spectral calibration profile

Guide.

Notes

44 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 3 Performing a Spectral Calibration
Evaluating the Spectral Calibration Data

b. Verify that the order of the peaks in the raw Red Yellow Blue Green
data profile from left to right are:
Sequencing
– 4-dye: red-yellow-blue-green
Fragment Analysis
– 4-dye: red-yellow-green-blue
– 5-dye: orange-red-yellow-green-blue

Are peaks in the Example of a 4-dye sequencing raw data profile

wrong order or
extraneous
Then Orange Red Yellow Green Blue
peaks adversely
affecting the
spectral profile?

Yes The calibration run

has failed. See the
Applied 3
Biosystems
3130/3130xl
Genetic Analyzers
Maintenance,
Troubleshooting, Example of a 5-dye fragment analysis raw data profile
and Reference
Guide.
No Go to step c.

c. Verify that the peaks in the spectral profile Peaks are distinct, regular and in the proper order – pass
do not contain gross overlaps, dips, or other
irregularities (see “Magnifying the Spectral
Profile or Raw Data” on page 46).

Are the peaks

November 16, 2004 2:09 pm, 03_SpectralCal.fm

separate and Then

distinct?

Yes The capillary has

passed. Go to
step 5.
No The calibration run Red peak is not distinct, regular or in the proper order – fail
has failed. See the
Applied
Biosystems
3130/3130xl
Genetic Analyzers
Maintenance,
Troubleshooting,
DRAFT

and Reference
Guide.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 45

 Chapter 3 Performing a Spectral Calibration
Evaluating the Spectral Calibration Data

5. Repeat steps 3 and 4 for each capillary in the

array.
6. Optional: Rename the spectral run. The spectral
file default name is the day, date, and time of the
run.
a. Click .

b. In the Rename Calibration dialog box, enter

a descriptive name for the spectral
calibration including the dye set, array
length and polymer type (optional).
c. Click .

Magnifying the Spectral Profile or Raw Data

1. In the tree pane of the Data Collection
software, click
GA Instruments > ga3130xl or
ga3130 > instrument

November 16, 2004 2:09 pm, 03_SpectralCal.fm

name > Spectral Viewer.
2. In the spectral profile or raw data display,
click-drag the cursor to create a box
around the area of interest.
Selecting an area to magnify in a spectral profile
3. Release the mouse button.
The Data Collection software displays the
selected region.
4. Press r to reset the view.
DRAFT

Magnified area of that spectral profile

Notes

46 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 3 Performing a Spectral Calibration
Activating a Spectral Calibration

Activating a Spectral Calibration

IMPORTANT! A run cannot start unless a calibration file that matches the dye set and
capillary array length combination to be used for the run, is active.

IMPORTANT! While the software does not force you to recalibrate spectrally after
changing polymer types, it is strongly recommended that you perform a spectral
calibration after a polymer type change.

IMPORTANT! Whenever you install or replace an array or switch dye sets, you must
either set the active spectral calibration for that dye set and array length combination or
perform a new spectral calibration and then activate it.

3
IMPORTANT! Every new spectral calibration is automatically the active one for that dye
set.

You may activate a previously created spectral calibration for a run as long as the
calibration matches the dye set and array length combination (and, for fragment analysis,
the polymer type) that you wish to use. Use an active spectral calibration for:
• Sequencing analysis applications that require a separate spectral calibration (for the
same dye set) for different capillary array lengths and polymer type
• Fragment analysis applications that require a separate spectral calibration (for the
same dye set) for different capillary array lengths and polymer type
• Repeat spectral calibrations where the original calibration is better than the second
one
November 16, 2004 2:09 pm, 03_SpectralCal.fm

Setting an Active 1. In the tree pane of the Data Collection software, click
Spectral GA Instruments > ga3130xl or ga3130 > instrument
Calibration name > Spectral Viewer.

IMPORTANT! If the Spectral Viewer window is blank and deactivated, then either:
–The spectral calibration for that dye set is not in the database
or,
–You changed the array length and you do not have a spectral calibration file
activated for that dye set and array length combination.

2. In the Dye Set drop-down list, select a dye set.

DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 47

 Chapter 3 Performing a Spectral Calibration
Activating a Spectral Calibration

3. In the List of Calibrations for Dye Set drop-down

list, select the spectral calibration you want to
use. The spectral profile and raw data is
displayed.

4. If the spectral calibration is acceptable, then click

. Otherwise, run a new spectral calibration.

November 16, 2004 2:09 pm, 03_SpectralCal.fm

DRAFT

Notes

48 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 3 Performing a Spectral Calibration
Examples of Passing Sequencing Spectral Calibrations

Examples of Passing Sequencing Spectral Calibrations

Dye Set Z Created
from Matrix
Standard

3
Dye Set Z Created
from a
Sequencing
Standard
November 16, 2004 2:09 pm, 03_SpectralCal.fm
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 49

 Chapter 3 Performing a Spectral Calibration
Examples of Passing Sequencing Spectral Calibrations

Dye Set E Created

from Matrix
Standard Set
DS-01

Dye Set E Created

from a
Sequencing
Standard

November 16, 2004 2:09 pm, 03_SpectralCal.fm

DRAFT

Notes

50 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 3 Performing a Spectral Calibration
Examples of Passing Fragment Analysis Spectral Calibrations

Examples of Passing Fragment Analysis Spectral

Calibrations
Dye Set G5
Created from
Matrix Standard
Set DS-33

Dye Set F Created

from Matrix
Standard Set
DS-32
November 16, 2004 2:09 pm, 03_SpectralCal.fm
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 51

 Chapter 3 Performing a Spectral Calibration
Examples of Passing Fragment Analysis Spectral Calibrations

Dye Set D
Created from
Matrix Standard
Set DS-30

Dye Set E5
Created from
Matrix Standard
Set DS-02

November 16, 2004 2:09 pm, 03_SpectralCal.fm

DRAFT

Notes

52 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 4

Autoanalysis and
Sequencing Analysis Software

Preparing the
Instrument

Performing a
Spatial Calibration

Performing a
Spectral Calibration

4
Create protocols
See page 59
Autoanalysis for automated
and Sequencing sequencing analysis
Analysis
Software
November 3, 2004 9:51 am, 04_SWSetup_Seq.fm

Create a
See page 77
Sequencing Analysis
Plate Record
Autoanalysis
and
SeqScape Software

Autoanalysis
and
Fragment Analysis
DRAFT

Running the
Instrument

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 53

 Chapter 4 Autoanalysis and Sequencing Analysis Software
Sequencing Analysis Software

Sequencing Analysis Software

See the Applied Biosystems DNA Sequencing Analysis Software v5.1 User Guide
(P/N 4346366) for details on sequencing analysis or the Sequencing Analysis
Software v5.2 User Bulletin titled New Features (P/N 4358355) for an update on
Sequencing Analysis Software v5.2.

Analyze your sequencing samples automatically using autoanalysis or manually.

Autoanalysis Perform autoanalysis of sequencing samples using features of the 3130/3130xl genetic
analyzer Data Collection software and Sequencing Analysis Software v5.2 or higher.
The Sequencing Analysis Software must be installed and registered with the
3130/3130xl genetic analyzer Data Collection software before you can create files
required for autoanalysis.
Autoanalysis can only be performed on the same computer that collected the sample
files. If you perform autoanalysis on samples, but wish to edit/review results on another
computer, transfer the analysis protocol to the Sequencing Analysis Software database.
To analyze samples on another computer, transfer the files to that location.

Manual Analysis If the run is not set up for autoanalysis, see the Applied Biosystems DNA Sequencing
Analysis Software v5.1 User Guide and the Sequencing Analysis Software v5.2 User
Bulletin - New Features.

File-Naming Some alphanumeric characters are not valid for user names or file names. Do not use the
Convention characters below:
spaces
\/:*?"<>|

November 3, 2004 9:51 am, 04_SWSetup_Seq.fm

IMPORTANT! An error message is displayed if you use any of these characters. You
must remove the invalid character to continue.

DRAFT

Notes

54 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 4 Autoanalysis and Sequencing Analysis Software
About Plate Records and Sequencing Analysis

About Plate Records and Sequencing Analysis

Overview Plate records are data tables in the instrument database that contain the following
information:
• Plate name, type, and owner
• Position of the sample on the plate (well number)
• Sample Name
• Mobility file (in Analysis Protocol)
• Comments about the plate and about individual samples
• Name of the run module and Dye set information (run modules specify the
conditions to run the samples)
• Name of the Analysis Protocol

Note: A plate record is similar to a sample sheet or an injection list that you may have
used with other ABI PRISM® instruments.

When to Create a Create a plate record for each plate of samples for the following types of runs:
Plate Record
• Spectral calibrations
• Sequencing Analysis Software
• SeqScape Software analysis 4
• GeneMapper® software
• Mixed (sequencing and fragment analysis samples - see the Applied Biosystems
3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference
Guide for creating a mixed plate record)
For runs to begin, you must create a plate record for and link it to a plate loaded on the
instrument. However, you can create plate records for new plates while a run is in
November 3, 2004 9:51 am, 04_SWSetup_Seq.fm

progress.

About a The Plate Editor displays an empty plate record for the application selected in the New
Sequencing Plate dialog box. The data fields within a given plate record vary depending on the
Analysis Plate selected application. This section describes the sequencing analysis plate record’s data
Record fields.
The table below describes required plate editor fields:

Parameters Description See Page

Instrument Protocol Contains the run module and dye set needed to run the 59
instrument.
DRAFT

Analysis Protocol Contains everything needed to analyze sequencing 62

data.
Results Group Defines the file type, the file name, file save locations, 70
analysis software and autoanalysis.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 55

 Chapter 4 Autoanalysis and Sequencing Analysis Software
About Plate Records and Sequencing Analysis

Elements of a Sequencing Analysis Plate Record

Plate Manager

Plate Record

Results Group Instrument Protocol Analysis Protocol

Results Group Instrument Analysis Protocol

Name Protocol Name Name

Analysis software Run type Basecaller and

and autoanalysis (Regular) DyeSet/Primer file

File storage Bases called

Run module
location (pure or mixed)

File and run folder Assigning Quality

Dye set
name preferences Values (QVs)

Post processing
(clear range
trimming)

IMPORTANT! For data collection and autoanalysis to succeed, each run of samples must
have an Instrument Protocol, an Analysis Protocol, and a Results Group assigned within
a plate record.

November 3, 2004 9:51 am, 04_SWSetup_Seq.fm

DRAFT

Notes

56 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 4 Autoanalysis and Sequencing Analysis Software
About Plate Records and Sequencing Analysis

A Blank
Sequencing 1 2 3 4 5 6
Analysis Plate
Record

Default is one sample run, to add

additional runs see page 79

Columns inserted in a plate record for a sequencing analysis run

Number and 4
Description
Column

1. Sample Name Name of the sample

2. Comment Comments about the sample (optional)
3. Priority A default value of 100 to each sample. Changing the value to a
smaller number increases the priority of that set of 16 or 4 samples to
run before the others in the injection list.
November 3, 2004 9:51 am, 04_SWSetup_Seq.fm

4. Results Group Some options:

• New: Opens the Results Group Editor dialog box
• Edit: Opens the Results Group Editor dialog box for the Results
Group listed in the cell
• None: Sets the cell to have no selected Results Group
• Select one of the available Results groups from the list
Note: You must have a Results Group selected for each sample
entered in the Sample Name column.
See “Results Group for Sequencing Analysis” on page 70.
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 57

 Chapter 4 Autoanalysis and Sequencing Analysis Software
About Plate Records and Sequencing Analysis

Number and
Description
Column

5. Instrument • New: Opens the Protocol Editor dialog box.

Protocol • Edit: Opens the Protocol Editor dialog box for the Instrument
Protocol listed in the cell.
• None: Sets the cell to have no selected protocol.
• List of Instrument Protocols: In alpha-numeric order.
Note: You must have an Instrument Protocol selected for each
sample entered in the Sample Name column.
See “Instrument Protocol for Sequencing Analysis” on page 59.
6. Analysis Protocol • New: Opens the Analysis Protocol Editor dialog box.
• Edit: Opens the Analysis Protocol Editor dialog box for the
Instrument Protocol listed in the cell.
• None: Sets the cell to have no selected protocol.
• List of Analysis Protocols: In alpha-numeric order
Note: You must have an Analysis Protocol selected for each sample
entered in the Sample Name column.
See “Analysis Protocol for Sequencing Analysis” on page 62.

November 3, 2004 9:51 am, 04_SWSetup_Seq.fm

DRAFT

Notes

58 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 4 Autoanalysis and Sequencing Analysis Software
Creating Protocols for Automated Sequencing Analysis

Creating Protocols for Automated Sequencing Analysis

If the appropriate instrument protocol, analysis
protocol, and results group have been created, proceed
to “Filling Out a Sequencing Analysis Plate Record”
on page 77.

Instrument Protocol for Sequencing Analysis

An instrument protocol contains all the settings
necessary to run the instrument: the protocol name,
type of run, run module, and dye set.

Do not edit the instrument

protocol currently being used, while the instrument is
running.

Creating an Instrument Protocol

1. In the tree pane of the Data Collection software,
click GA Instruments > ga3130xl or
ga3130 > Protocol Manager.
4

Create instrument
protocols here
November 3, 2004 9:51 am, 04_SWSetup_Seq.fm

Create analysis
protocols here
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 59

 Chapter 4 Autoanalysis and Sequencing Analysis Software
Creating Protocols for Automated Sequencing Analysis

2. In the Instrument Protocol section, click

.
The Protocol Editor opens.

3. Complete the Protocol Editor:

a. Type a name for the protocol. 3a

b. Type a description for the protocol

(optional). 3b

c. Select Regular in the Type drop-down list.

3c
3d
3e

3f

d. Select the correct run module for your run.

See “Sequencing Resolution Performance
and Specifications” on page 3.

Note: To customize a run module, see the

Applied Biosystems 3130/3130xl Genetic
Analyzers Maintenance, Troubleshooting,

November 3, 2004 9:51 am, 04_SWSetup_Seq.fm

and Reference Guide.

DRAFT

Notes

60 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 4 Autoanalysis and Sequencing Analysis Software
Creating Protocols for Automated Sequencing Analysis

e. Select the correct Dye Set for your run by

using the table below.
POP-4 POP-6
POP-7 Polymer
Polymer Polymer

RapidSeq36

RapidSeq36
LongSeq80

LongSeq80
UltraSeq36

UltraSeq36

FastSeq50
StdSeq50

StdSeq50

StdSeq50
Chemistry Dye Set

BigDye® Terminator v3.1 Cycle Sequencing Kit Z_BigDye ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓

V3
ABI PRISM® dGTP BigDye® Terminator v3.0 — — — — — — — — — —
Cycle Sequencing Ready Reaction Kit
BigDye® Terminator v1.1 Cycle Sequencing Kit E_BigDye ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓
V1
ABI PRISM® dGTP BigDye® Terminator Cycle — — — — — — — — — —
Sequencing Kit*
ABI PRISM® dRhodamine Dye Terminator ✓ ✓ ✓ ✓ ✓ — — — — —
Cycle Sequencing Ready Reaction Kit
ABI PRISM® BigDye® Primer Cycle Sequencing — — — ✓ ✓ — — — — —
Kits
*dGTP kits are not supported on capillary electrophoresis instruments due to compressions on certain sequence context regions; you can
run the kits if you do not care about the compression issues.

f. Click . 4
Importing an Instrument Protocol
1. Click in the Instrument Protocols pane
of the Protocol Editor window to display the
standard File Import dialog box.
November 3, 2004 9:51 am, 04_SWSetup_Seq.fm

2. Navigate to the location of the .xml file you want

to import.

3. Select the .xml file and click Open.

Exporting an Instrument Protocol

1. In the Instrument Protocols pane, highlight the

protocol you want to export.

2. Click to display the standard File

Export dialog box.
DRAFT

3. Browse to the desired folder location.

4. Click .

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 61

 Chapter 4 Autoanalysis and Sequencing Analysis Software
Analysis Protocol for Sequencing Analysis

Analysis Protocol for Sequencing Analysis

An analysis protocol contains all the settings
necessary for analysis and post processing:
• Protocol name – The name, description of the
analysis protocol, and the sequence file formats
to be used
• Basecalling settings – The basecaller,
DyeSet/Primer file, and analysis stop point to be
used
• Mixed Bases (Optional) – When two bases are
found at the same position. Define the percent
value of the second highest to the highest peak
• Clear Range – The high quality sequence
remaining after trimming low quality sequences
typically found at the beginning and ends of the
sequence. The clear range can be based on base
positions, sample quality values, and/or number
of ambiguities (Ns) present

Note: If you created an appropriate analysis protocol

in the Sequencing Analysis software, you can use it in
Data Collection software.

IMPORTANT! Do not delete an analysis protocol

during a run while it is being used for that run.
Autoanalysis will not be performed if you do so.

Creating an Analysis Protocol

November 3, 2004 9:51 am, 04_SWSetup_Seq.fm

See the Applied Biosystems DNA Sequencing Analysis
Software v5.2 User Guide (P/N 4346366) for more
information on analysis protocols.

1. In the Analysis Protocol section of the Protocol

Manager, click .
If more than one analysis application is installed
on the data collection computer, the Analysis
Applications dialog box opens.

Note: When you name your analysis protocol,

assign a version name to help you distinguish
DRAFT

your analysis protocols.

Notes

62 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 4 Autoanalysis and Sequencing Analysis Software
Analysis Protocol for Sequencing Analysis

2. Select Sequencing Analysis, then click

to open the Analysis Protocol Editor dialog box.

3. In the General tab:

a. Enter a unique name and description for the
new protocol.
3a
b. Select the appropriate Sequence File
formats settings.

Option Creates…
Write .Seq File A .seq file for printing the
check box sequence as text file or for
use in other software.
• Use ABI format with 3b 4
Applied Biosystems
software.
• Use FASTA format with
other software.
Write Standard A .scf file to use with other
Chromatogram software. When created,
Format file the .scf extension is not
November 3, 2004 9:51 am, 04_SWSetup_Seq.fm

(.scf) appended to the file name.

Write Phred A .phd.1 file to use with
(.phd.1) File other software if you used
the KB™ basecaller.
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 63

 Chapter 4 Autoanalysis and Sequencing Analysis Software
Analysis Protocol for Sequencing Analysis

4. Select the Basecalling tab.

a. See “3130/3130xl Genetic Analyzer 4a
Basecaller and DyeSet/Primer Files” on
page 66 to select your basecaller and 4c
DyeSet primer file.

Note: Sequencing Analysis Software and

3130/3130xl genetic analyzer Data
4d
Collection software filter .mob file choices
to match the chosen .bcp file.

4b

b. In the Processed data pane, select True or

Flat Profile.

Option Used to display data as processed traces scaled...

Uniformly - the average height of peaks in the region of strongest signal is about
equal to a fixed value. The profile of the processed traces will be very similar to
that of the raw traces.

Semi-locally - the average height of peaks in any region is about equal to a fixed
value. The profile of the processed traces will be flat on an intermediate scale (>
about 40 bases).
Note: This option is applied to data that is analyzed with the KB™ basecaller

November 3, 2004 9:51 am, 04_SWSetup_Seq.fm

only. If you use the ABI basecaller, the profile option reverts to True Profile.

c. If desired, select one or more stop points for

data analysis.
d. Select your Threshold Quality option.

Option Function

With the KB™ basecaller, use this setting to assign a base to every
position, as well as the QV.

With the KB basecaller, use this setting to assign Ns to base with

QVs less than the set point. The QV is still displayed.
DRAFT

Notes

64 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 4 Autoanalysis and Sequencing Analysis Software
Analysis Protocol for Sequencing Analysis

5. Select the Mixed Bases tab.

Note: This function is active with the KB

Basecaller only.

a. For mixed bases only, select Use Mixed

Base Identification.
b. Use the default setting of 25% or change the
5a
detection level by entering a new value or
dragging the % line up or down.
5b
Note: Do not use less than 15% as your
detection limit.

6. Select the Clear Range tab.

Note: The clear range is the region of sequence

that remains after excluding the low-quality or
4
error prone sequence at both the 5´ and 3´ ends.

Select one or more Clear Range methods. If you

apply multiple methods, the smallest clear range
results.
November 3, 2004 9:51 am, 04_SWSetup_Seq.fm

Use with ABI and

7. Click to save the protocol and close the KB Basecallers

Sequence Analysis Protocol Editor dialog box.

Use with
KB Basecaller

Use with ABI and

KB Basecallers
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 65

 Chapter 4 Autoanalysis and Sequencing Analysis Software
Analysis Protocol for Sequencing Analysis

3130/3130xl Genetic Analyzer Basecaller and DyeSet/Primer Files

Basecaller and DyeSet/Primer Files Used with BigDye® Terminator Chemistry and KB Basecalling

DNA Sequencing KB Basecalling Run

Polymer DyeSet/Primer Basecaller
Chemistry Module

BigDye® Terminator v1.1 POP-4™ UltraSeq36_POP4 KB_3130_POP4_BDTv1.mob [Link]

Cycle Sequencing Kit
StdSeq50_POP4
LongSeq80_POP4
™
POP-6 RapidSeq36_POP6 KB_3130_POP6_BDTv1.mob
StdSeq50_POP6
POP-7™ UltraSeq36_POP7 KB_3130_POP7_BDTv1.mob
RapidSeq36_POP7
FastSeq50_POP7
StdSeq50_POP7
LongSeq80_POP7
®
BigDye Terminator v3.1 POP-4 UltraSeq36_POP4 KB_3130_POP4_BDTv3_.mob
Cycle Sequencing Kit
StdSeq50_POP4
LongSeq80_POP4
POP-6 RapidSeq36_POP6 KB_3130_POP6_BDTv3.mob
StdSeq50_POP6
POP-7 UltraSeq36_POP7 KB_3130_POP7_BDTv3.mob
RapidSeq36_POP7
FastSeq50_POP7
StdSeq50_POP7
LongSeq80_POP7

November 3, 2004 9:51 am, 04_SWSetup_Seq.fm

Basecaller and DyeSet/Primer Files Used with BigDye® Terminator Chemistry and ABI Basecalling

DNA
ABI Basecalling Run
Sequencing Polymer Basecaller DyeSet/Primer
Module
Chemistry

BigDye® POP-4™ UltraSeq36_POP4 Basecaller- DT3130POP4LR{BD}v1.

Terminator v1.1 [Link] mob
Kit
LongSeq80_POP4 Basecaller-
3130POP4_80cmv3.bcp
POP-6™ RapidSeq36_POP6 Basecaller- DT3130POP6{BD}[Link]
[Link]
DRAFT

StdSeq50_POP6 Basecaller-
[Link]

Notes

66 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 4 Autoanalysis and Sequencing Analysis Software
Analysis Protocol for Sequencing Analysis

Basecaller and DyeSet/Primer Files Used with BigDye® Terminator Chemistry and ABI Basecalling (continued)
BigDye POP-4 UltraSeq36_POP4 Basecaller- DT3130POP4{BDv3}v1.m
Terminator v3.1 [Link] ob
Cycle
LongSeq80_POP4 Basecaller-
Sequencing Kit
3130POP4_80cmv3.bcp
POP-6 RapidSeq36_POP6 Basecaller- DT3130POP6{BDv3}v1.m
[Link] ob
StdSeq50_POP6 Basecaller-
[Link]
ABI PRISM® POP-4 UltraSeq36_POP4 Basecaller- DT3130POP4{dRhod}v2.
dRhodamine [Link] mob
Dye Terminator
LongSeq80_POP4 Basecaller-
Cycle
3130POP4_80cmv3.bcp
Sequencing
Ready Reaction POP-6 RapidSeq36_POP6 Basecaller- DT3130POP6{dRhod}v2.
Kit [Link] mob
StdSeq50_POP6 Basecaller-
[Link]

Dye Primer Chemistry

Basecaller and DyeSet/Primer Files Used for Dye Primer Chemistry

DNA
ABI Basecalling Run
Sequencing
Chemistry
Polymer
Module
Basecaller DyeSet/Primer 4
ABI PRISM® POP-6 RapidSeq36_POP6 Basecaller- DP3130POP6{BD
BigDye® Primer [Link] -21M13}[Link]
Cycle
StdSeq50_POP6 Basecaller- DP3130POP6{BD
Sequencing Kit
[Link] -21M13Rev}[Link]
November 3, 2004 9:51 am, 04_SWSetup_Seq.fm
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 67

 Chapter 4 Autoanalysis and Sequencing Analysis Software
Analysis Protocol for Sequencing Analysis

Editing and Deleting Analysis Protocols

Editing an Analysis Protocol

1. In the Analysis Protocols pane in the Analysis
Protocol Manager, highlight the protocol you
want to edit.

2. Click .

3. Make changes in the General, Basecalling,

Mixed Bases and Clear Range tabs, if
appropriate.

4. Click to save the protocol and close the

Analysis Protocol Editor dialog box.

Deleting an Analysis Protocol

IMPORTANT! Do not delete an analysis protocol

during a run while it is being used for that run.
Autoanalysis will not be performed if you do so. You
must first delete any plate records using the analysis
protocol before you can delete or modify the
analysis protocol for these plate records.

1. In the Analysis Protocols pane in the Analysis

Protocol Manager, highlight the protocol you
want to delete.

November 3, 2004 9:51 am, 04_SWSetup_Seq.fm

2. Click to display the Deletion
Confirmation dialog box.

3. Click .

DRAFT

Notes

68 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 4 Autoanalysis and Sequencing Analysis Software
Analysis Protocol for Sequencing Analysis

Exporting an Analysis Protocol

1. In the Analysis Protocols pane in the Analysis
Protocol Manager, highlight the protocol you
want to export.

2. Click to display the standard File

Export dialog box.

3. Browse to the desired folder location.

4. Click Save.
Importing an Analysis Protocol
1. Click to display the standard File
Import dialog box.

2. Browse for the .xml file to import and click

Open.

Note: For multiple applications, select the

appropriate application to associate with the
analysis protocol.

4
November 3, 2004 9:51 am, 04_SWSetup_Seq.fm
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 69

 Chapter 4 Autoanalysis and Sequencing Analysis Software
Results Group for Sequencing Analysis

Results Group for Sequencing Analysis

A Results Group is a component within Data
Collection that organizes samples and certain user
settings under a single name. It is called a Results
Group because it is used to name, sort, and deliver
samples that result from a run.

Creating a Results Group

1. In the tree pane of the Data Collection software,
click GA Instruments > Results Group.

2. Click to display the Results Group Editor

window.

3. Complete the General tab:

a. Type a unique Results Group Name. The
name can be used in grouping sample files.
b. Type a Results Group Owner (optional).

November 3, 2004 9:51 am, 04_SWSetup_Seq.fm

The owner name can be used in naming and
sorting sample files.
3a
c. Type a Results Group Comment (optional). 3b
3c

DRAFT

Notes

70 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 4 Autoanalysis and Sequencing Analysis Software
Results Group for Sequencing Analysis

4. Select the Analysis tab, then:

a. Select Sequencing Analysis from the
Analysis Type drop-down list.
b. In the Analysis Actions section, select Do
Autoanalysis, if you want your data 4a
automatically analyzed after a run.

Note: Login ID and password are not 4b

required for Sequencing Analysis software.

5. Select the Destination tab, then use the default

destination or define a new location for data
storage.

To use … Then …

default location* skip to step 6. 5a

custom location complete steps a-b.

5b
a. Click Use Custom Location, then click 5c 4
to navigate to a different save
location.
b. Click to test the Location path
name connection:

Then a message box

November 3, 2004 9:51 am, 04_SWSetup_Seq.fm

If it…
displays …

Passes Test succeeded:

<“path”>.
Fails Test failed:<“path”>.

*Sample File Destinations

Locations where sample files are placed during extraction:
• Default Destination, default folder naming: E:\AppliedBiosystemsUDC\DataCollection\data\<instrument type>\
<instrument name>\run folder
• Default Destination, custom folder naming: E:\AppliedBiosystemsUDC\DataCollection\data\top custom folder\
subfolders, etc.
DRAFT

• Custom Destination, default folder naming: Destination\<instrument type>\<instrument name>\run folder

• Custom Destination, custom folder naming: Destination\top customer folder\subfolders, etc.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 71

 Chapter 4 Autoanalysis and Sequencing Analysis Software
Results Group for Sequencing Analysis

6. Select the Naming tab.

Use the Naming tab to customize sample file and
run folder names. You have two options:
• Use the default names for the folder and
Sample
sample file. File Name
Format pane
• Use custom names for the folder and sample
file. See “Optional: Completing Sample File
Name Format Pane” on page 73 for
elements of the Naming tab.

Note: Sample name, run folder name, and path

name, combined, can total no more than 250 Run Folder
Name
characters. Format pane

November 3, 2004 9:51 am, 04_SWSetup_Seq.fm

DRAFT

Notes

72 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 4 Autoanalysis and Sequencing Analysis Software
Results Group for Sequencing Analysis

Optional: Completing Sample File Name

Format Pane

Note: The default sample file naming for sequencing

analysis is:
seq_<capillary number>_<wellposition>.ab1

1. Select the Naming tab.

2. Type a prefix for the file name in the Prefix box.

Your entry is shown in the Example line.

3. Select the symbol that separates the Format

elements in the file name from the Name
4
Delimiter drop-down list. Only one delimiter
symbol may be chosen.
November 3, 2004 9:51 am, 04_SWSetup_Seq.fm

4. Click the Format list and then select the

components that you want in the sample name.

Note: All the samples from a single run can be

placed in the same run or results folder, so the
name of every sample from a single run should
be different. Most of the Format options are not
different between samples, so select at least one
of the options that make the sample names
unique within a run.
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 73

 Chapter 4 Autoanalysis and Sequencing Analysis Software
Results Group for Sequencing Analysis

If a unique identifier is not included in the name, Warning message

a warning message displays. Select from the
elements to make a unique sample file name.
Examples are:
– Well position
– Capillary number
– Run sequence number
– Plate Quadrant

Note: some identifiers, such as well position,

capillary number and plate quadrant are not
unique in multiple sample instances. Plate
Quadrant is not a unique identifier for a 96-well
plate.

As you select the elements for the file name, they

are placed in the Example line. An additional
element drop-down menu displays allowing you
the option of selecting an additional element.

November 3, 2004 9:51 am, 04_SWSetup_Seq.fm

The names of the Format elements eventually
truncate, but the Example field remains visible
(up to 72 characters).

Note: Resize the Results

Group window horizontally
to view the element options.
DRAFT

Notes

74 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 4 Autoanalysis and Sequencing Analysis Software
Results Group for Sequencing Analysis

5. Type the suffix for the file name in the Suffix

box.

Note: The File Extension field displays the file

extension generated from the Analysis Type
specified on the Analysis tab (see page 71). For
example, Sequencing Analysis produces sample
files with an .ab1 extension.

Optional: Run Folder/Sub-Folder Name

Format Pane

Note: The default run folder naming for sequencing

analysis is Run_<Instrumentname>_<Dateand
TimeofRun>_<RunSeq#>.

Follow the same steps described for the Sample File

Name Format pane (see page 73) to change the sub-
folder name within the run folder. Make the sub-
folder name unique, such as using the Run Folder
name.

Saving a Results Group

4
Click from any tab once all the elements
within the Results Group have been chosen.

Note: Even if you create a custom run folder location,

the system generates a separate default run folder that
contains the log file.
November 3, 2004 9:51 am, 04_SWSetup_Seq.fm

Importing and Exporting a Results Group

Results Groups can be imported from, or exported to,
XML files allowing sharing of identical Results
Groups between instruments.

Importing a Results Group

1. In the tree pane of the Data Collection software,

click GA Instruments > Results Group.

2. Click to display the standard File

DRAFT

Import dialog box.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 75

 Chapter 4 Autoanalysis and Sequencing Analysis Software
Results Group for Sequencing Analysis

3. Navigate to the file you want to import.

Note: Import file type is .xml (XML file).

4. Click .

Exporting a Results Group

1. In the tree pane of the Data Collection software,

click GA Instruments > Results Group.

2. Click the Results Group name to select it.

3. Click .
A standard file export dialog box displays with
the chosen Results Group name.

4. Navigate to the location where you want to save

the exported file.

5. Click .

Note: If there is a name conflict with a Results

Group that already exists at the save location,
then duplicate the Results group. Duplication
copies the settings into a similar Results Group
without the risk of user error when copying it
manually (see procedure below).

Duplicating a Results Group

1. Click the Results Group name.

November 3, 2004 9:51 am, 04_SWSetup_Seq.fm

2. Click .

Note: When you duplicate a Results Group, you

are asked to type a name for the new Results
Group and for the analysis application type.

DRAFT

Notes

76 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 4 Autoanalysis and Sequencing Analysis Software
Filling Out a Sequencing Analysis Plate Record

Filling Out a Sequencing Analysis Plate Record

Creating a Sequencing Analysis Plate
Record
1. In the tree pane of the Data Collection software,
click GA Instruments > ga3130xl or
ga3130 > Plate Manager.

2. Click to display the New Plate Dialog

dialog box.

3. Complete the information in the New Plate

Dialog:
a. Type a name for the plate.
b. Type a description for the plate (optional).
c. Select your sequencing application in the 3a
Application drop-down list.
d. Select 96-well or 384-well in the Plate Type 3b
drop-down list.
3c
e. Type a name for the owner and operator.
3d
f. Click to open the Sequencing 4
3e
Analysis Plate Editor.
3f

3f
November 3, 2004 9:51 am, 04_SWSetup_Seq.fm
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 77

 Chapter 4 Autoanalysis and Sequencing Analysis Software
Filling Out a Sequencing Analysis Plate Record

Completing a Sequencing Analysis Plate

Record
1. In the Sample Name column of a row, enter a 1 2 3 4
sample name, then click the next cell. The value
100 automatically displays in the Priority
column.

2. In the Comments column, enter any comments

or notations for the sample.

3. In the Priority column, change the priority value,

if desired. A lower number for each 4 or 16 set,
receives a higher run priority.

4. In the Results Group 1 column, select a group

from the drop-down list (see page 70) or create a
new Results Group.
5. In the Instrument Protocol 1 column, select a 5 6
protocol from the drop-down list (see page 59) or
create a new instrument protocol.

6. In the Analysis Protocol 1 column, select a

protocol from the drop-down list (see page 62) or
create a new analysis protocol.

7. Complete the plate record based on the samples

loaded in your plate:
• For the single runs that use the same
samples and protocols – Highlight the entire
row, then select Edit > Fill Down Special.

November 3, 2004 9:51 am, 04_SWSetup_Seq.fm

Based on your plate type (96- or 384-well)
and capillary array (16 or 4 capillaries), the
software automatically fills in the
appropriate well numbers for a single run
or
• For entire plates that use the same samples
and protocols – Highlight the entire row,
then select Edit > Fill Down to fill down
the entire plate editor.
• For plates with different samples and
protocols – complete the entries manually.
DRAFT

Notes

78 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 4 Autoanalysis and Sequencing Analysis Software
Filling Out a Sequencing Analysis Plate Record

8. To do more than one injection of the same

sample, select Edit > Add Sample Run.
Results Group, Instrument Protocol and Analysis
Protocol columns are added to the right end of
the plate record.

9. Complete the columns for the additional runs.

10. Click .

Note: After clicking OK in the Plate Editor, the

completed plate record is stored in the Plate
Manager [Link] plate record can be
searched for, edited, duplicated, exported, or
deleted in the Plate Manager.

4
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DRAFT

Notes

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 Chapter 4 Autoanalysis and Sequencing Analysis Software
Filling Out a Sequencing Analysis Plate Record

November 3, 2004 9:51 am, 04_SWSetup_Seq.fm

DRAFT

Notes

80 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 5

Autoanalysis and
SeqScape Software

Preparing the
Instrument

Performing a
Spatial Calibration

Performing a
Spectral Calibration

Autoanalysis
and Sequencing
Analysis
Software
November 3, 2004 9:51 am, 05_SWSetup_SeqScape.fm

5
Autoanalysis
and
SeqScape Software

Create protocols
for automated See page 88
SeqScape Software Analysis
Autoanalysis
and
Fragment Analysis

Create a
See page 101
SeqScape Software
DRAFT

Plate Record
Running the
Instrument

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 81

 Chapter 5 Autoanalysis and SeqScape Software
SeqScape Software

SeqScape Software
Analyzing your sequencing samples may be done by autoanalysis or manual analysis.

Autoanalysis Use the ABI PRISM® SeqScape® software to automatically analyze Applied Biosystems
3130/3130xl Genetic Analyzers sequencing data. Perform autoanalysis only on the same
instrument computer that collected the sample files. You can configure the software
packages to perform data collection and then data analysis without requiring user
interaction.
Install and register the SeqScape software with the 3130/3130xl genetic analyzer Data
Collection software before creating required files for autoanalysis.
See Appendix B in the SeqScape Software User Guide v2.5 (P/N 4359442), for more
details on setting up autoanalysis.

Required Autoanalysis requires three software packages:

Software
• 3130/3130xl genetic analyzer Data Collection software
Packages
The Data Collection software runs the instrument and collects fluorescent data from
samples. For autoanalysis to occur, the software must communicate with
downstream software.
Analysis parameters used for data collection as well as that created in SeqScape
software are accessible in Data Collection software.
• Autoanalysis Manager
The Autoanalysis Manager software is part of the integration between the data
collection, SeqScape, and GeneMapper® software. It can queue messages and track
their processing status. Each message is considered a batch job, whether it contains

November 16, 2004 2:09 pm, 05_SWSetup_SeqScape.fm

a single sample, samples from a result group, or an entire run of samples.
Autoanalysis Manager is installed by Seqscape or GeneMapper software when
loaded on a system with Data Collection software.
• A version of SeqScape software without a user interface
This SeqScape software version is identical to the regular software version except
that there is no user interface. The Autoanalysis Manager opens and uses this
version of software to analyze the data in the projects.
The automated processing version and the standard version of SeqScape software
are installed from the SeqScape Software installation CD.

IMPORTANT! When installing SeqScape software on a computer that is connected to a

3130/3130xl genetic analyzer, the Data Collection software must be running. Otherwise,
the SeqScape software does not register with the Data Service. See Chapter 2 in the
SeqScape Software User Guide v2.5, for information on installing the software.
DRAFT

Notes

82 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 5 Autoanalysis and SeqScape Software
About Plate Records and Seqscape Software

Importing Reports In the SeqScape Software v2.5, select Tools > Options [Link] can set the options to
and Projects After automatically import:
Autoanalysis
• Reports after autoanalysis
• Projects after autoanalysis
See the SeqScape Software User Guide v2.5 (P/N 4359442) for more details.

File-Naming Some alphanumeric characters are not valid for user names or file names. Do not use the
Convention invalid characters below:
spaces
\/:*?"<>|

IMPORTANT! An error message is displayed if you use any of these characters. You
must remove the invalid character to continue.

Manual Analysis See the SeqScape Software User Guide v2.5 (P/N 4359442) for information on
performing manual analysis.

About Plate Records and Seqscape Software

Requirements Successful automatic analysis requires that:
• SeqScape software is installed properly
• SeqScape software is registered and the appropriate user IDs have been created
November 3, 2004 9:51 am, 05_SWSetup_SeqScape.fm

• Autoanalysis Manager software is running

• The 3130/3130xl genetic analyzer is set up to run, and samples are prepared
• Files for a Data Collection software plate record are available: 5
– An instrument protocol
– An analysis protocol
– A results group assigned within a plate record

When to Create a Create a plate record for each plate of samples for the following types of runs:
Plate Record
• Spectral calibrations
• Sequencing Analysis Software
• SeqScape Software analysis
• GeneMapper® software
DRAFT

• Mixed (sequencing and fragment analysis samples - see the Applied Biosystems
3130/3130xl Genetic Analyzers Maintenance, Troubleshooting and Reference
Guide for creating a mixed plate record)

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 83

 Chapter 5 Autoanalysis and SeqScape Software
About Plate Records and Seqscape Software

For runs to begin, you must create a plate record for and link it to a plate loaded on the
instrument. However, you can create plate records for new plates while a run is in
progress.

SeqScape The Plate Editor displays an empty plate record for the application selected in the New
Software Plate Plate dialog box. The data fields within a given plate record vary depending on the
Record Overview application. This section describes the SeqScape Plate Record’s data fields.

IMPORTANT! For data collection and SeqScape software autoanalysis to succeed, each
run of samples must have an instrument protocol, an analysis protocol, and a results
group assigned within a plate record. You are also required to have a project, project
template, and specimen information.

The table below describes required plate editor fields.

Parameters Description See Page

Instrument Protocol Contains the run module and dye set needed to run 88
the instrument.
Created in Data Collection software.
Analysis Protocol Contains everything needed to analyze sequencing 92
data.
Created in Data Collection software or SeqScape
software. If you prefer to use analysis protocols
created in SeqScape software, then select “Always
use this protocol” - in the SeqScape software
analysis defaults settings.
Results Group Defines the file type, the file name, file save locations, 98
default analysis protocols linked to sample injections,

November 3, 2004 9:51 am, 05_SWSetup_SeqScape.fm

and user name and password.
Created in Data Collection software.
Project A group of related sequences that share the same See the
reference or for which there is no explicit reference. SeqScape
Software
Project Template Contains a reference data group (RDG), analysis
User Guide
defaults, and display settings.
v2.5 for more
Specimen The container that holds all the sample data as information
assembled contigs from a biological source or PCR
product
DRAFT

Notes

84 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 5 Autoanalysis and SeqScape Software
About Plate Records and Seqscape Software

Elements of a
SeqScape Plate Plate Manager

Record
Plate Record

Data Collection SeqScape software

software files: files:

Project Template
Results Group Instrument Protocol Analysis Protocol* - Analysis Protocol*
- Analysis Defaults
- RDG
Results Group Instrument Analysis Protocol - Display Settings
Name Protocol Name Name

Analysis software Run type Basecaller and

and autoanalysis (Regular) DyeSet/Primer file Project

File storage Bases called

Run module
location (pure or mixed) Specimen

File and run folder Assigning Quality

Dye set
name preferences Values (QVs)

Post processing
(clear range
trimming)

Filter settings

*You can create Analysis Protocols in either

SeqScape or Data Colletion software
November 3, 2004 9:51 am, 05_SWSetup_SeqScape.fm

5
DRAFT

Notes

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 Chapter 5 Autoanalysis and SeqScape Software
About Plate Records and Seqscape Software

SeqScape A Seqscape software plate record displaying the columns and descriptions is shown
Software Plate below.
Record

1 2 3 4 5 6 7 8 9

Default is one sample run, to add runs

see page 103

Number and Column Description

November 3, 2004 9:51 am, 05_SWSetup_SeqScape.fm

1. Sample Name Name of the sample.
2. Comment Comments about the sample (optional).
3. Priority A default value of 100 to each sample. Changing the value to a smaller number
causes that set of 16 or 4 samples to run to before the others in the injection list.
4. Project Select one of the available Project from the list that was created in Data Collection or
SeqScape software.
5. Project Template Completed automatically based on the Project selected.
6. Specimen Select one of the available Specimen from the list that was created in Data
Collection or SeqScape software.
DRAFT

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 Chapter 5 Autoanalysis and SeqScape Software
About Plate Records and Seqscape Software

Number and Column Description

7. Results Group Some options:

• New: Opens the Results Group Editor dialog box
• Edit: Opens the Results Group Editor dialog box for the Results Group listed in
the cell
• None: Sets the cell to have no selected Results Group
• Select one of the available Results groups from the list
Note: You must have a Results Group selected for each sample entered in the
Sample Name column.
See “Creating a Results Group” on page 98.
8. Instrument Protocol • New: Opens the Protocol Editor dialog box.
• Edit: Opens the Protocol Editor dialog box for the Instrument Protocol listed in
the cell.
• None: Sets the cell to have no selected protocol.
• List of Instrument Protocols: In alpha-numeric order.
Note: You must have an Instrument Protocol selected for each sample entered in
the Sample Name column.
See “Creating an Instrument Protocol” on page 88.
9. Analysis Protocol • New: Opens the Analysis Protocol Editor dialog box.
• Edit: Opens the Analysis Protocol Editor dialog box for the Instrument Protocol
listed in the cell.
• None: Sets the cell to have no selected protocol.
• List of Analysis Protocols: In alpha-numeric order
Note: You must have an Analysis Protocol selected for each sample entered in the
Sample Name column.
See “Creating an Analysis Protocol” on page 93.
November 3, 2004 9:51 am, 05_SWSetup_SeqScape.fm

5
DRAFT

Notes

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 Chapter 5 Autoanalysis and SeqScape Software
Creating Protocols for Automated SeqScape Software Analysis

Creating Protocols for Automated SeqScape Software

Analysis
If the appropriate SeqScape software protocols and
results group have been created, proceed to “Filling
Out a SeqScape Software Plate Record” on page 101.

Instrument Protocol for SeqScape Software

An instrument protocol contains all the necessary
settings to run the instrument:
• Protocol name
• Type of run
• Run module
• Dye set

Creating an Instrument Protocol

1. In the tree pane of the Data Collection software,
click GA Instruments > ga3130 or
ga3130xl > Protocol Manager.

Create
instrument

November 3, 2004 9:51 am, 05_SWSetup_SeqScape.fm

Create analysis
protocols here

2. In the Instrument Protocols section, click

to open the Protocol Editor.
DRAFT

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 Chapter 5 Autoanalysis and SeqScape Software
Creating Protocols for Automated SeqScape Software Analysis

3. Complete the Protocol Editor:

a. Type a name for the protocol. 3a

b. Type a description for the protocol 3b

(optional).
c. Select Regular in the Type drop-down list.
3c
3d
3e

3f

d. Select the correct run module for your run.

See “Sequencing Resolution Performance
and Specifications” on page 3 to see a list of
modules or the Applied Biosystems
3130/3130xl Genetic Analyzers
Maintenance, Troubleshooting and
Reference Guide to modify a default
module.
November 3, 2004 9:51 am, 05_SWSetup_SeqScape.fm

5
DRAFT

Notes

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 Chapter 5 Autoanalysis and SeqScape Software
Creating Protocols for Automated SeqScape Software Analysis

e. Select the correct Dye Set for your run using

the table below.
POP-4 POP-6
POP-7 Polymer
Polymer Polymer

RapidSeq36

RapidSeq36
LongSeq80

LongSeq80
UltraSeq36

UltraSeq36

FastSeq50
StdSeq50

StdSeq50

StdSeq50
Chemistry Dye Set

BigDye® Terminator v3.1 Cycle Sequencing Kit Z_BigDye ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓

V3
ABI PRISM® dGTP BigDye® Terminator v3.0 — — — — — — — — — —
Cycle Sequencing Ready Reaction Kit
BigDye® Terminator v1.1 Cycle Sequencing Kit E_BigDye ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓ ✓
V1
ABI PRISM® dGTP BigDye® Terminator Cycle — — — — — — — — — —
Sequencing Kit*
ABI PRISM® dRhodamine Dye Terminator Cycle ✓ ✓ ✓ ✓ ✓ — — — — —
Sequencing Ready Reaction Kit
ABI PRISM® BigDye® Primer Cycle Sequencing — — — ✓ ✓ — — — — —
Kits
*dGTP kits are not supported on capillary electrophoresis instruments due to compressions on certain sequence context
regions; you can run the kits if you do not care about the compression issues.

f. Click .

November 3, 2004 9:51 am, 05_SWSetup_SeqScape.fm

DRAFT

Notes

90 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 5 Autoanalysis and SeqScape Software
Creating Protocols for Automated SeqScape Software Analysis

Importing an Instrument Protocol

1. Click in the Instrument Protocols pane
of the Protocol Editor window to display the
standard File Import dialog box.

2. Navigate to the location of the .xml file you want

to import.

3. Select the .xml file and click Open.

Exporting an Instrument Protocol

1. In the Instrument Protocols pane, highlight the

protocol you want to export.

2. Click to display the standard File

Export dialog box.

3. Browse to the desired folder location.

4. Click .
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5
DRAFT

Notes

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 Chapter 5 Autoanalysis and SeqScape Software
Creating Protocols for Automated SeqScape Software Analysis

Analysis Protocol for SeqScape Software

About Analysis An analysis protocol contains all the settings necessary for analysis and post processing:
Protocols
• Protocol name – The name, description of the analysis protocol, and the sequence
file formats to be used
• Basecalling settings – The basecaller, DyeSet/Primer file, and analysis stop point
to be used
• Mixed Bases – (Optional) – When two bases are found at the same position. Define
the percent value of the second highest to the highest peak
• Clear Range – The high quality sequence remaining after trimming low quality
sequences typically found at the beginning and ends of the sequence. The clear
range can be based on base positions, sample quality values, and/or number of
ambiguities (Ns) present
• Filter – The settings that define which samples will be used in the assembly

Note: If you created an appropriate analysis protocol in the SeqScape software, you can
use it in the Data Collection software. See Appendix B in the SeqScape Software User
Guide v2.5 (P/N 4359442) for more information on autoanalysis and analysis protocols.

IMPORTANT! Do not delete the current analysis protocol being used, during a run.
Autoanalysis will not be performed if you do so.

IMPORTANT! You are required to select the Always use this Analysis Protocol in
Analysis Defaults > Analysis Protocol in the Seqscape software if you want to use it for
SeqScape analysis. See the SeqScape Software User Guide v2.5 (P/N 4359442) for more

November 3, 2004 9:51 am, 05_SWSetup_SeqScape.fm

information.

DRAFT

Notes

92 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 5 Autoanalysis and SeqScape Software
Creating Protocols for Automated SeqScape Software Analysis

Creating an Analysis Protocol

IMPORTANT! If you created an appropriate analysis

protocol in SeqScape software, you can use it in the
Data Collection software. You can also create an
analysis protocol in the SeqScape software.

1. In the Analysis Protocol section of the Protocol

Manager, click .
If more than one analysis application is installed
on the data collection computer, the Analysis
Applications dialog box opens.

2. Select SeqScape, then click to open the

Analysis Protocol Editor dialog box.
November 3, 2004 9:51 am, 05_SWSetup_SeqScape.fm

3. In the General tab, enter a unique name and

description (optional) for the new protocol. 5
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 93

 Chapter 5 Autoanalysis and SeqScape Software
Creating Protocols for Automated SeqScape Software Analysis

4. Select the Basecalling tab, then:

a. Select the appropriate basecaller and
DyeSet primer based on the chemistry,
capillary array length and polymer type you
are using. The dye set primer files displayed
are based on the basecaller selected.
See “3130/3130xl Genetic Analyzer
Basecaller and DyeSet/Primer Files” on
page 66 for a table on basecallers and
dyeset/primer files.

Note: SeqScape Software and the Data

Collection software filter .mob file choices
to match the chosen .bcp file.

b. In the Processed data pane, select True or

Flat Profile.

Option Function

Displays data as processed traces scaled uniformly. The average peak height in
the region of strongest signal is about equal to a fixed value. The profile of the
processed traces is similar to that of the raw traces.

Displays data as processed traces scaled semi-locally. The average peak height in
any region is about equal to a fixed value. The profile of the processed traces is
flat on an intermediate scale (> about 40 bases).
Note: This option is applied to data analyzed with the KB™ basecaller only. If you
use the ABI basecaller, the profile option reverts to True Profile.

November 3, 2004 9:51 am, 05_SWSetup_SeqScape.fm

c. If desired, select one or more stop points for
data analysis.
d. Select your Threshold Quality option.

Option setting Function using KB basecaller

Assigns a base to every position, as well as the QV.

Assigns Ns to bases with QVs less than the set point. The QV will
still be displayed.
DRAFT

Notes

94 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 5 Autoanalysis and SeqScape Software
Creating Protocols for Automated SeqScape Software Analysis

5. Select and fill in the Mixed Bases tab:

Note: This function is active with the KB

basecaller only.

a. For mixed bases only, select Use Mixed

Base Identification.
b. Use the default setting of 25% or change the
detection level by entering a new value or
dragging the % line up or down.

Note: Do not use less than 15% as your

detection limit.

6. Select the Clear Range tab, then, if desired,

select one or more stop points for data analysis.
Select the recommended settings, which are the
default settings:
a. Use Quality values, fewer than 4 bases out
of 20 have QVs less than 20.
b. Use reference trimming.

Note: The clear range is the region of the

sequence that remains after excluding the low-
quality or error-prone sequence at both the 5´ and
November 3, 2004 9:51 am, 05_SWSetup_SeqScape.fm

3´ ends.

5
DRAFT

Notes

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 Chapter 5 Autoanalysis and SeqScape Software
Creating Protocols for Automated SeqScape Software Analysis

7. Select the Filter tab, then, if desired, change one

or more of the [Link] the recommended
settings, which are the default settings:
a. Maximum Mixed Bases (%): 20
b. Maximum Ns (%): 10.0
c. Minimum Clear Length (bp): 50
d. Minimum Sample Score: 20

8. Click to save the protocol and close the

Analysis Protocol Editor dialog box.

Editing an Analysis Protocol

1. In the Analysis Protocols pane in the Analysis
Protocol Manager, highlight the protocol you
want to edit.

2. Click .

3. Make changes in the General, Basecalling,

November 3, 2004 9:51 am, 05_SWSetup_SeqScape.fm

Mixed Bases and Clear Range tabs, as
appropriate.

4. Click to save the protocol and close the

Analysis Protocol Editor dialog box.

DRAFT

Notes

96 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 5 Autoanalysis and SeqScape Software
Creating Protocols for Automated SeqScape Software Analysis

Deleting an Analysis Protocol

IMPORTANT! Do not delete an analysis protocol

during a run while it is being used for that run or
Autoanalysis will not be performed. Also, you must
first delete any plate records using the analysis
protocol before you can delete or modify the
analysis protocol for these plate records.

1. In the Analysis Protocols pane in the Analysis

Protocol Manager, highlight the protocol you
want to delete.

2. Click .
The Deletion Confirmation dialog box displays.

3. Click .

Exporting an Analysis Protocol

1. In the Analysis Protocols pane in the Analysis

Protocol Manager, highlight the protocol you
want to export.

2. Click to display the standard File

Export dialog box.
November 3, 2004 9:51 am, 05_SWSetup_SeqScape.fm

3. Browse to the desired folder location.

4. Click Save. 5
Importing an Analysis Protocol

1. Click to display the standard File

Import dialog box.

2. Browse to the .xml file to import and click Open.

Note: For multiple applications, select the

appropriate application to associate with the
analysis protocol.
DRAFT

Notes

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 Chapter 5 Autoanalysis and SeqScape Software
Creating Protocols for Automated SeqScape Software Analysis

Results Group for SeqScape Software

A Results Group is a component within Data
Collection that organizes samples and certain user
settings under a single name. It is called a Results
Group because it is used to name, sort, and deliver
samples that result from a run.

Creating a Results Group

1. In the tree pane of the Data Collection software,
click GA Instruments > Results Group.

2. Click .
The Results Group Editor window displays.

3. Complete the General tab:

a. Type a Results Group Name. The name can
be used in naming and sorting sample files.
It must be unique (see page for a list of
accepted characters).
b. Optional: Type a Results Group Owner. The
owner name can be used in naming and
3a
sorting sample files.
3b

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c. Optional: Type a Results Group Comment. 3c

4. Select the Analysis tab, then:

a. Select SeqScape_ computer name in the
Analysis Type drop-down list.
b. Select Do Autoanalysis in the Analysis
Actions section. 4a

c. Type a valid SeqScape Software Login ID

and Password in the text boxes.
4b
Note: Failure to use the proper login and
password causes your samples not to be
analyzed automatically.
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Notes

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 Chapter 5 Autoanalysis and SeqScape Software
Creating Protocols for Automated SeqScape Software Analysis

5. Select the Destination tab, then use the default

destination or define a new location for data
storage.

To use … Then …

default location* skip to step 6 5a

custom location complete steps a-c

5a
a. Click Use Custom Location, then click 5b
to navigate to a different save
location.
b. Click to test the Location path
name connection:

Then a message box

If it…
displays …

Passes Test succeeded:

<“path”>.
Fails Test failed:<“path”>.

6. Select the Naming tab, then define custom

names for the sample file and the run folder
name. See “Optional: Completing Sample File
Name Format Pane” on page 73 for more
detailed information.

7. Click to save and close the Results

November 3, 2004 9:51 am, 05_SWSetup_SeqScape.fm

Group Editor.

*Sample File Destinations

Locations where sample files are placed during extraction:
• Default Destination, default folder naming: E:\AppliedBiosystemsUDC\DataCollection\data\<instrument type>\
<instrument name>\run folder
• Default Destination, custom folder naming: E:\AppliedBiosystemsUDC\DataCollection\data\top custom folder\
DRAFT

subfolders, etc.
• Custom Destination, default folder naming: Destination\<instrument type>\<instrument name>\run folder
• Custom Destination, custom folder naming: Destination\top customer folder\subfolders, etc.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 99

 Chapter 5 Autoanalysis and SeqScape Software
Creating Protocols for Automated SeqScape Software Analysis

Importing and Exporting a Results Group

Note: Importing or exporting of SeqScape software

Results Groups are not supported for transfer between
separate computers.

1. In the tree pane of the Data Collection software,

click GA Instruments > Results Group.

2. Click to open a File Import dialog box.

3. Navigate to the file you want to import.

Note: Import file type is .xml (XML file).

4. Click .
Note: When you import or duplicate a Results
Group, you are asked to type a name for the new
Results Group and for the analysis application
type.

Exporting a Results Group

1. In the tree pane of the Data Collection software,

click GA Instruments > Results Group.

2. Click the Results Group name to select it.

3. Click .

November 3, 2004 9:51 am, 05_SWSetup_SeqScape.fm

A standard File Export dialog box displays with
the chosen Results Group name.

4. Navigate to the location where you want to save

the exported file.

5. Click .

Note: If there is a name conflict with a Results

Group that already exists at the save location, the
Results groups can be duplicated to copy settings
into a similar Results Group without the risk of
user error when copying it manually (see
“Duplicating a Results Group” on page 100).
DRAFT

Duplicating a Results Group

1. Click the Results Group to select it.

Notes

100 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 5 Autoanalysis and SeqScape Software
Filling Out a SeqScape Software Plate Record

2. Click .

Note: When you import or duplicate a Results

Group, you are asked to type a name for the new
Results Group and for the analysis application
type.

Filling Out a SeqScape Software Plate Record

Creating a SeqScape Software Plate
Record
1. Click the Plate Manager icon in the navigation
pane.

2. Click .
The New Plate Dialog dialog box opens.

3. Complete the New Plate dialog box:

a. Type a name for the plate.
b. Type a description for the plate (optional).
3a
c. Select SeqScape_computer name in the
Application drop-down list.
3b
d. Select 96-well or 384-well in the Plate Type
drop-down list.
3c
November 3, 2004 9:51 am, 05_SWSetup_SeqScape.fm

e. Type a name for the owner. 3d

f. Type a name for the operator. 3e
3f 5
g. Click .
The SeqScape Plate Editor opens.

3g
DRAFT

Notes

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 Chapter 5 Autoanalysis and SeqScape Software
Filling Out a SeqScape Software Plate Record

Completing a SeqScape Software Plate

Record
1. In the Sample Name column of a row, enter a 1 2 3 4 5
sample name, then click the next cell. The value
100 automatically display in the Priority column.

2. In the Comments column, enter any additional

comments or notations for the sample.

3. In the Priority column, change the priority value,

if desired. A lower number for each 4 or 16 set,
receives a higher run priority. (See the Applied
Biosystems 3130/3130xl Maintenance,
Troubleshooting, and Reference Guide for
changing priority values).

4. In the Project column, select a project from the

drop-down list or create a new project with the
corresponding project template.
Based on the project you select, the project
template is filled in automatically.

5. In the Specimen column, select or create a

specimen.
6. In the Results Group 1 column, select a group 6 7 8
from the drop-down list (see page 98).

7. In the Instrument Protocol 1 column of the row,

November 3, 2004 9:51 am, 05_SWSetup_SeqScape.fm

select a protocol from the drop-down list (see
page 88).

8. In the Analysis Protocol 1 column of the row,

select a protocol from the drop-down list (see
page 93).

9. To complete the rest of the plate record based on

the samples loaded in your plate, do one of the
following:
• For the same samples and protocols –
Highlight the entire row, then select Edit >
Fill Down Special.
Based your plate type (96- or 384-well) and
DRAFT

capillary array (16 or 4 capillaries), the

software automatically fills in the
appropriate well numbers for a single run.

Notes

102 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 5 Autoanalysis and SeqScape Software
Filling Out a SeqScape Software Plate Record

• For the same samples and protocols –

Highlight the entire row, then select Edit >
Fill Down.
• For the different samples and protocols –
Complete the entries manually.
10. If you want to do more than one run, then select
Edit > Add Sample Run.
Additional Results Group, Instrument Protocol
and Analysis Protocol columns are added to the
right end of the plate record.
Add additional runs by selecting Edit > Add
Sample Run again.

11. Complete the columns for the additional runs.

12. Click to save, then close the plate record.

Note: After clicking OK within the Plate Editor,

the completed plate record is stored in the Plate
Manager [Link] plate record can be
searched for, edited, exported, or deleted in the
Plate Manager.

For sample preparation and running the instrument,

see Chapter 7, “Running the Instrument.”
November 3, 2004 9:51 am, 05_SWSetup_SeqScape.fm

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Notes

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 Chapter 5 Autoanalysis and SeqScape Software
Filling Out a SeqScape Software Plate Record

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Notes

104 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 6

Autoanalysis and Fragment Analysis

Preparing the
Instrument

Performing a
Spatial Calibration

Performing a
Spectral Calibration

Autoanalysis
and Sequencing
Analysis
Software
November 3, 2004 9:51 am, 06_SWSetup_FA.fm

Autoanalysis
and
SeqScape Software

Create protocols See page 112

for automation
Autoanalysis
and 6
Fragment Analysis

Create a
GeneMapper Software See page 123
Plate Record
DRAFT

Running the
Instrument

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 105

 Chapter 6 Autoanalysis and Fragment Analysis
GeneMapper Software

GeneMapper Software
Analyze your fragment analysis samples automatically using autoanalysis or manually.

Note: This chapter is written for both GeneMapper® Software v3.7 or higher and
GeneMapper® ID Software v3.2. Graphic examples are from GeneMapper software
v3.7.

GeneMapper Perform autoanalysis of fragment analysis samples with features of the 3130/3130xl
Software v3.7 and Data Collection and GeneMapper software using the same instrument computer that
GeneMapper ID collected the sample files or on a remote computer.
Software v3.2
• Autoanalysis can be performed on the same instrument computer that collected the
sample files or on another computer using the remote analysis feature of
GeneMapper software.
• After autoanalysis, if you wish to edit/review results on another computer, then
transfer the GeneMapper software project, analysis methods, size standards, panel,
and bin set information to the other GeneMapper software database. All
components need to be exported and imported individually.
• When completing the plate record, fill in the instrument protocol and other
information for Data Collection software to complete the run.
• When creating a new Results Group for a set of samples to be autoanalyzed, check
the Do Autoanalysis check box and enter the appropriate GeneMapper Software
user name and password. For remote analysis, define a default location for sample
file storage.

File-Naming Some alphanumeric characters are not valid for user names or file names. Do not use the
Convention invalid characters below:
spaces

November 3, 2004 9:51 am, 06_SWSetup_FA.fm

\/:*?"<>|

IMPORTANT! An error message is displayed if you use any of these characters. You
must remove the invalid character to continue.

Manual Analysis For information on manual analysis, see the GeneMapper Software v3.7 User Guide
(PN 4359413) or GeneMapper ID Software V3.1 User Guide (PN 4338775), or the User
Bulletin titled GeneMapper ID Software v3.2, Subject: New Features and Installation
Procedures for GeneMapper ID Software v3.2 (PN 4352543).
DRAFT

Notes

106 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 6 Autoanalysis and Fragment Analysis
GeneMapper Software

About Fragment When GeneMapper software is installed on a computer that has 3130/3130xl genetic
Analysis and Data analyzer Data Collection software, two applications are available through the Results
Collection Group Editor (see page 115):
• GeneMapper-Generic
• GeneMapper-<Computer Name>

GeneMapper- Use GeneMapper-Generic to generate .fsa files, without performing autoanalysis. When
Generic completing the Sample Sheet, fill in basic information for the Data Collection software
to complete the run; all other GeneMapper software related fields are text entries. Text
entries are useful if you are using other software analysis applications or choose to
analyze your samples in GeneMapper software on another computer, but do not have the
same entries in the GeneMapper software database stored on the Data Collection
computer. For example, if you have a customized size standard definition on another
GeneMapper software computer, you can type in that size standard name in the size
standard text field and it will populate that column in your GeneMapper software
project.

GeneMapper- Use GeneMapper-<Computer Name> for autoanalysis. The Size Standard, Analysis
<Computer Method, and Panel columns in the Sample Sheet window read directly from the
Name> GeneMapper software database. Create these components in GeneMapper software prior
to setting up the plate record for a run. New entries cannot be created for these columns
once you are in the plate editor dialog box. If you create a new GeneMapper software
component while the plate record dialog box is open, the columns will not update. The
plate record must be closed and reopened to update the GeneMapper
software components. For more information see, “Creating Protocols for Automated
Fragment Analysis” on page 112.
November 3, 2004 9:51 am, 06_SWSetup_FA.fm

6
DRAFT

Notes

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 Chapter 6 Autoanalysis and Fragment Analysis
About GeneMapper Software Plate Records

About GeneMapper Software Plate Records

A plate record is similar to a sample sheet or an injection list that you may have used
with other ABI PRISM® instruments.
Plate records are data tables in the instrument database that store information about the
plates and the samples such as:
• Plate name, type, and owner
• Position of the sample on the plate (well number)
• Comments about the plate and about individual samples
• Dye set information (in Instrument protocol)
• Name of the run module where run modules specify information about how samples
are run (in Instrument protocol)

When to Create a Create a plate record for each plate of samples for the following types of runs:
Plate Record
• Spectral calibrations
• Sequencing Analysis Software
• SeqScape Software analysis
• GeneMapper® software
• Mixed (sequencing and fragment analysis samples - see the Applied Biosystems
3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference
Guide for creating a mixed plate record)
For runs to begin, you must create a plate record for and link it to a plate loaded on the
instrument. However, you can create plate records for new plates while a run is in
progress.
Files needed to create a GeneMapper software plate record:

November 3, 2004 9:51 am, 06_SWSetup_FA.fm

See
Parameters Description
Page

Instrument Contains everything needed to run the instrument. 112

Protocol
Results Group Defines the file type, the file name, autoanalysis, and file save 115
locations that are linked to sample injections.

IMPORTANT! For data collection and auto-analysis to be successful, each run of

samples must have an Instrument Protocol, a Results Group and files created in
GeneMapper software assigned within a plate record.
DRAFT

Notes

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 Chapter 6 Autoanalysis and Fragment Analysis
About GeneMapper Software Plate Records

Elements of a GeneMapper software plate record

Plate Manager

Plate Record

Data Collection GeneMapper software

software files: definitions:

Size standard
Results Group Instrument Protocol

Results Group Instrument Analysis method

Name Protocol Name

Analysis software Run type Bin set

and autoanalysis (Regular)

File storage Panel

Run module
location

File and run folder SNP Set

Dye set
name preferences
November 3, 2004 9:51 am, 06_SWSetup_FA.fm

6
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Notes

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 Chapter 6 Autoanalysis and Fragment Analysis
About GeneMapper Software Plate Records

1 2 3 4 5 6 7 8 9 10 11

Defaults to one sample run, to add additional runs see page 125

Blank GeneMapper software plate record

Columns inserted in a plate record for a fragment analysis run

Number and Column Description

1. Sample Name Name of the sample

2. Comment Comments about the sample (optional)
3. Priority A default value of 100 to each sample. Changing the value to a
smaller number causes that set of 16 or 4 samples to run to
before the others in the injection list.

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4. Sample Type Use to identify the sample as Sample, Positive Control, Allelic
Ladder or Negative Control.
5. Size Standard • GeneMapper-Generic (optional):
IMPORTANT! For GeneMapper-<Computer Manually enter size standards in the text field
Name> ONLY: • GeneMapper-<Computer Name>:
Create the Size Standard, Panel, and Analysis Select a saved size standard from the drop-down list
Method in GeneMapper software before creating a
new plate
6. Panel • GeneMapper-Generic (optional):
IMPORTANT! For GeneMapper-<Computer Manually enter panels in the text field
Name> ONLY: • GeneMapper-<Computer Name>:
Create the Size Standard, Panel, and Analysis Select a saved panel from the drop-down list
DRAFT

Method in GeneMapper software before creating a

new plate

Notes

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 Chapter 6 Autoanalysis and Fragment Analysis
About GeneMapper Software Plate Records

Number and Column Description

7. Analysis Method • GeneMapper-Generic (optional):

IMPORTANT! For GeneMapper <Computer Manually enter analysis methods in the text field
Name> ONLY: • GeneMapper-<Computer Name>:
Create the Size Standard, Panel, and Analysis Select a saved analysis method from the drop-down list
Method in GeneMapper software before creating a
new plate
8. SNP Set • GeneMapper-Generic (optional):
IMPORTANT! For GeneMapper <Computer Manually enter SNP set in the text field
Name> ONLY: • GeneMapper-<Computer Name>
The SNP set, created in the GeneMapper software,
links a SNP name to a marker name.
9. Three User-defined columns Optional text entries
10. Results Group Options:
• New: Opens the Results Group Editor dialog box
• Edit: Opens the Results Group Editor dialog box for the
Results Group listed in the cell
• None: Sets the cell to have no selected Results Group
• Select one of the available Results groups from the list
Note: You must select a Results Group for each sample
entered in the Sample Name column.
See “Results Group for Fragment Analysis” on page 115.
11. Instrument Protocol Options:
• New: Opens the Protocol Editor dialog box.
• Edit: Opens the Protocol Editor dialog box for the
Instrument Protocol listed in the cell.
• None: Sets the cell to have no selected protocol.
• List of Instrument Protocols: In alpha-numeric order.
Note: You must select an Instrument Protocol for each
November 3, 2004 9:51 am, 06_SWSetup_FA.fm

sample entered in the Sample Name column.

See “Results Group for Fragment Analysis” on page 115.

6
DRAFT

Notes

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 Chapter 6 Autoanalysis and Fragment Analysis
Creating Protocols for Automated Fragment Analysis

Creating Protocols for Automated Fragment Analysis

If the appropriate fragment analysis protocols and
results group have been created, proceed to “Creating
a GeneMapper Software Plate Record” on page 123.

Instrument Protocol for Fragment Analysis

An instrument protocol contains all the settings
necessary to run the instrument:
• Protocol name
• Type of run
• Run module
• Dye set

Creating an Instrument Protocol

1. In the tree pane of the Data Collection software,
click GA Instruments > ga3130xl or
ga3130 > Protocol Manager.

Create
instrument

Create analysis
protocols here

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2. In the Instrument Protocols section, click
to open the Protocol Editor.
DRAFT

Notes

112 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 6 Autoanalysis and Fragment Analysis
Creating Protocols for Automated Fragment Analysis

3. Complete the Protocol Editor:

a. Type a name for the protocol. 3a

b. Type a description for the protocol

(optional). 3b

c. Select Regular in the Type drop-down list.

3c
3d
3e

3f

d. Using the table below, select the run module

for your run. To customize a run module,
see the Applied Biosystems 3130/3130xl
Genetic Analyzers Maintenance,
Troubleshooting, and Reference Guide on
modifying a module.

Capillary Array
Application or Kit Length Run Module
(cm)

SNaPshot® Multiplex System 22 SNP22_POP4_1

36 SNP36_POP4_1
• LMS v2.5 22 FragmentAnalysis22_POP4_1
• ABI PRISM® Mouse Mapping 36 FragmentAnalysis36_POP4_1
Set v1.0
FragmentAnalysis36_POP7_1
• Custom oligos
• Stockmarks 50 FragmentAnalysis50_POP4_1
November 3, 2004 9:51 am, 06_SWSetup_FA.fm

®
• AFLP FragmentAnalysis50_POP6_1
FragmentAnalysis50_POP7_1
• AmpFlSTR® COfiler® 36 HIDFragmentAnalysis36_POP4_1
• AmpFlSTR Profiler Plus®
• AmpFlSTR SGM Plus®
• AmpFlSTR Profiler Plus ID
• AmpFlSTR SEfiler™ 6
™
• AmpFlSTR Yfiler
• Other 4-Dye AmpFlSTR
• AmpFlSTR Identifiler
• Other 5-Dye AmpFlSTR
DRAFT

Notes

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 Chapter 6 Autoanalysis and Fragment Analysis
Creating Protocols for Automated Fragment Analysis

e. Using the table below, select the correct Dye

Set for your run.

Matrix Standard
Application or Kit Dye Set
Set

Custom oligos D DS-30

• ABI PRISM Mouse Mapping Set v1.0 D DS-31
• Custom oligos
• AmpFlSTR COfiler F DS-32
• AmpFlSTR Profiler Plus
• AmpFlSTR SGM Plus
• AmpFlSTR Profiler Plus ID
• Other 4-Dye AmpFlSTR
• AFLP
• Stockmarks -Canine and Bovine
ABI PRISM SNaPshot Multiplex System E5 DS-02
• ABI PRISM Linkage Mapping Set v2.5 G5 DS-33
• Custom Oligos
• AmpFlSTR Identifiler™
• AmpFlSTR SEfiler
• AmpFlSTR Yfiler
• Other 5-Dye AmpFlSTR
• Stockmarks-Equine

f. Click .

Importing an Instrument Protocol

1. Click in the Instrument Protocols pane

November 3, 2004 9:51 am, 06_SWSetup_FA.fm

of the Protocol Editor window to display the
standard File Import dialog box.

2. Navigate to the location of the .xml file you want

to import.
3. Select the .xml file and click Open.
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Notes

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 Chapter 6 Autoanalysis and Fragment Analysis
Creating Protocols for Automated Fragment Analysis

Exporting an Instrument Protocol

1. In the Instrument Protocols pane, highlight the

protocol you want to export.

2. Click to display the standard File

Export dialog box.

3. Browse to the desired folder location.

4. Click .

Results Group for Fragment Analysis

A Results Group is a component within Data
Collection that organizes samples and certain user
settings under a single name. It is called a Results
Group because it is used to name, sort, and deliver
samples that result from a run.

Creating a Results Group for Autoanalysis

1. In the tree pane of the Data Collection software,
click GA Instruments > Results Group.

2. Click to open the Results Group Editor

window.
November 3, 2004 9:51 am, 06_SWSetup_FA.fm

6
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Notes

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 Chapter 6 Autoanalysis and Fragment Analysis
Creating Protocols for Automated Fragment Analysis

3. Complete the General tab:

a. Type a unique Results Group Name. The
name can be used in naming and sorting
sample files.
b. Optional: Type a Results Group Owner. The
owner name can be used in naming and
sorting sample files.
3a
c. Optional: Type a Results Group Comment. 3b
3c

4. Select the Analysis tab, then:

a. Click Analysis Type and then select one of
the following:

If You Select ... Then ...

None Only raw data files are 4a

generated.
4c
GeneMapper- Autoanalysis is not
4d
Generic enabled and only .fsa files
are generated.
4b
GeneMapper- Autoanalysis of completed
<Computer runs is enabled.

November 3, 2004 9:51 am, 06_SWSetup_FA.fm

Name>
Steps b, c, and d below
apply only to
GeneMapper-<Computer
Name> (not GeneMapper-
Generic).

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b. Select an option in the Analysis Actions

section using the table below.

Use with Setting from Automated

If You Select … Then …
Processing Tab (page 118)

Do Autoanalysis Samples are analyzed after each run of When every run completes
16 or 4 samples.
Do Autoanalysis and Samples are analyzed after all pending Only when the result group is complete
Results Entry Group samples using the same results group
Complete have been run.

c. Type the Login ID.

d. Type the login password.

Note: The login ID and password relate to the

GeneMapper software UserName and Password.
These items can only be created through the
GeneMapper software Options Users tab.
Autoanalysis will fail if the incorrect username
and password are entered.

5. Select the Destination tab, then use the default

destination or define a new location for data
storage.

To use a … Then …

default location* skip to step 6. 5a

custom location complete steps a-b.
5b
Use for remote analysis 5c
using GeneMapper v3.7
November 3, 2004 9:51 am, 06_SWSetup_FA.fm

*Sample File Destinations 6

Locations where sample files are placed during extraction:
• Default Destination, default folder naming: E:\AppliedBiosystemsUDC\DataCollection\data\<instrument type>\
<instrument name>\run folder
• Default Destination, custom folder naming: E:\AppliedBiosystemsUDC\DataCollection\data\top custom folder\
DRAFT

subfolders, etc.
• Custom Destination, default folder naming: Destination\<instrument type>\<instrument name>\run folder
• Custom Destination, custom folder naming: Destination\top customer folder\subfolders, etc.

Notes

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 Chapter 6 Autoanalysis and Fragment Analysis
Creating Protocols for Automated Fragment Analysis

a. Click Use Custom Location, then click

to navigate to a different save
location.
b. Click to test the Location path
name connection:

Then a message box

If it…
displays …

Passes Test succeeded:

<“path”>.
Fails Test failed:<“path”>.

6. Select the Naming tab to customize sample file Sample File Name Format
and run folder names.

Note: The default sample file naming for

fragment analysis is:
frag_<capillary number>_<wellposition>.fsa

Note: Sample name, run folder name, and path

name, combined, can total no more than 250
characters.

For defining the elements of the Naming tab, see

page 119.

Run Folder Name Format pane

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7. Select the Automated Processing tab. Select an
autoanalysis
In “Autoanalysis is performed” select when you option
want your samples autoanalyzed using the table
below.

Use with Settings from Analysis Tab

If You Select … Then …
(page 117)

Only when the result group Samples are analyzed after all pending Do Autoanalysis and Results Entry
is complete samples using the same results group Group Complete
have been run.
When every run completes Samples are analyzed after each run of Do Autoanalysis
16 or 4 samples.
DRAFT

8. Click to save the Results Group.

Notes

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Creating Protocols for Automated Fragment Analysis

Completing the Sample File Name Format Pane

1. Type a prefix for the file name in the Prefix box.
Anything that you type here is shown in the
Example line.

2. Click the Name Delimiter list choose the

symbol that will separate the Format elements in
the file name (see step 3 below). Only one
delimiter symbol may be chosen.

3. Click the Format list and then select the

components that you want in the sample name.

Note: All the samples from a single run can be

placed in the same run or results folder; the name
of every sample from a single run should be
different. Most of the Format options will not be
different between samples; select at least one of
the options to make the sample names unique
within a run.

If a unique identifier is not included in the name,

a warning message [Link] from the
elements to make a unique sample file name.
November 3, 2004 9:51 am, 06_SWSetup_FA.fm

Examples are:
– Well position
– Capillary number
– Run sequence number
– Plate Quadrant
Warning message
Note: Some identifiers, such as well position, 6
capillary number and plate quadrant are not
unique in multiple sample instances. Plate
Quadrant is not a unique identifier for a 96-well
plate.
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 Chapter 6 Autoanalysis and Fragment Analysis
Creating Protocols for Automated Fragment Analysis

As you select the elements for the file name, they

are placed in the Example line. An additional
element drop-down menu displays allowing you
the option of selecting an additional element.

The names of the Format elements eventually

truncate, but the Example field remains visible
(up to 72 characters).

4. Click the Suffix box (optional) and type the

suffix for the file name.
The File Extension field displays the file
extension generated from the Analysis Type

November 3, 2004 9:51 am, 06_SWSetup_FA.fm

specified on the Analysis tab (see page 116). For
example, Sequencing Analysis produces sample
files with an .ab1 extension.

Run Folder/Sub-Folder Name Format Pane

Follow the same steps described above for the Sample
File Name Format pane (see page 119) to change the
sub-folder name within the run folder.
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Importing and Exporting a Results Group

Importing or exporting of GeneMapper software
Results Groups are not supported for transfer between
separate computers.

Importing a Results Group

1. In the tree pane of the Data Collection software,

click GA Instruments > Results Group.

2. Click .
A standard File Import dialog box displays.

3. Navigate to the file you want to import.

Note: Import file type is .xml (XML file).

4. Click .
Note: When you import or duplicate a Results
Group, you are asked to type a name for the new
Results Group and for the analysis application
type.

Exporting a Results Group

1. In the tree pane of the Data Collection software,

click GA Instruments > Results Group.

2. Click the Results Group name to select it.

3. Click .
November 3, 2004 9:51 am, 06_SWSetup_FA.fm

A standard file export dialog box displays with

the chosen Results Group name.

4. Navigate to the location where you want to save

the exported file.

5. Click .
6
Note: If there is a name conflict with a Results
Group that already exists at the save location, the
Results groups can be duplicated in order to copy
settings into a similar Results Group without the
risk of user error when copying it manually (see
DRAFT

“Duplicating a Results Group” on page 122).

Notes

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 Chapter 6 Autoanalysis and Fragment Analysis
Creating Protocols for Automated Fragment Analysis

Duplicating a Results Group

1. Click the Results Group.

2. Click .

Note: When you import or duplicate a Results

Group, you are asked to type a name for the new
Results Group and for the analysis application
type.

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Notes

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 Chapter 6 Autoanalysis and Fragment Analysis
Creating a GeneMapper Software Plate Record

Creating a GeneMapper Software Plate Record

Creating the Plate Record for Autoanalysis
1. In the tree pane of the Data Collection software,
click GA Instruments > ga3130xl or
ga3130 > Plate Manager.

2. Click to open New Plate Dialog.

3. Complete the information in the New Plate

Dialog:
a. Type a name for the plate.
b. Type a description for the plate (optional).
c. Select your GeneMapper application in the
Application drop-down list. 3a

d. Select 96-well or 384-well in the Plate Type

3b
drop-down list.
e. Type a name for the owner.
3c
f. Type a name for the operator. 3d
g. Click . 3e
The GeneMapper software Plate Editor 3f
opens.

3g
November 3, 2004 9:51 am, 06_SWSetup_FA.fm

6
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 Chapter 6 Autoanalysis and Fragment Analysis
Creating a GeneMapper Software Plate Record

Completing a GeneMapper Software Plate

Record for Autoanalysis

1. In the Sample Name column of a row, enter a 1 2 3 4 5

sample name, then click the next cell. The value
100 automatically display in the Priority column.

2. In the Comment column, enter any additional

comments or notations for the sample.

3. In the Priority column, change the priority value,

if desired.

4. In the Sample Type column, select a sample type

from the drop-down list.

5. In the Size Standard column, select a size

standard from the drop-down list.
6. In the Panel column, select a panel from the 6 7 8 9
drop-down list.

7. In the Analysis Method column, select a method

from the drop-down list.

8. In the Snp Set column, select a SNP set from the

drop-down lis if applicable, otherwise select
None.

9. Enter text for User-Defined columns 1 to 3.

10. In the Results Group 1 column, create a new 9 10 11
Results Group or select a group from the drop-

November 3, 2004 9:51 am, 06_SWSetup_FA.fm

down list (see page 115).

11. In the Instrument Protocol 1 column, create a

new instrument protocol or select a protocol from
the drop-down list (see page 112).

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 Chapter 6 Autoanalysis and Fragment Analysis
Creating a GeneMapper Software Plate Record

12. To complete the plate record:

• For the same samples and protocols –
Highlight the entire row, then select Edit >
Fill Down Special.
Based on your plate type (96- or 384-well)
and capillary array (16 or 4 capillaries), the
software automatically fills in the
appropriate well numbers for a single run.
• For the same samples and protocols –
Highlight the entire row, then select Edit >
Fill Down.
• For the different samples and protocols –
Complete the entries manually.
13. To do more than one run, select Edit > Add
Sample Run.
Additional Results Group, Instrument Protocol
and Analysis Protocol columns are added to the
right end of the plate record.
Add additional runs by selecting Edit > Add
Sample Run again.

14. Complete the columns for the additional runs.

15. Click to save, then close the plate record.

IMPORTANT! After clicking OK in the Plate

Editor, the plate record is stored in the Plate
Manager database and can now be located,
edited, exported, or deleted.
November 3, 2004 9:51 am, 06_SWSetup_FA.fm

6
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 Chapter 6 Autoanalysis and Fragment Analysis
Creating a GeneMapper Software Plate Record

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Notes

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 Chapter 7

Running the Instrument

Preparing the
Instrument

Prepare samples and See page 128

Heading 1text
plate assemblies
Performing a
Spatial Calibration

Place Plate onto See page 128

Heading 1text
Autosampler
Performing a
Spectral Calibration

Heading
Link the Plate
1text See page 128
Autoanalysis
and Sequencing
Analysis
Software
November 16, 2004 12:37 pm, 07_RunInstrument.fm

See page 129

Schedule
Heading 1text
a run
Autoanalysis
and
SeqScape Software

See page 130

Run
Heading
the instrument
1text
Autoanalysis
and
Fragment Analysis

Set up for See page 134

continuous operation
DRAFT

Running the
Instrument
7

Notes

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 Chapter 7 Running the Instrument
Preparing Samples and Plate Assemblies

Preparing Samples and Plate Assemblies

Review Table
Generalized sample preparation and plate assembly
procedures are discussed in Chapter 3, “Performing a
Spectral Calibration,” on page 27.

Topic... See

Sample Preparation “Preparing the Calibration Standard” on page 31 and “Loading

Samples” on page 32 to review handling samples.
Follow your individual kit protocol to prepare sample load
volume:
10 to 30 µL for a 96-well plate
5 to 15 µL for a 384-well plate
Sealing plates and plate assembly “Seal the plate:” on page 33.
Placing plate assemblies in the instrument “Placing the Plate Assembly into the Instrument” on page 39.
Searching for plate records to link to a plate “Running the Spectral Calibration Plate” on page 40.

Linking and Unlinking a Plate

Link a plate on the autosampler to your newly created
plate record before running the plate.
Select the desired plate record, then click the plate
position indicator corresponding to the plate position

November 16, 2004 12:37 pm, 07_RunInstrument.fm

in the instrument. The plate position (A or B) displays
in the link column.

Note: The 3130 genetic analyzer has only one plate

position (B) to link a plate record.

The plate position indicator changes from yellow to

green when linked and the green run button
becomes active.
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Notes

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 Chapter 7 Running the Instrument
Linking and Unlinking a Plate

Unlinking a Plate Record

1. Click the plate record that you want to unlink.
1
2. Click .

Viewing the Run Schedule

For more information on run scheduling and sample
injection order, see “Plate Mapping” on page 161.

To verify that runs are scheduled correctly:

1. In the tree pane of the Data Collection software,

click GA Instruments > ga3130xl or
ga3130 > instrument name > Run
Scheduler > Run View.

2. Select a row for any run. The corresponding

wells to be injected for that run are highlighted in
November 16, 2004 12:37 pm, 07_RunInstrument.fm

the plate diagram.

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Notes

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 Chapter 7 Running the Instrument
Running the Instrument

Running the Instrument

Starting the Run

1. Verify that the active spectral calibration matches

your dye set and capillary array length for all
scheduled runs.
To change the active spectral calibration, see
“Activating a Spectral Calibration” on page 47.
To create a new spectral calibration, see
“Creating a Spectral Instrument Protocol” on
page 35.
2. Click the green button in the toolbar.

3. The Processing Plates dialog box opens, then

click .

The software automatically performs a run

validation:
• If the validation passes, the run starts
• If any of the validation test fails, the run
does not start. Check the event log for
information.

November 16, 2004 12:37 pm, 07_RunInstrument.fm

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 Chapter 7 Running the Instrument
Running the Instrument

Starting the Autoanalysis Manager for

SeqScape and/or GeneMapper Software
Use the Autoanalysis Manager (AAM) software with
SeqScape® and/or GeneMapper® software to
automatically analyze the data.

1. Select Start > Programs > Applied Biosystems

> Autoanalysis Manager > Autoanalysis
Manager 3.0.

Note: Autoanalysis Manager does not start

automatically. Open Autoanalysis Manager to
receive messages from the data collection
software for autoanalysis in SeqScape and/or
GeneMapper software.

The Autoanalysis Manager window opens.

2. Quit the SeqScape and/or GeneMapper software.

November 16, 2004 12:37 pm, 07_RunInstrument.fm

No other interaction with the AAM software is

needed until the runs finish. See “Using
Autoanalysis Manager Software” on page 155 on
how to use the Autoanalysis Manager.
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 Chapter 7 Running the Instrument
Running the Instrument

Basic Run Module Automated module steps when the run starts
Steps
Module Steps Approximate Time

Turn Oven On N/A

Wait for oven to equilibrate 1 min 40 sec
Initialize autosampler
Fill Array 3-4 min
PreRun 3 min
Inject samples 10 to 30 sec
Start separation 10 min
Ramp voltage
Collect Data Variable
Run ends: Until next run starts
Leave oven on
Laser to idle
Total time prior to separation:
• Oven unheated: ~25 min
• Oven at set temperature: ~6.5 min

To customize a run module, see the Applied Biosystems 3130/3130xl Genetic Analyzers
Maintenance, Troubleshooting and Reference Guide.

Note: The PostBatch Utility, which runs automatically, turns off both the oven and the
laser at end of a batch of runs.

DNA Sequencing Approximate run times of common DNA sequencing analysis runs

November 16, 2004 12:37 pm, 07_RunInstrument.fm

Run Times
Type of Run Run Module Run Time (min)

Ultra rapid UltraSeq36_POP4 40

UltraSeq36_POP7 35
Rapid RapidSeq36_POP6 60
RapidSeq36_POP7
Fast FastSeq50_POP7 60
Standard StdSeq50_POP4 100
StdSeq50_POP6 150
StdSeq50_POP7 120
DRAFT

Long read LongSeq80_POP4 210

LongSeq80_POP7 170

Notes

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 Chapter 7 Running the Instrument
Controlling the Run

Fragment Approximate run times of common fragment analysis runs

Analysis Run
Times Run Time
Type of Run Run Modules
(min)

High Throughput, Small Size FragmentAnalysis22_POP4 20

Fragment Analysis
SNP22_POP4 20

Standard Fragment Analysis FragmentAnalysis36_POP4 45

HIDFragmentAnalysis36_POP4 45
SNP36_POP4 30
FragmentAnalysis36_POP7 35
FragmentAnalysis50_POP4 65
FragmentAnalysis50_POP6 90
FragmentAnalysis50_POP7 50

For the latest size standard modules (for example, run modules for the LIZ 1200 system),
go to [Link] then click the link for Support, then Software
Downloads, then GeneScan™ Size Standards, then Run Modules.

Controlling the Run

Using the Toolbar Use the toolbar at the top of the data collection software window to control the run.
January 17, 2007 7:11 pm, 07_RunInstrument.fm

Click ... Description

Starts the run

Start Run
Stops the current run, and all other
scheduled runs

Stop
Completes the current run, then stops
all other scheduled runs
DRAFT

Stop After Current Run

Notes

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 Chapter 7 Running the Instrument
Set Up for Continuous Operation

Click ... Description

Stops the current run, then starts the

other scheduled runs

Skip to Next Run

Pauses the current run a

Pause Run
a Pausing the instrument for too long, especially after sample injection, will adversely
affect data quality.

Set Up for Continuous Operation

Overview Use the continuous run feature to create and link a plate during a run. You can:
• Run one or more plates
• Remove the plate(s) once samples have run
• Link and run additional plates
When using the continuous run feature:
• Only mount or unmount plates when the instrument is paused.
• Create the plate record before pausing the instrument to make linking more
efficient, reducing long pauses.
• Link new plates after a run has resumed.

Adding or During a run, you can mount and unmount plates while the instrument is paused. The
Replacing a Plate plate record can be created, then linked after the run has been resumed.

January 17, 2007 7:11 pm, 07_RunInstrument.fm

During a Run
If the plate is in use, see “Adding, Replacing, or Removing a Plate During a Run” on
page 135.

IMPORTANT! Pausing the instrument for too long, especially after sample injection, will
affect data quality.
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 Chapter 7 Running the Instrument
Set Up for Continuous Operation

Adding, Replacing, or Removing a Plate

During a Run
Replace a completed plate or add a new plate to an
unused plate bay (3130xl genetic analyzer only).

1. Prepare your plate and create the plate record.

2. Click (Pause).
In the Pause dialog box, read the pause warning,
then click to pause the run.

The Resume run dialog box opens when the run

is paused.

IMPORTANT! Do not click OK to resume the

run. Temporarily ignore the dialog box.

3. Remove the old plate, if applicable.

a. Press the Tray button to bring the
autosampler forward.
b. Open the instrument door.
c. Remove the old plate.

4. Mount the new plate.

November 16, 2004 12:37 pm, 07_RunInstrument.fm

5. Close the door.

6. Click OK in the Resume Run dialog box.

7. In the Completed Run dialog box, click to
continue if the samples have been injected, or
click to abort the run and return the
instrument to an idle state.

IMPORTANT! If you click OK, the instrument

will continue running the current run regardless
of whether the samples have actually been
injected or not. If the samples have not been
DRAFT

injected, the samples will be injected from the

new plate.
7

Notes

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 Chapter 7 Running the Instrument
Set Up for Continuous Operation

8. Search for the plate record, then link the new

plate.
The new plate runs after the current plate
completes all scheduled injections.

Note: If you unmount the currently running

plate prior to the first frame of data being
collected but after sample injection (clicked OK
to continue), the plate status changes to
processed even though the run is actually
continuing.

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Set Up for Continuous Operation

Viewing Data During a Run

Run Scheduler > In the tree pane of the Data Collection software, click
Plate View GA Instruments > ga3130xl or ga3130 > instrument name > Run
Scheduler > Plate View.

Note: The Run Scheduler and Plate View windows display the same
information.
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 Chapter 7 Running the Instrument
Set Up for Continuous Operation

Run Scheduler > In the tree pane of the Data Collection software, click
Run View GA Instruments > ga3130xl or ga3130 > instrument name > Run
Scheduler > Run View to monitor the status of the scheduled runs.

Note: For default load maps, see Appendix A, “Plate Mapping.”

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 Chapter 7 Running the Instrument
Set Up for Continuous Operation

Instrument Status In the tree pane of the Data Collection software, click
GA Instruments > ga3130xl or ga3130 > instrument name > Instrument
Status to monitor the status of the instrument or the current run.

Open the Event Log to monitor System Status must be Array and polymer information
system messages ‘Ready’ before a run starts
November 16, 2004 12:37 pm, 07_RunInstrument.fm

System Status changes from green to flashing

red when errors occur, see Event Log.
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 Chapter 7 Running the Instrument
Set Up for Continuous Operation

Instrument Condition Sensor States Pane

The color of the indicator provides a quick way to check the status of the item to the left.
See the table below for a definition of each color.

A green box A red box A yellow box

For...
indicates... indicates... indicates...

Laser Laser is off Laser is on Laser is idle

EP Electrophoresis is off Electrophoresis is on —
Oven Oven is off Oven is on —
Front Doors Doors are closed Doors are open —
Oven Door Door is closed Door is open —
Autosampler Autosampler is homed Autosampler is forward —

Events Box
The Events box lists the:
• Instrument’s recent actions
• Status of each capillary as passed or failed at the end of a spectral calibration
• Calibration data at the end of a spatial calibration
Some of the events listed in the Events box provide information for service engineers.

Errors Box
The Errors box lists errors that have occurred during the current run.
Some of the error messages provide information for service engineers. A “fatal” error
usually requires that you restart the data collection software.

November 16, 2004 12:37 pm, 07_RunInstrument.fm

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 Chapter 7 Running the Instrument
Set Up for Continuous Operation

Instrument Status In the tree pane of the Data Collection software, click GA Instruments >
> EPT Chart ga3130xl or ga3130 > instrument name > Instrument Status > EPT
Chart. The EPT chart displays real-time electrophoresis (EP) data during a run.
November 16, 2004 12:37 pm, 07_RunInstrument.fm
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 Chapter 7 Running the Instrument
Set Up for Continuous Operation

Instrument Status In the tree pane of the Data Collection software, click GA Instruments >
> Event Log ga3130xl or ga3130 > instrument name > Instrument Status > Event
Log. The Event log itemizes events such as errors and general information for all data
collection steps.
Clear error messages by clicking Clear Errors. The System Status light flashes red until
all errors are cleared. Take corrective action based on error message.

Note: This view can also be used to monitor spectral calibration results in real time to
verify the capillary-by-capillary processing status.

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Clear Errors changes the System status from red to green (ready state).

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 Chapter 7 Running the Instrument
Set Up for Continuous Operation

Capillaries Viewer In the tree pane of the Data Collection software, click GA Instruments > ga3130
or ga3130xl > instrument name > Capillaries Viewer. Use the Capillary Viewer
to examine the quality of the raw data during a run for several capillaries at once.

Click individual colors to view or hide them

Select check boxes

of capillaries to
display

Raw,
multicomponented
data
November 16, 2004 12:37 pm, 07_RunInstrument.fm

Check Boxes
Select the check boxes of the capillaries to view their electropherograms. The capillaries
are displayed in the order in which the boxes are checked. The more boxes that are
selected, the slower the refresh window rate.

Raw Data An electropherogram is a graph of relative dye concentration against time, plotted for
each dye. The displayed raw data has been corrected for spectral overlap
(multicomponented).

How to Zoom

To zoom in and out:

DRAFT

1. Select a rectangular area over the area of interest by holding down the mouse
button. Release the mouse button to zoom in.
7
2. Click to return to full view.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 143

 Chapter 7 Running the Instrument
Set Up for Continuous Operation

Cap/Array Viewer In the tree pane of the Data Collection software, click GA Instruments > ga3130
or ga3130xl > instrument name > Cap/Array Viewer. Use the window during a
run to examine the quality of your data, which is displayed as color data for the entire
capillary array. You can view all the capillaries (vertical axis) as a function of time/scan
numbers (horizontal axis).

Click individual colors to view or hide them

Raw data
display for
selected
capillary (4)

Capillary
order Electrophero-
gram
displays

November 16, 2004 12:37 pm, 07_RunInstrument.fm

0 End

How to Zoom

To zoom in and out:

1. Select a rectangular area over the area of interest by holding down the mouse
button. Release the mouse button to zoom in.

2. Click to return to full view.

DRAFT

Notes

144 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 7 Running the Instrument
Working with Data in The Run History View

Working with Data in The Run History View

Run History Components

Elements of the Use the Run History utility only with completed runs stored in the local 3130/3130xl
Run History Utility genetic analyzer Data Collection database. It does not provide real-time viewing of
collecting runs.
In the left tree pane, click the icon next to the function to launch it.

Elements Within the Run History Utility

Icon Element Displays the...

EPT Viewer Electrophoresis data of the run, such as voltage, current,

and oven temperature profiles.

Event Log Event messages associated with the run.

Instrument Instrument protocol and run module settings used for the
Protocol run.

Spatial Spatial calibration associated with the run.

Calibration
Viewer
Capillaries Individual electropherogram for each sample in the run.
Viewer

Cap/Array Array view of the run.

Viewer
November 16, 2004 12:37 pm, 07_RunInstrument.fm

Spectral Spectral calibration used for the run.

Viewer

Reextraction Extraction and analysis status for all samples in the run.
See “Viewing Autoextraction Results” on page 147 for
more details.

Note: If Cleanup Database has been used, you cannot view processed data in Run History.
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 145

 Chapter 7 Running the Instrument
Viewing Data from a Completed Run in the Data Collection Software

Viewing Data from a Completed Run in the Data Collection

Software
View data using two formats within the 3130/3130xl
genetic analyzer Data Collection software under the
Run History icon:
• In the Cap/Array Viewer window (in much the
same way that you might view the gel file output
from an ABI PRISM ® slab gel instrument).
• In the Capillary Viewer window, capillary-by-
capillary.

Viewing Data from a Completed Run

1. In the tree pane of the Data Collection software,
click GA Instruments > ga3130xl or
ga3130 > Run History to select the run you
want to view.

2. Search for your run by either Barcode or

Advanced search.

3. After choosing the run, click the run history

elements, such as Cap/Array Viewer or the
Capillary Viewer from the left tree pane to look
at the run data.

November 16, 2004 12:37 pm, 07_RunInstrument.fm

DRAFT

Notes

146 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 7 Running the Instrument
Viewing Autoextraction Results

Viewing Autoextraction Results

Overview After a run is completed, extraction and analysis is performed automatically, using the
settings in the Plate Editor and the Results Group. View the results of extraction and
analysis in the Reextraction Panel. Reextract samples with the same settings, or with
different Analysis Protocols or Results Groups. This process can be useful for
many reasons:
• The destination location may not have been available during extraction.
• Some samples may have failed analysis and a different Analysis Protocol might be
more successful.
• Samples might be saved in different locations, or with no analysis at all to
save space.
• Sample names may need to be edited.

Sample File Locate the Results Group’s Naming Tab and check the Destination Tab and Run Folder
Destinations Name Format to find the sample file destination.

Effects of Changes made in the Reextraction Panel to a Results Group, Analysis protocol, sample
Changes Made in names, or Comments, also change in the original plate record. The original plate
the Reextraction information is overwritten.
Panel
November 16, 2004 12:37 pm, 07_RunInstrument.fm
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 147

 Chapter 7 Running the Instrument
Viewing Autoextraction Results

Selecting and Queuing Samples for

Extraction
Queue individual samples for reextraction to
experiment with different Analysis Protocols for
samples that have failed initial extraction.

1. Click (Run History).

2. Enter the plate name for a plate that has been

completed, or click Search. Plates that have runs
still pending cannot be reextracted. All the runs
from that plate appear in the window.

3. Select a run from the list.

4. Click (Reextraction) in the left tree pane to

display the Reextraction window.

5. Click the check boxes in the Extract column to

select the samples to be reextracted.

November 16, 2004 12:37 pm, 07_RunInstrument.fm

6. Click Extract to start the reextraction.

Note: Reextracted sample files are saved in the

original folder that data was extracted to unless
this destination was changed through the Results
Group.

DRAFT

Notes

148 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 7 Running the Instrument
Viewing Autoextraction Results

Elements of the Reextraction Window

All the samples are displayed with the results of
extraction and analysis.

Note: Sort the columns of the re-extraction panel by

holding the shift key and then clicking on a column
header.

Reextraction Window for Sequencing Analysis

Use check boxes to

select samples to Results of extraction and analysis
be reextracted Select a run
November 16, 2004 12:37 pm, 07_RunInstrument.fm

Click here to start extraction

Use these buttons if several samples

are highlighted
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 149

 Chapter 7 Running the Instrument
Viewing Autoextraction Results

Reextraction Window for Fragment Analysis

Use check boxes to select

samples to be reextracted Select a run Results of extraction

Click here to start extraction

Use these buttons if several

November 16, 2004 12:37 pm, 07_RunInstrument.fm

samples are highlighted

DRAFT

Notes

150 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 7 Running the Instrument
Viewing Autoextraction Results

Results Column The results of extraction and analysis are color coded in the Results column. The
following table lists the colors and their values for Sequencing Analysis.

Color Value

Red Extraction or analysis failed

Note: Descriptive messages can be viewed by resizing the Results column to
view all text.
Yellow Warnings for extraction or analysis
Note: Descriptive messages can be viewed by resizing the Results column to
view all text.
Green Successful extraction (with no analysis intended), or successful extraction
and analysis.

The Results column, by default, shows only the beginning of any processing message.
The entire message and the sample file location can be viewed by expanding the cell.
There is a tooltip view for each sample results message.

Tooltip view. Access by placing the cursor over the sample of interest
November 16, 2004 12:37 pm, 07_RunInstrument.fm

Drag the cell’s edge to expand the column

DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 151

 Chapter 7 Running the Instrument
Viewing Autoextraction Results

Expanded column

Quality Column The Quality column represents the quality values for an entire sequence. Quality Values
are only assigned to analyzed samples when using the KB™ Basecaller.
Colors displayed and their associated value range

Color Quality Value Range

Red < 15
Orange ≥ 15 and < 20
Yellow ≥ 20 and < 30
Green > 30

November 16, 2004 12:37 pm, 07_RunInstrument.fm

Note: For more information on KB Basecaller and Quality Values, see the Applied
Biosystems DNA Sequencing Analysis Software v5.1 User Guide, PN 4346366.

The column is empty (white) if:

• Analysis was not performed
• Analysis failed
• ABI Basecaller was used for analysis. This basecaller does not assign
Quality Values. DRAFT

Notes

152 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 7 Running the Instrument
Viewing Autoextraction Results

Results Group and Analysis Protocol

Columns
You can edit and make changes for reextraction to the
Results Group and the Analysis Protocol (Analysis
Method in the GeneMapper ® software).

Note: Select an entire column in the Reextraction

window by clicking on the column header. For
example, clicking on the Extract column header
selects all samples. Clicking the Uncheck or Check
buttons at the bottom of the window, enables or
disables the check boxes for each sample. The fill-
down command (Ctrl+D) works the same here as in
the Plate Editor for easier information input.

Sorting the Samples

1. Hold down the shift key while clicking on the

column header to sort samples according to the
column properties.

2. Shift-click again to sort them in reverse order.

Sort by:
• Capillary number
• Well position
• Results
• Quality
• Extract column
November 16, 2004 12:37 pm, 07_RunInstrument.fm

Note: For example, bring all of the failed

analysis or extraction samples to the top of the
column. Now they can be viewed without having
to scroll down to each sample individually.
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 153

 Chapter 7 Running the Instrument
Viewing Autoextraction Results

Reextracting Selected Samples

1. Expand the Results column cells for any yellow

or red results to see a description of the warning
or failure.

2. If desired, select a new Results Group, or edit the

current one. Selecting a new Results Group
allows you to turn off autoanalysis, change the
samples and folder naming options, the location
where they are placed, and the owner of the
Results Group.

3. If desired, change the Analysis Protocol to

experiment with different ways of analyzing the
sample, using a different basecaller for example.

4. Check the check box in the Extract column for

the samples you wish to extract again.

5. Click Extract.

Note: Reextraction creates an entirely new

sample file and does not replace the previously
saved sample file. The presence of a previous
sample file has no effect on the creation of a new
sample file. If the same naming options that are
used for reextraction are identical to those used
previously, a number is appended to the
filename. For example, if the first sample is,
“sample 01.ab1” then the second sample would

November 16, 2004 12:37 pm, 07_RunInstrument.fm

be, “sample 01 (1).ab1.”

DRAFT

Notes

154 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 7 Running the Instrument
Using Autoanalysis Manager Software

Using Autoanalysis Manager Software

Use Autoanalysis Manager software with SeqScape and/or GeneMapper software. The
Autoanalysis Manager software is installed by the SeqScape or GeneMapper software
installation CD.
Autoanalysis occurs in the following sequence:

1. When data collection software finishes a run, the Message Service sends the
message “Run Completed.”

2. The Autoanalysis Manager receives the message, and the job is submitted. The job
appears in the General tab.

3. The Autoanalysis Manager polls for jobs every 2 minutes and opens the automated
processing version of SeqScape and/or GeneMapper software to analyze the data.

4. At the end of analysis, the status in the Autoanalysis Manager is updated.

Files Created The data collection software stores the sample files in the location specified in the results
group. The Autoanalysis Manager copies the files into the Data Store for SeqScape or
GeneMapper processing.
To maintain sufficient storage space on your hard drive, delete or transfer unnecessary
sample files to a different network or CD.

Autoanalyzed Note: If your GeneMapper or SeqScape software was opened during autoanalysis, then
Samples close your analysis application and relaunch the Autoanalysis Manager.

Once an internal message from the instrument is received by the Autoanalysis Manager,
November 16, 2004 12:37 pm, 07_RunInstrument.fm

it opens the automated processing version of SeqScape and/or GeneMapper software to

autoanalyze the samples. The standard user version of SeqScape and/or GeneMapper
software must be closed in order for autoanalysis to begin.
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 155

 Chapter 7 Running the Instrument
Using Autoanalysis Manager Software

Components
The Autoanalysis Manager has two or three tabs:
• General tab
• GeneMapper tab, if GeneMapper v3.7 or GeneMapper ID v3.2 software is installed
• SeqScape tab, if SeqScape software is installed

General Tab The General tab shows the jobs that have been submitted and their status.

Command Buttons in the General Tab

Command Button Functions in the General Tab

Button Name Function

Delete Job Deletes an individual job/project from the Autoanalysis Manager

November 16, 2004 12:37 pm, 07_RunInstrument.fm

list.
Does not delete sample files, SeqScape or GeneMapper
software project.
Delete Completed Jobs Deletes all completed jobs/projects from the Autoanalysis
Manager list. Only successful jobs are deleted.
Does not delete sample files, SeqScape or GeneMapper
software projects.
Move Job Up The active job/project is always given a queue number of 1. Once
job 1 is finished analyzing, job 2 becomes job 1 and all other
Move Job Down
numbers are changed accordingly. Use the Move Up/Down
buttons if you want to rearrange the analysis order.
DRAFT

Notes

156 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Chapter 7 Running the Instrument
Using Autoanalysis Manager Software

GeneMapper The GeneMapper software tab shows the jobs that have been submitted and their status.
Software Tab

Command Buttons in the GeneMapper Software Tab

Command Button Functions in the GeneMapper Software Tab

Button Name Function

Configure Schedule • Next Analysis Time:

Enables you to set a start time for autoanalysis. Before this
time arrives, autoanalysis of projects will not occur.
• Periods restricting automated analysis:
Enables you to set times during which autoanalysis will not
occur. Useful if you know that you are going to be reviewing
November 16, 2004 12:37 pm, 07_RunInstrument.fm

data during a certain time period and don’t want to be

bothered by the “Runs ready for processing” dialog box. Runs
build up in the queue until the restricting time period is over at
which time the runs will be autoanalyzed.
• Automatic Deletion of Completed Jobs:
Enables you to set the software to automatically delete
successfully completed jobs. Jobs that failed or have not been
analyzed will not be deleted. Only the Autoanalysis Manager
job is deleted, sample files and GeneMapper software projects
are not.
Edit Properties Enables you to change the following settings:
• Job/Project Name
• UserName: GeneMapper software UserName
• Password: Matching password for GeneMapper software
DRAFT

UserName
• Queue position: Enter a new queue position number for the
project 7

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 157

 Chapter 7 Running the Instrument
Using Autoanalysis Manager Software

Button Name Function

Requeue Job • Samples that need to be autoanalyzed have queue numbers

listed in the # column.
• Samples that are already analyzed or failed, have a blank cell
in the # column.
To resubmit a job for autoanalysis, use the Requeue Job
button to assign a queue number to that job.
Delete Job • Deletes an individual job/project from the AutoAnalysis
Manager list.
Does not delete sample files or GeneMapper software project.
Delete Completed Jobs • Deletes all completed jobs/projects from the AutoAnalysis
Manager list. Only successful jobs are deleted.
Does not delete sample files or GeneMapper software
projects.

November 16, 2004 12:37 pm, 07_RunInstrument.fm

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Notes

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 Chapter 7 Running the Instrument
Using Autoanalysis Manager Software

SeqScape The SeqScape software tab shows the jobs, project, and status information.
Software Tab

Command Button Functions in the SeqScape Software Tab

Button Name Function

Details Displays the project in the navigation pane

Resubmit Submits a job for analysis

Edit Properties Edits the name and password (active only if analysis failed)
Delete Deletes a job from the Autoanalysis Manager
November 16, 2004 12:37 pm, 07_RunInstrument.fm
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 159

 Chapter 7 Running the Instrument
Viewing Analyzed Data

Viewing Analyzed Data

Locating Sample Analyzed sample files are extracted into a run folder defined in the Naming tab of your
Files Results Group, and placed in a location defined in the Destination tab.
The default location is:
E:\AppliedBiosystems\UDC\Data Collection\Data\ <instrument type>\<instrument
name>\<Run Name>

November 16, 2004 12:37 pm, 07_RunInstrument.fm

Locating Sample Files

Locate the reextracted data in the location defined by the Results Group or the default
destination location.

Viewing Sample Use the Sequencing Analysis, SeqScape, or the GeneMapper Software to view re-
Files extracted sample electropherogram data, both raw, and analyzed.

Sample file type File extension

Sequencing, SeqScape .ab1

Fragment analysis .fsa
DRAFT

Notes

160 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Appendix A

Plate Mapping

Injection Scheduling
Samples are scheduled for injection based on their position in a 96-or 384-well plate and
the capillary number. Study the appropriate plate mapping patterns described in “96-
Well Plate Mapping” or “384-Well Plate Mapping” to arrange your samples according to
your preferred injection priority.
The injection schedule system is based on the:
• Order of the linked plates (3130xl instrument only). See page 128 for linking plate
information.
• Sample priority value in the plate record.
If all priorities are set to 100 (default), then runs are scheduled as outlined below. See the
Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and
Reference Guide on “Run Priority Scheduling”.

Capillary Array Map

The capillary numbers in the capillary array are shown in the layout below. The capillary
array layout is the same for both 96- and 384-well plates.
Capillary Number Layout
November 3, 2004 9:51 am, A_Appendix.fm
DRAFT

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 161

Appendix A
96-Well Plate Mapping

96-Well Plate Mapping

3130xl Genetic For a 96-well plate, injections are made from every well in two consecutive rows,
Analyzer starting with an odd row. A full 96-well plate requires six runs to inject all samples. See
the examples below where samples (grey) and capillary number (number) positions can
affect your number of runs.

Efficient Sample Placement Inefficient Sample Placement

Inject 48 samples using three runs Inject 32 samples using four runs
H

A
15 13 11 9 7 5 3 1

1
15 13 11 9 7 5 3 1

1
Run 1 Run 1
16 14 12 10 8 6 4 2

2
16 14 12 10 8 6 4 2

2
15 13 11 9 7 5 3 1 3 15 13 11 9 7 5 3 1

3
Run 2 Run 2
16 14 12 10 8 6 4 2
4

16 14 12 10 8 6 4 2

4
15 13 11 9 7 5 3 1
5

15 13 11 9 7 5 3 1

5
Run 3 Run 3
16 14 12 10 8 6 4 2
6

16 14 12 10 8 6 4 2

6
15 13 11 9 7 5 3 1

7
Run 4
16 14 12 10 8 6 4 2

8
3130 Genetic For a 96-well plate, injections are made from four consecutive wells in a row. A full plate
Analyzer of 96 sample requires 24 runs to inject all samples once.
In the following example of a 96-well plate, the gray circles represent samples and the
number in the well indicates capillary number. It takes four runs to inject 16 samples.
H

Run 2 4 3 2 1 4 3 2 1
Run 1
1

Run 4 4 3 2 1 4 3 2 1 Run 3
2

November 3, 2004 9:51 am, A_Appendix.fm

3

DRAFT

Notes

162 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Appendix A
384-Well Plate Mapping

384-Well Plate Mapping

3130xl Genetic For a 384-well plate, injections are made from every other well and every other row. A
Analyzer full plate of 384 samples requires 24 runs to inject all samples once.
The example below is the injection pattern for the first four injections, starting with well
A01. The light gray circles represent samples and the dark gray circles indicate the
injection pattern.

Run 1 Run 2

GR1316c
GR1316c

P
O
N
M
L
K
J
I
H
G
F
E
D
C
B
A
P
O
N
M
L
K
J
I
H
G
F
E
D
C
B
A

1
1

2
2

3
3

4
4

5
5

6
6
Run 3 Run 4
GR1316c

GR1316c
P
O
N
M
L
K
J
I
H
G
F
E
D
C
B
A

P
O
N
M
L
K
J
I
H
G
F
E
D
C
B
A
1

1
2

2
3

3
4

4
5

5
6

6
3130 Genetic For a 384-well plate, injections are made from every other well. A full plate of 384
Analyzer sample requires 96 runs to inject all samples once.
The example below is the injection pattern for the first six injections, starting with well
A01. The light gray circles represent samples and the dark gray circles indicate the
injection pattern.

Run 1 Run 2 Run 3

November 3, 2004 9:51 am, A_Appendix.fm

P
O
N
M
L
K
J
I
H
G
F
E
D
C
B
A

P
O
N
M
L
K
J
I
H
G
F
E
D
C
B
A
P
O
N
M
L
K
J
I
H
G
F
E
D
C
B
A

1
1

2
2

3
3

4
4

5
5

6
6

Run 4 Run 5 Run 6

P
O
N
M
L
K
J
I
H
G
F
E
D
C
B
A
P
O
N
M
L
K
J
I
H
G
F
E
D
C
B
A

P
O
N
M
L
K
J
I
H
G
F
E
D
C
B
A
1
1

1
2
2

2
3
3

3
4
4

4
5
5

5
DRAFT

6
6

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 163

Appendix A
384-Well Plate Mapping

November 3, 2004 9:51 am, A_Appendix.fm

DRAFT

Notes

164 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 Index

Numerics GeneMapper Software, computer name 107

manually, fragment analysis documentation 106
3130 basecaller and DyeSet/Primer files 66, 67 manually, Seqscape software documentation 83
manually, sequencing documentation 54
A sequencing 54
Autoanalysis Manager
ABI PRISM® BigDye® Primer Cycle Sequencing Kits
components 155
table, dye sets and standards 29
explained 82
ABI PRISM® dGTP BigDye® Terminator Cycle general tab 156
Sequencing Ready Reaction Kit, table of dye starting 131
set and standards 29 using 155
ABI PRISM® dGTP BigDye® Terminator v 3.0 Cycle autoextraction
Sequencing Ready Reaction Kit overview 147
table of dye set and standards 29 Automated Processing tab 118
ABI PRISM® dRhodamine Terminator Cycle Sequencing automated SeqScape analysis 82
Kit automatic analysis, before you start 83
table of information 29
autosampler 18
Activating spectral calibration 47
function 11
AmpFlSTR kits
matrix standard 30
table of dye sets, filter, modules 5 B
analysis protocol barcode reader 6
deleting 68, 97 barcode, type of search 40
editing 68, 96 basecaller and DyeSet/Primer files 66
export 69, 97
general description 55 basecaller files 66, 67
import 69, 97 BigDye® Terminator chemistry, information tables 66
options 58 BigDye® Terminator v3.1 Cycle Sequencing Kit
options, SeqScape software 87 table, dye set and standard 29
analysis, manual 54, 83, 106 biohazardous waste, handling xx
analyzing GeneMapper Software data 160 bold text, when to use ix
anode buffer reservoir buffer
November 3, 2004 1:23 pm, 3130UserGuide_IX.fm

filling 19 hazards 32
function 11 making 16
Applied Biosystems buffer fill-line 12
contacting xi
SAMPLE DOCUMENT

buffer reservoir, anode, illustration of 12

customer feedback on documentation x
Information Development department x buffer valve pin, illustration of 12
Technical Support xi
array length, polymer type, table 36 C
array port, illustration of 12 calibration standards
assembling the plate 34 types, fragment analysis 30
assumptions for using this guide ix types, sequencing 29
Australian EMC standards xxiii Canadian safety standards xxiii
autoanalysis cap/array viewer 144
capillaries viewer 143

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 165

capillary array viewing analyzed sequencing data 160
function 11 viewing complete run 146
illustration of 12 Data Collection software
installing or replacing 13 starting 9
capillary array knob and tip, illustration of 12 data collection software, starting 9
capillary array length destinations 147
polymer type, table 36 detection cell block and heater
cathode buffer reservoir, filling 17 function 11
CAUTION documentation
description xiv GeneMapper Software User Guide (PN) 106
example xv related x
Change Polymer Type Wizard, using 15 double-tapered ferrule, illustration of 12
characters dye primer chemistry, information table 67
acceptable 54, 83, 106 dye set
check valve fragment analysis 30, 114
diagram of 12 table, sequencing 29
chemical safety xviii Dye Terminator chemistry, files 66
chemical safety guidelines xix DyeSet/Primer files 66, 67
chemical waste list of 64, 94
hazards xx
safety xx E
safety guidelines xx
chemical waste disposal, guidelines xx E dye set, sequencing kit table 61
computer electrical hazard symbol xvi
assigning a unique name 9 electrical safety xxi
starting 7 electrical shock hazards xxi
condition number, spectral calibration 42 electrical symbols, on instruments xv
conventions electrode, illustration of 12
bold text ix electromagnetic compatibility standards. See EMC
IMPORTANTS! ix
standards
in this guide ix
italic text ix electropherogram, definition 143
menu commands ix EMC standards xxiii
Notes ix Australian xxiii
user attention words ix Canadian xxiii
conventions, safety xiv European xxiii
creating EPT chart 141
analysis protocol for autoanalysis 62, 93 ergonomic safety xxii
GeneMapper Software plate record for errors box 140

November 3, 2004 1:23 pm, 3130UserGuide_IX.fm

autoanalysis 123
SeqScape Software plate record 101 European EMC standards xxiii
Sequencing Analysis plate record for European safety standards xxiii
autoanalysis 77 event log 142
SAMPLE DOCUMENT
customer feedback, on Applied Biosystems icon, displays 145
documents x events, box 140

D F
DANGER file extension 160
description xiv file naming, invalid characters 54
example xv
fill down special, function 38
data
fill line, anode buffer reservoir 19
how to zoom 143
viewing 137 filter set

166 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 fragment analysis 5 physical xxi
find all plate search 40 repetitive motion xxii
fragment analysis
data analysis 160 I
filter set 5 illustration of 12
kit types 5
passing profiles, spectral calibration 51 IMPORTANT
run modules 113 description xiv
run, average time 133 example xv
function 11 IMPORTANTS!, description ix
Information Development department, contacting x
G Install Array Wizard
using 13
GeneMapper Software
installation category xxi
computer name 107
elements 109 instrument
generic 107 condition, status 140
instrument protocol 108 diagram of interior 11
plate records 108 documentation x
results group 108 EPT status 141
GeneMapper Software tab 157 layout 2
operation 130
GeneMapper™ Software and GeneMapper™ ID setup 12
Software 106 starting the system 8
general hazard symbol xvi instrument operational safety, instructions for xviii
guidelines instrument protocol
chemical safety xix creating 35
chemical waste disposal xx creating for SeqScape software 88
chemical waste safety xx creating, for fragment analysis 109, 112
waste disposal xx general description 55
icon, displays 145
H options, SeqScape software 87
options,s equencing 58
hard drive space, automatic checking 132 instrument status 139
hazard icons interconnect tube 12
accompanying safety alert words xiv
components xiv invalid characters in names 54, 83, 106
described xiv italic text, when to use ix
in documents xiv
on instruments xiv, xvi
See also hazard symbols
K
See also safety symbols KB basecalling run modules 66
November 3, 2004 1:23 pm, 3130UserGuide_IX.fm

hazard symbols
electrical xvi L
general xvi
hot surface xvi labels, instrument safety xvi
SAMPLE DOCUMENT

in documents xv laser hazard xxi

laser hazard xvi symbol xvi
moving parts xvi warnings xxii
on instruments xvi laser safety xxi
See also hazard icons laser classification xxi
See also safety symbols requirements xxii
hazards Launching Data Collection software 9
chemical waste xx
layout, instrument 2
electrical shock xxi
laser xxi length of read, definition 3
moving parts xxi linking a plate 128
moving/lifting instrument xvii

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 167

LOR definition 3 P
lower polymer block 11 pausing a run 133
lower polymer block, illustration of 12 PDP motor cover, illustration of 12
Luer fitting, illustration of 12 physical hazard safety xxi
physical hazards xxi
M piston, illustration of 12
manual analysis, fragment analysis documentation 106 plate assembly
manual analysis, Seqscape software documentation 83 diagram 34
manual analysis, sequencing documentation 54 placing in instrument 39
matrix standard plate editor, filling in 37
fragment analysis 30 plate manager, access 37
matrix standards plate record
fragment analysis 114 creating 37
preparing for sequencing 31 creating for GeneMapper Software
sequencing 29 autoanalysis 123
menu commands, conventions for describing ix creating for SeqScape Software 101
creating for Sequencing Analysis autoanalysis 77
mixed plate record 55 discussed 55, 83, 108
modules elements, sequencing analysis 56
fragment analysis 4, 5 linking and unlinking 128
KB basecalling 66 mixed 55
sequencing 3 search 40
spectral 36 plate view 137
mounting pin, illustration of 12 plates
moving and lifting linking and unlinking from plate records 128
computer xviii sealing 33
monitor xviii polymer
moving and lifting instrument, safety xvii array length, table 36
moving parts changing to new type 15
hazard xxi replenishing or changing 14
hazard symbol xvi when to add or change 14
safety xxi polymer delivery pump
MSDSs diagram 12
description xviii polymer supply bottle cap with hole, illustration of 12
obtaining xix polymer supply bottle, illustration of 12
referring to xix, xx
polymer supply tube illustration of 12
when to review xviii
protocol manager, access 35
N pump block 12
function 11

November 3, 2004 1:23 pm, 3130UserGuide_IX.fm

Naming pump chamber, illustration of 12
tab, fragment analysis 118
Notes, description ix
Q
SAMPLE DOCUMENT

O quality column 152

quality value range 152
O-ring, illustration of 12
Q-value, spectral calibration 42
oven
function 11
overflow hole, illustration of 12 R
overvoltage category (rating) xxi radioactive waste, handling xx
overvoltage rating xxi reader, barcode 6

168 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

 reextraction conventions xiv
editing Results Group, Analysis Protocol, Analysis electrical xxi
Method 153 ergonomic xxii
results column 151 instrument xvii
selected samples 154 instrument operation xviii
selecting 148 laser xxi
window elements 149 moving and lifting instrument xvii
reextraction panel moving parts xxi
effects of changes made in 147 physical hazard xxi
standards xxiii
repetitive motion hazard xxii workstation xxii
Replenish Polymer Wizard safety alert words
using 15 accompanying hazard icons xiv
reservoirs CAUTIONS xiv
filling 17 DANGERS xiv
positions on the autosampler 18 description xiv
resolution IMPORTANTS xiv
fragment analysis 4 WARNINGS xiv
results column, reextraction 151 safety labels, on instruments xvi
Results Group safety requirements, laser xxii
creating for sequencing analysis 70 safety standards
creating, fragment analysis 115 Canadian xxiii
creating, SeqScape software 98 European xxiii
editor, GeneMapper 107 U.S. xxiii
general description 55 safety symbols
importing and exporting 100 on instruments xvi
options 57 See also hazard symbols
options, SeqScape software 165
sample file 147
run default location 160
fragment analysis 133 type 160
requires plate record 55, 84, 108
samples
sensor states 140
sequencing, average time 132 autoanalyzing 155
starting 130 loading 32
starting, stopping, skipping, pausing 133 sensor states 140
viewing data 137 SeqScape software tab 159
run history utility 145 SeqScape Software v2.5
run modules autoanalysis 82
automated steps, description 132 plate editor 84
selecting for fragment analysis 113 plate record elements 85
selecting spectral 36 user guide P/N 82
run schedule, viewing 129 sequencing
November 3, 2004 1:23 pm, 3130UserGuide_IX.fm

run scheduler automated, creating protocols 59

spatial 22 automation, required files 55
verifying schedule 129 data, automating the analysis 82
SAMPLE DOCUMENT

matrix standards 31
run time passing profiles, spectral calibration 49
fragment analysis 4 plate editor 55
spectral calibration 41 run time 132
running buffer, making and storing 16 specifications 3
spectral run modules 36
S viewing analyzed data 160
sequencing chemistry
safety
supported kits 28
before operating the instrument xvii
service console, using 9
chemical xviii
chemical waste xx set (activate) spectral calibration 47

Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide 169

software, starting 9 U
spatial calibration unlinking a plate 129
accepting or rejecting 24
Update Cap Array Info
creating 22
evaluating profiles 23 using 13
examples of profiles 25 US safety standards xxiii
viewer 145 user attention words, described ix
when required 22 utility, run history 145
specifications
fragment analysis 4
sequencing 3 V
spectral calibration viewer
creating plate record 37 cap/array 144
evaluating results 43 capillaries 143
pass/fail status 42 icons and display information 145
passing profiles, fragment analysis 51 spectral 145
passing profiles, sequencing 49
performing a 37 W
preparing standards for 31
run times 41 WARNING, description xiv
set spectral calibration 47 waste disposal, guidelines xx
when to perform 28 water seal, illustration of 12
spectral calibration standard, types 29
water trap
spectral viewer 145 illustration of 12
spectral viewer, blank or deactivated 47 wizard
standards Replenish Polymer Wizard, using 15
EMC xxiii Update Cap Array Info, using 13
safety xxiii workstation safety xxii
starting
run 133 Z
spectral calibration run 40
status Z dye set, sequencing kit table 61
instrument 139
service console 9
status lights
on instrument startup 8
stopping a run 133
supported sequencing chemistry kits 28
symbols
hazard xvi

November 3, 2004 1:23 pm, 3130UserGuide_IX.fm

hot surface xvi
symbols on instruments
electrical xv
safety xvi
SAMPLE DOCUMENT

T
tables
summary 3
Technical Support, contacting xi
text conventions ix
toolbar 133
training, information on xi

170 Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide

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6/2010
Part Number 4352715 Rev. D