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Getting Started Guide
Applied Biosystems SOLiD™ 3 System
SETS v3.0 Getting Started Guide
SOLiD Experimental Tracking Software (SETS)
Getting Started Guide
Applied Biosystems SOLiD™ 3 System
SETS v3.0 Getting Started Guide
SOLiD Experimental Tracking Software (SETS)
For Research Use Only. Not for use in diagnostic procedures.
This user guide is the proprietary material of Life Technologies or its subsidiaries and is protected by laws of copyright. The
customer of the SOLiD™ 3 System is hereby granted limited, non-exclusive rights to use this user guide solely for the purpose of
operating the SOLiD™ 3 System. Unauthorized copying, renting, modifying, or creating derivatives of this user guide is
prohibited.
Information in this document is subject to change without notice.
APPLIED BIOSYSTEMS DISCLAIMS ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT, EXPRESSED OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR
PURPOSE. TO THE FULLEST EXTENT ALLOWED BY LAW, IN NO EVENT SHALL APPLIED BIOSYSTEMS BE
LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY, OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR
SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH
OR ARISING FROM THIS DOCUMENT, INCLUDING BUT NOT LIMITED TO THE USE THEREOF, WHETHER OR NOT
FORESEEABLE AND WHETHER OR NOT APPLIED BIOSYSTEMS IS ADVISED OF THE POSSIBILITY OF SUCH
DAMAGES.
TRADEMARKS:
Life Technologies, Applied Biosystems, AB (Design) and GeneAmp are registered trademarks and MicroAmp and SOLiD are
trademarks of Applied Biosystems LLC, or its subsidiaries in the US and/or certain other countries.
Covaris is a trademark of Covaris, Inc.
AmpliTaq and AmpliTaq Gold are registered trademarks of Roche Molecular Systems, Inc.
All other trademarks are the sole property of their respective owners.
© Copyright 2009, Applied Biosystems. All rights reserved.
Part Number 4389302 Rev. C
02/2009
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SOLiD™ 3 System – SETS v3.0 Getting Started Guide
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Safety information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
How to use this guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . viii
How to obtain support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
Chapter 1 SETS Software Overview . . . . . . . . . . . . . . . . . . . . . . . 1
SOLiD™ 3 System Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
SETS Software Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
SETS Homepage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Chapter 2 Prepare Run Settings . . . . . . . . . . . . . . . . . . . . . . . . . . 7
ICS and SETS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
SOLiD™ 3 System Software Workflow Relationship . . . . . . . . . . . . . . . . . 9
Log In to SETS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Set Analysis Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Load a Reference Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Chapter 3 Monitor the Run in SETS . . . . . . . . . . . . . . . . . . . . . . 27
View Run Metrics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
View Cycle Scans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
View Sample Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Troubleshoot Failed Jobs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
View History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Cancel Analysis Midstream . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Cluster Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
System Logs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
RSS Feed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
iv SOLiD™ 3 System – SETS v3.0 Getting Started Guide
Contents
Chapter 4 View Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
View Overall Run Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
View Sample Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
View Analysis Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Master Report Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Chapter 5 Perform Reanalysis . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Primary Reanalysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Secondary Reanalysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
Chapter 6 Support Multiplexing . . . . . . . . . . . . . . . . . . . . . . . . . 93
Multiplexing and Barcodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
View Multiplexing Series in SETS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Setup a Multiplexing Run in ICS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
Multiplexing Series Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Chapter 7 Manage Administrative Tasks . . . . . . . . . . . . . . . . . 101
Global SETS and Export . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
Auto-Export in SETS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
Manual Export in SETS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
Event Notifications and Email Services . . . . . . . . . . . . . . . . . . . . . . . . 109
Alerts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
Delete Runs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Manage Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Appendix A Web Services . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
Appendix B Software License Agreement . . . . . . . . . . . . . . . . . . 119
Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
vi SOLiD™ 3 System – SETS v3.0 Getting Started Guide
Contents
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SOLiD™ 3 System – SETS v3.0 Getting Started Guide
Preface
Safety information
Note: For general safety information, see this Preface and
Appendix C, “Safety” on page 117. When a hazard symbol and
hazard type appear by a chemical name or instrument hazard, see the
“Safety” Appendix for the complete alert on the chemical or
instrument.
Safety alert words Four safety alert words appear in Applied Biosystems user
documentation at points in the document where you need to be aware
of relevant hazards. Each alert word—IMPORTANT, CAUTION,
WARNING, DANGER—implies a particular level of observation or
action, as defined below:
IMPORTANT! – Indicates information that is necessary for proper
instrument operation, accurate chemistry kit use, or safe use of a
chemical.
CAUTION! – 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.
WARNING! – Indicates a potentially hazardous situation that,
if not avoided, could result in death or serious injury.
DANGER! – 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.
Preface
How to use this guide
viii SOLiD™ 3 System – SETS v3.0 Getting Started Guide
How to use this guide
Text conventions This guide uses the following conventions:
•Bold text indicates user action. For example:
Ty pe 0, then press Enter for each of the remaining fields.
•Italic text indicates new or important words and is also used for
emphasis. For example:
Before analyzing, always prepare fresh matrix.
• A right arrow symbol () separates successive commands you
select from a drop-down or shortcut menu. For example:
Select FileOpenSpot Set.
Right-click the sample row, then select View Filter
View All Runs.
User attention
words
Two user attention words appear in Applied Biosystems user
documentation. Each word implies a particular level of observation
or action as described below:
Note: – Provides information that may be of interest or help but is
not critical to the use of the product.
IMPORTANT! – Provides information that is necessary for proper
instrument operation, accurate chemistry kit use, or safe use of a
chemical.
Preface
How to obtain support
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SOLiD™ 3 System – SETS v3.0 Getting Started Guide
How to obtain support
For the latest services and support information for all locations, go
to:
www.appliedbiosystems.com
At the Applied Biosystems web site, you can:
• Access worldwide telephone and fax numbers to contact
Applied Biosystems Technical Support and Sales facilities.
• 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.
Preface
How to obtain support
xSOLiD™ 3 System – SETS v3.0 Getting Started Guide
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Chapter 1
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SOLiD™ 3 System – SETS Software Getting Started Guide
SETS Software Overview
This chapter covers:
■SOLiD™ 3 System Overview . . . . . . . . . . . . . . . . . . . . . . . . . 2
■SETS Software Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
■SETS Homepage. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
SETS Software Overview
Prepare Run Settings
Monitor the Run in SETS
View Reports
Perform Reanalysis
Support Multiplexing
Manage Administrative Tasks
Chapter 1 SETS Software Overview
SOLiD™ 3 System Overview1
2SOLiD™ 3 System – SETS Software Getting Started Guide
SOLiD™ 3 System Overview
SOLiD™
Technology
The Applied Biosystems SOLiD™ 3 System provides parallel
sequencing of clonally amplified DNA fragments linked to magnetic
beads. The sequencing methodology is based on sequential ligation
with dye-labeled oligonucleotides. All fluorescently labeled
oligonucleotide probes are present simultaneously, competing for
incorporation. After each ligation, fluorescence is measured before
another round of ligation takes place.
This ligation-based chemistry eliminates dephasing. The use of a
two-base encoding mechanism, which interrogates each base twice
for errors during sequencing, discriminates between true
polymorphisms and system noise. The SOLiD™ Analyzer software
allows customers to monitor the runs in real-time, and provides basic
data analysis tools.
The SOLiD™ 3 System consists of:
•SOLiD
™ Analyzer
• All ancillary equipment
• ICS software, which is described in the Applied Biosystems
SOLiD™ 3 System Instrument Operation Guide (PN 4402739)
•SOLiD
™ Experiment Tracking System (SETS) software, which
is described in this document
Chapter 1 SETS Software Overview
SETS Software Overview 1
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SOLiD™ 3 System – SETS Software Getting Started Guide
SETS Software Overview
Overview The SOLiD™ Experiment Tracking System (SETS) software is a
web-based application for viewing real-time data and completed run
analysis reports from a SOLiD™ Analyzer. The SOLiD™ Analyzer
system uses ligation-based sequencing, then filters data to remove
missing calls, nonligations, and/or redundancies.
Data are analyzed at two levels:
• Primary analysis, which involves:
– Image alignment
– Color assignment
– Color calls
– Quality value assignments
• Secondary analysis, which compares color space calls to a
reference sequence
Opening SETS When using the SOLiD™ Analyzer computer, you can access SETS
by:
• Typing in the SETS software URL, supplied by the Applied
Biosystems Field Service Engineer:
This address opens the SETS software to the homepage and you are
automatically logged-in as a “guest” user. As a guest, you can only
view analyzed data and reports. Log in to the software to perform
other functions. See “Log In to SETS” on page 10.
Chapter 1 SETS Software Overview
SETS Homepage1
4SOLiD™ 3 System – SETS Software Getting Started Guide
SETS Homepage
The SETS software opens to the homepage where you can view real-
time and completed-run data generated by the SOLiD™ Analyzer.
The homepage is divided into three sections:
• Error Messages
• In-Progress or Most Recent Runs (per flowcell)
• Recent Analyses
At the upper left-hand corner, you can see the current login
information, including instrument name and SETS user:
Chapter 1 SETS Software Overview
SETS Homepage 1
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SOLiD™ 3 System – SETS Software Getting Started Guide
Error Messages When there are error messages, the Log Messages section displays
them at the top of the homepage. You can scroll through the
messages or click to remove all messages from the field.
For more information on log messages, see Chapter 3, System Logs.
In Progress or Most
Recent Run
This section displays status of a current run or results for the most
recently completed run. Flowcell 1 displays on the left-hand side of
the window; flowcell 2 displays on the right side.
To understand more about your run, click or More
Information within each flowcell section.
Chapter 1 SETS Software Overview
SETS Homepage1
6SOLiD™ 3 System – SETS Software Getting Started Guide
Run Metrics provides quality metrics in the form of traffic lights to
help you assess the progress and measurable quality of the run. More
Information allows you to view analyzed data for a particular run.
For details on monitoring a run, see Chapter 3, Monitor the Run in
SETS.
Note: At any time you can return to the SETS homepage by clicking
the button on the main menu at the top of the screen.
Recent Analyses This section displays the progress of data analysis for individual
samples.
For every analysis, you can see:
• run name
• sample name
• date created
• last closed stage
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Chapter 2
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SOLiD™ 3 System – SETS Software Getting Started Guide
Prepare Run Settings
This chapter covers:
■ICS and SETS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
■SOLiD™ 3 System Software Workflow Relationship. . . . . . . . 9
■Log In to SETS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
■Set Analysis Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
■Load a Reference Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . 25
SETS Software Overview
Prepare Run Settings
Monitor the Run in SETS
View Reports
Perform Reanalysis
Support Multiplexing
Manage Administrative Tasks
Chapter 2 Prepare Run Settings
ICS and SETS2
8SOLiD™ 3 System – SETS Software Getting Started Guide
ICS and SETS
To understand the relationship of the two software components in the
SOLiD™ 3 System and how a user would interact between the two in
a typical workflow, refer to the “SOLiD™ 3 System Software
Workflow Relationship” on page 9.
Analysis Settings Before you start a run on the SOLiD™ Analyzer using the
Instrument Control Software (ICS), open the SETS software and
select the secondary analysis settings. To use a reference sequence
not listed in the drop-down list, upload your reference and add it to
the list. For details, see:
•“Set Analysis Parameters” on page 11
•“Load a Reference Sequence” on page 25
Secondary analysis (sequence data alignments to a reference
sequence) will not occur without a preloaded reference sequence.
IMPORTANT! For more complex genomes, such as the human
genome, secondary analysis should occur on a different cluster from
the one that controls the SOLiD™ 3 System. Sequencing data from
complex genomes are often analyzed in smaller batches, for instance,
one chromosome at a time.
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