Applied Biosystems
3730 and 3730xl Getting Started Guide Rev E
Getting Started Guide
200 Pages

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Page 1
USER GUIDE
Applied Biosystems® 3730/3730xl DNA Analyzer Getting Started Publication Number 4359476 Revision E
For Research Use Only. Not for use in diagnostic procedures.
The information in this guide is subject to change without notice. DISCLAIMER LIFE TECHNOLOGIES CORPORATION AND/OR ITS AFFILIATE(S) DISCLAIM ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT, EXPRESSED OR IMPLIED, INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NON-INFRINGEMENT. TO THE EXTENT ALLOWED BY LAW, IN NO EVENT SHALL LIFE TECHNOLOGIES AND/OR ITS AFFILIATE(S) 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. Limited Use Label License No. 358: Research Use Only Notice to Purchaser: The purchase of this product conveys to the purchaser the limited, non-transferable right to use the purchased amount of the product only to perform internal research for the sole benefit of the purchaser. No right to resell this product or any of its components is conveyed expressly, by implication, or by estoppel. This product is for internal research purposes only and is not for use in commercial applications of any kind, including, without limitation, quality control and commercial services such as reporting the results of purchaser's activities for a fee or other form of consideration. For information on obtaining additional rights, please contact [email protected] or Out Licensing, Life Technologies Corporation, 5791 Van Allen Way, Carlsbad, California 92008. Limited Use Label License No. 481: Sequencing or Fragment Analysis Intellectual Property Notice to Purchaser: This product is optimized for use in the DNA sequencing or fragment analysis methods covered by patents owned and/or controlled by Life Technologies Corporation ("LTC"). LTC does not convey any right or license under these patents, whether expressly, by implication, by estoppels, or otherwise, to the purchaser by the purchase of this product to use the DNA sequencing or fragment analysis methods. Notwithstanding the foregoing, a limited license to use the DNA sequencing or fragment analysis methods covered by such patents can be obtained for certain research and development activities (a) through the purchase of certain LTC reagents when such reagents are used in conjunction with an authorized LTC instrument, or (b) directly from LTC. For information on obtaining additional rights to practice the DNA sequencing or fragment analysis methods, please contact [email protected] or Out Licensing, Life Technologies Corporation, 5791 Van Allen Way, Carlsbad, California 92008. LIMITED LICENSE The Applied Biosystems® 3730 and 3730xl DNA Analyzers include patented technology licensed from Hitachi, Ltd. as part of a strategic partnership between Life Technologies and Hitachi, Ltd., as well as patented technology of Life Technologies. TRADEMARKS All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. © 2014 Thermo Fisher Scientific Inc. All rights reserved.
Contents
Revision history... vii
Chapter 1
Preparing the Instrument
1
Instrument and Parts... 2 Polymer Delivery Pump Detail... 3 Overview... 4 Troubleshooting Instrument Status Lights... 6 Starting the 3730/3730xl Analyzer Data Collection Software... 9 Installing the Capillary Array... 10 Replacing the Polymer... 12 Preparing Buffer and Filling the Reservoirs... 14 Placing Reservoirs into the Instrument... 18
Chapter 2
Performing Spatial Calibration
21
Overview... 22 Performing Spatial Calibration... 22 Evaluating the Calibration Data
Chapter 3
... 24
Performing Spectral Calibration For Sequencing and Fragment Analysis
29
Overview... 30 Preparing the Spectral Calibration Chemistry... 32 Creating a Spectral Instrument Protocol... 36 Creating a Spectral Calibration Plate Record... 39 Loading the Plate into the Instrument... 41 Running the Spectral Calibration Plate... 42 Evaluating the Spectral Calibration Data... 45 Examples of Passing Sequencing Spectral Calibrations... 49 Example of a Passing Fragment Analysis Spectral Calibration... 51 Spectral Viewer... 52 Troubleshooting... 55
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Chapter 4
Setting Up the Software for DNA Sequencing
57
Plate Records and Sequencing Analysis... 58 Creating Required Settings for Automated Sequencing Analysis... 62 Creating and Completing a Sequencing Analysis Plate Record... 80 Fill Down Special... 83
Chapter 5
Setting Up the Software for Fragment Analysis
89
3730/3730xl Analyzer Data Collection and GeneMapper® Software... 90 GeneMapper® Software Plate Records... 93 Components of a GeneMapper® Software Plate Record... 94 Creating Required Settings for Automated Fragment Analysis... 97 Creating and Completing a GeneMapper® Software Plate Record... 110 Filling Down the Plate Record... 113
Chapter 6
Running the Instrument
117
Working with Plate Assemblies... 118 Placing Plate Assemblies into the Instrument... 122 Scheduling Runs... 123 Default Load Maps... 127 Barcode Readers... 130 Running the Instrument: Manual vs Auto Mode... 132 Starting the Run... 135 Controlling the Run... 137 Monitoring the Status of the Run... 138 Viewing Real-Time Electrophoresis Data... 140 Viewing Event History... 141 Viewing Electropherogram Data... 142 Viewing the Run History Data... 144 Viewing the Results of Autoextraction... 146
Appendix A Parts List
153
Appendix B Dye Sets: G5, G5-RCT, Any4Dye, Any4dye-HDR, and Any5Dye
155
Dye Sets G5 and G5-RCT For Fragment Analysis... 155 Creating a Spectral Calibration for Dye Sets Any4Dye, Any4Dye–HDR, or Any5Dye . 157 Regular Runs Using Any4Dye or Any5Dye Dye Sets... 161
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Applied Biosystems® 3730/3730xl DNA Analyzer Getting Started Guide
Appendix C Instrument Warranty Information
165
Computer Configuration... 165 Limited Product Warranty... 165 Damages, Claims, and Returns... 167
Support
169
Obtain SDSs... 169 Obtain support... 169 Limited Product Warranty... 169
Safety
171
Chemical Waste Safety... 177
Index
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Applied Biosystems® 3730/3730xl DNA Analyzer Getting Started Guide
About This Guide
IMPORTANT! Before using this product, read and understand the information the “Safety” section in this document.
Revision history Revision E
Date September 2014
Description Update laser information in Safety section.
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Applied Biosystems® 3730/3730xl DNA Anayzers Getting Started Guide
Chapter 1
Preparing the Instrument
Preparing the Instrument
Performing Spatial Calibration
See page 9
Start the 3730/3730xl Data Collection Software
Performing Spectral Calibration for Sequencing and Fragment Analysis
See page 10 Setting Up the Software for DNA Sequencing
Install the capillary array
Setting Up the Software for Fragment Analysis
See page 12
Replace the polymer Running the Instrument
Performing Maintenance
See page 14
Prepare buffer and fill the reservoirs
Audit Trails and Access Control
Notes
Applied Biosystems® 3730/3730xl DNA Analyzer Getting Started Guide
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1
Chapter 1 Preparing the Instrument Instrument and Parts
Instrument and Parts Polymer Delivery Pump (PDP)
Capillary array
Pump Block Interconnect tube Polymer supply tube Lower polymer block Polymer reservoir
Anode buffer jar
Stacker door Oven door
Interior light button
Waste reservoir
Status lights
Stacker door indicator light
Power button (on/off)
Tray button
Buffer reservoir Water reservoir
description 4
Notes
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Applied Biosystems® 3730/3730xl DNA Analyzer Getting Started Guide
Chapter 1 Preparing the Instrument Polymer Delivery Pump Detail
Polymer Delivery Pump Detail 1 Mounting pin PDP motor cover
PDP motor
Syringe fitting
Capillary array tip
Water seal Waste fitting Water trap
Capillary array
Piston Mounting pin Capillary array knob
Pump chamber
Double-tapered ferrule Array port
Pump block Check valve
Interconnect tube
Buffer valve pin
Polymer supply tube
Polymer supply bottle cap with hole
Mounting pin
Lower polymer block Mounting pin
O-ring Electrode
Overflow hole Buffer fill-line
Buffer jar (67mL anode reservoir) Polymer supply bottle
Notes
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Chapter 1 Preparing the Instrument Overview
Overview This chapter explains how to prepare the instrument for a run by installing the capillary array, buffer, and reservoirs.
Powering On the Computer and 3730/3730xl Analyzer Instrument 1. Press the power button on the monitor to power it on.
2. Press the power button on the computer to power it on.
3. In the Log On to Windows dialog box: a. In the User Name field, enter your user
name. b. In the Password field, enter your password. c. Click
.
4. Close the oven door. 5. Close the stacker drawer. Stacker drawer
6. Close the instrument door. Instrument door
7. Wait until the monitor displays the desktop of the Windows® operating system.
8. Press the power button on the 3730/3730xl Analyzer instrument to power it on.
Notes
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Applied Biosystems® 3730/3730xl DNA Analyzer Getting Started Guide
Chapter 1 Preparing the Instrument Overview
The Status Lights Status • The instrument is ready
1
Status Light
Action
Solid Green
Go to page 9.
• An automated wizard operation is in progress with the instrument door closed • A run is in progress
Flashing Green
• The instrument cannot communicate with the computer.
Solid Yellow
Go to page 7.
• The instrument is downloading firmware
Flashing Yellow
Go to page 7.
Solid Red
Go to page 7.
• The instrument is performing diagnostics • The oven door is open • The instrument door is open • The buffer reservoir is not installed • The capillary array is not installed • An automated wizard operation is in progress with the instrument door open • The instrument has detected a problem
Notes
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Chapter 1 Preparing the Instrument Troubleshooting Instrument Status Lights
Troubleshooting Instrument Status Lights Flashing Yellow
To determine the source of the problem:
1. Press on the instrument door to ensure that it is closed. If the 3730/3730xl Analyzer instrument displays the green status light, then the instrument door was open. Go to page 9
Instrument door
2. If the 3730/3730xl Analyzer instrument continues to display the flashing yellow light: a. Open the instrument door. b. Press on the oven door to verify that it is
closed. Oven door
c. Close the instrument door. d. If the 3730/3730xl Analyzer instrument
displays the green status light, then the oven door was open. Go to page 9
3. If the 3730/3730xl Analyzer instrument continues to display the flashing yellow light: a. Open the instrument door.
OK – Go to page 9.
b. Open the oven door. c. Check that the buffer reservoir and capillary
array are installed.
Capillary array (installed)
d. Close the oven door.
Buffer reservoir (installed)
e. Close the instrument door.
OK – Go to page 9.
Capillary array (not installed) Buffer reservoir (not installed)
Capillary array (installed) Buffer reservoir (not installed)
Notes
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Applied Biosystems® 3730/3730xl DNA Analyzer Getting Started Guide
Chapter 1 Preparing the Instrument Troubleshooting Instrument Status Lights
Solid Yellow Light To determine the source of the problem, verify that the:
1
1. Monitor displays the desktop of the Windows operating system. 2. Ethernet cable is connected to the back of the 3730/3730xl Analyzer instrument. 3. Other end of the Ethernet cable is connected to the computer. 4. Instrument door is closed. 5. Buffer, water, and waste reservoirs are in place. 6. 3730 Analyzer User account password is functional. If the instrument continues to display the solid yellow light, contact Applied Biosystems technical support or your service representative for further assistance.
Solid Red Light To determine the source of the problem:
1. If the instrument continues to display the solid red light: a. Power off the instrument. b. Wait for 30 seconds. c. Power on the instrument.
2. If the instrument continues to display the solid red light: a. Start the 3730/3730xl Analyzer Data Collection Software as explained page 9. b. In the navigation pane of the Data Collection Software, double-click
GA Instruments > Status > Event Log.
ga3730 >
instrument name > Instrument
Notes
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Chapter 1 Preparing the Instrument Troubleshooting Instrument Status Lights
c. In the Event Log view, find the last message in the log file. d. Using the error code, perform the required tasks to fix the problem.
3. If the instrument continues to display the solid red light, contact technical support or your service representative for further assistance.
Notes
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Applied Biosystems® 3730/3730xl DNA Analyzer Getting Started Guide
Chapter 1 Preparing the Instrument Starting the 3730/3730xl Analyzer Data Collection Software
Starting the 3730/3730xl Analyzer Data Collection Software 1
1. Select
> All Programs > Applied Biosystems > Unified Data Collection > Run Unified Data Collection v3.0. The data collection software opens the Service Console dialog box.
Red circles indicate that applications of the data collection software are not running.
Wait for the Service Console dialog box to open the applications of the data collection software.
Not running
Starting
Running
When all applications are running (green squares), the Data Collection software opens the Data Collection Viewer.
Applications of the data collection software are running
Notes
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Chapter 1 Preparing the Instrument Installing the Capillary Array
Installing the Capillary Array CHEMICAL HAZARD. POP 7™ polymer may cause eye, skin, and respiratory tract irritation. Read the MSDS, and follow the handling instructions. Wear appropriate protective eyewear, clothing, and gloves. Use for research and development purposes only.
CHEMICAL HAZARD. Running Buffer with EDTA causes eye, skin, and respiratory tract irritation. Read the MSDS, and follow the handling instructions. Wear appropriate protective eyewear, clothing, and gloves. Required Materials
• Capillary array, 96- or 48-capillary • Lab wipes, lint-free • Gloves Guidelines for Capillary Use
• Do not bend the capillaries • Store capillary arrays using a buffer reservoir and the header shipping cover. For storage information refer to the Maintenance and Troubleshooting Guide PN 4359473).
Header shipping cover
Installing a New or Used Capillary Array IMPORTANT! Wear gloves when you
Buffer reservoir
handle the capillary array.
Failure to use the Install Array wizard when changing capillary arrays can result in degraded analysis data.
1. Close the instrument door. 2. In the Data Collection software, select GA Instruments > instrument name >.
ga3730 >
Notes
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Applied Biosystems® 3730/3730xl DNA Analyzer Getting Started Guide
Chapter 1 Preparing the Instrument Installing the Capillary Array
3. On the toolbar, select Wizards > Install Array Wizard.
1
4. Install the array as instructed by the Array wizard.
5. Perform a spatial calibration (see page 22).
o
Notes
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Chapter 1 Preparing the Instrument Replacing the Polymer
Replacing the Polymer Note: You can omit this section if you have installed
a capillary array using the Install Array wizard during the initial activation of the instrument.
CHEMICAL HAZARD. POP 7™ polymer may cause eye, skin, and respiratory tract irritation. Read the MSDS, and follow the handling instructions. Wear appropriate protective eyewear, clothing, and gloves. Use for research and development purposes only.
Required Materials • POP-7™ polymer • Wipes, lint-free • Gloves
Guidelines for Polymer Use • Check the polymer blocks and lines daily for bubbles. • Ensure that you have enough polymer for operation: – A 96-capillary run uses approximately 250 µL of polymer – A 48-capillary run uses approximately 110 µL of polymer.
When to Replace the Polymer =
Replace the polymer on the instrument: • Weekly (polymer lifetime is 7 days at 25 °C) • If insufficient polymer remains for the planned run set
IMPORTANT! Failure to replace expired/old polymer
may lead to loss of resolution and data quality.
Notes
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Applied Biosystems® 3730/3730xl DNA Analyzer Getting Started Guide