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Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide (PN 4477854A)

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User Guide: 3130/3130xl Genetic Analyzers, 3130 Series Data Collection Software 4 - Maintenance, Troubleshooting and Reference

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USER GUIDE
Applied Biosystems� 3130/3130xl Genetic Analyzers
3130 Series Data Collection Software 4
MAINTENANCE, TROUBLESHOOTING, AND REFERENCE
Publication Part Number 4477854 Rev. A Revision Date May 2012

For Research Use Only. Not for use in diagnostic procedures.
The information in this guide 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. 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. NOTICE TO PURCHASER: LIMITED USE LABEL LICENSE NO: 358: Research Use Only The purchase of this product conveys to the purchaser the limited, non-transferable right to use 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 outlicensing@lifetech.com or Out Licensing, Life Technologies, 5791 Van Allen Way, Carlsbad, California 92008.
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.
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
The trademarks mentioned herein are the property of Life Technologies Corporation or their respective owners.
Applied Biosystems, AmpFlSTR, BigDye, Cofiler, GeneMapper, Identifiler, POP-4, Profiler, Profiler Plus ID, SeqScape, SGM Plus, SNaPshot, StockMarks, Variant Reporter, and Yfiler are registered trademarks and AB (Design), Applera, Hi-Di, KB, POP, POP-6, POP-7, and SEfiler are trademarks of Applied Biosystems or its subsidiaries in the U.S. and/or certain other countries.
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.
� 2012 Life Technologies Corporation. All rights reserved.

Contents

Chapter 1

Maintenance

Polymer Delivery Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Performing Maintenance Tasks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 Routine Cleaning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 Resetting the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 Moving and Leveling the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 Shutting Down the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 Wizards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 Flushing and Filling the Water Trap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 Fluids and Waste . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 Capillary Array . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 Storing Capillary Arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 Autosampler Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 Manual Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Chapter 2

Computer Maintenance

Computer Task Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 Working With Drives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 Hard Disk and Database Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34 Archiving Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 Defragmenting the Computer Hard Drive . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 Deleting Records from the Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Chapter 3

Managing Software License for 3130 Series

Data Collection Software 4

Manage software licenses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 Obtain and activate a software license . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 Renew a software license . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

Chapter 4 Troubleshooting

Instrument Startup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 Instrument Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 Spatial Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 Spectral Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52 Plate Linking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 Run Performance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 5

Data Collection Software Advanced Functions

Customizing Run Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68 Run Priority Scheduling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70 Edit > Fill Down Special Option for Plate Records . . . . . . . . . . . . . . . . . . . . . . . . . . 73 Multi-application (Mixed) Plate Record . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

Chapter 6

Reference Tables

Sequencing Summary Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84 Fragment Analysis Run Module Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89 Run Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93

Appendix A Parts List

Documentation and Support

Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97 Obtaining SDSs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97 Obtaining Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98 Computer Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98 Limited Product Warranty . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98

Safety

Symbols on instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99 Safety alerts on this instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100 Instrument safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101 Safety and electromagnetic compatibility (EMC) standards . . . . . . . . . . . . . . . . . . 104 Chemical safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105 Biological hazard safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107 Safety Labels on Instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107 Workstation Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108

Index

109

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 1
Maintenance 1

Overview

This chapter covers the following topics:
Polymer Delivery Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Performing Maintenance Tasks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 Routine Cleaning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 Resetting the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 Moving and Leveling the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 Shutting Down the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 Wizards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 Flushing and Filling the Water Trap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 Fluids and Waste . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 Capillary Array . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 Storing Capillary Arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 Autosampler Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 Manual Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 1 Maintenance
Polymer Delivery Pump

Polymer Delivery Pump

Syringe fitting
Water seal Waste fitting
Water trap Mounting pin
Piston Pump chamber
Pump block
Check valve

Components of the polymer delivery pump (PDP) are identified in the drawing below.

Mounting pin

PDP motor

PDP motor cover

Capillary array tip

Capillary array Capillary array knob

Double-tapered ferrule Array port

Polymer supply tube

Interconnect tube

Polymer supply bottle cap with
hole
Polymer supply bottle
Electrode

GR2459

Mounting pin
O-ring

Buffer valve pin Lower polymer block Mounting pin
Overflow hole Buffer fill-line
Buffer jar (16 mL anode reservoir)

Notes
6

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 1 Maintenance
Performing Maintenance Tasks

Performing Maintenance Tasks
1
Overview This section lists common tasks required to maintain your Applied Biosystems
3130/3130xl Genetic Analyzers in good working condition. The tasks are divided into tables based on how often you should perform each task.

Wear appropriate protection, including gloves, laboratory goggles, and coat whenever you work with the fluids used on this instrument, or parts that may come into contact with these fluids.

Daily Tasks Perform these tasks at least once per day.

Maintenance Task
Ensure adequate levels of buffer and water in reservoirs.
Ensure the plate assemblies are properly assembled. IMPORTANT! The holes in the plate retainer must align with the holes in the septa, or the capillary tips will be damaged.
Ensure the plate assemblies are positioned on the plate deck properly. Plates should sit snugly on the deck. IMPORTANT! Never use warped plates.
Check the level of buffer in the buffer jar. Ensure that the overflow hole faces the front of the instrument and is not occluded.
Change the water and 1X run buffer in the reservoirs on the instrument and ensure that the outside of the assemblies are dry. Do not simply `top off' liquids. Full replacement is critical.
Check for bubbles in the pump block, lower polymer block, interconnect tube, polymer supply tube, and channels.
Remove all bubbles with the Bubble Remove Wizard.
Check the loading-end header to ensure the capillary tips are not crushed or damaged.
Check the level of polymer in the bottle to ensure sufficient volume for runs.
Check the pump block and the lower polymer block to ensure they fit securely on the instrument.
Clean the instrument surfaces.
Check for leaks around the array knob, interconnecting tube nuts, and check valve.

Frequency Before each run Before each run
Before each run
Before each run
Every 48 hours
Daily or before each run
Daily or before each run
Daily or before each run Daily
Daily Daily

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 1 Maintenance
Performing Maintenance Tasks

Weekly Tasks Perform these tasks at least once per week.

Maintenance Task Replace the polymer using the Replenish Polymer Wizard.
Flush the water trap. See "Flushing and Filling the Water Trap" on page 17. Check the storage conditions of the used arrays. Restart the computer and instrument. Check hard disk space.

Frequency
Weekly or as needed Weekly Weekly Weekly Weekly

Monthly Tasks Perform these tasks at least once per month.

Maintenance Task
Run the Water Wash Wizard. Flush the array port during this Wizard, whether or not bubbles are present in the array port. Defragment the hard drive.

Frequency Monthly or as
needed
Monthly

As-Needed Tasks Perform these tasks as needed.
Maintenance Task Clean the drip tray. Change the array. Remove any dried polymer from the capillary tips. Use a lint-free wipe moistened with deionized water. Clean buffer and water reservoirs each time before using a different polymer.

Frequency As needed As needed As needed
As needed

Notes
8

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 1 Maintenance
Routine Cleaning

Routine Cleaning
1
General Cleaning

1. Ensure the oven and instrument doors are closed.
2. Press the Tray button on the front of the
instrument to move the autosampler to the forward position.

Tray button

IMPORTANT! Never use organic solvents to clean the instrument.

3. Wipe off any liquid on or around the autosampler
using a lint-free tissue.
4. Clean off any polymer build-up (crystals) on the
instrument including the capillary tips and the stripper plate with deionized water and lint-free tissue.
5. Clean the array port knob, plug, or opening
threads of these parts with moistened lab wipes.
6. Clean out the drip trays with deionized water and
lint-free tissue.
Resetting the Instrument
Reset the instrument when: � A fatal error as indicated by the red status light � The instrument does not respond to the 3130 Series Data Collection Software 4

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 1 Maintenance
Resetting the Instrument
Two procedures can reset the instrument: � Press the reset button through the pin hole on the front of the instrument to dump and reload the firmware and to reset the electronics. Try this method first. � Shut down and restart the computer and the instrument.
Resetting With the Reset Button
1. Close the instrument doors.
2. Using a long narrow implement, such as a
straightened paper clip, press the reset button on the front of the instrument.

Resetting by Powering Down
1. Close the instrument doors.
2. Power off the instrument by pressing the on/off
button on the front of the instrument.
3. Restart the computer.
a. Select Start > Turn off Computer. b. In the dialog box, select Restart, then click
OK.
IMPORTANT! Wait until the computer has completely restarted before proceeding.
4. Turn on the instrument, then wait for the solid
green light.
5. Launch the Data Collection software (Service
Console applications start automatically).

Reset button On/Off button

Notes
10

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 1 Maintenance
Moving and Leveling the Instrument

Moving and Leveling the Instrument
1
PHYSICAL INJURY HAZARD. Do not attempt to lift the instrument or any other heavy objects unless you have received related training. Incorrect lifting can cause painful and sometimes permanent back injury. Use proper lifting techniques when lifting or moving the instrument. Two or three people are required to lift the instrument, depending upon instrument weight.

1. Remove the following components from the
instrument: � Any plate assemblies from the autosampler. � Water and buffer reservoirs from the autosampler. � Capillary array, by selecting Instrument Shutdown Wizard. (See "Performing a Long-Term Shutdown" on page 14.) � Anode buffer reservoir.
2. Switch off the breaker on the back of the
instrument.
3. Disconnect the power cord and the Ethernet
cable.
IMPORTANT! While moving the instrument, avoid any shock or vibration.

4. Move the instrument. 5. Place the bubble level on the autosampler deck. 6. Turn the instrument legs to level the instrument.

To move the instrument corner ...
up down

Turn the leg ...
right (clockwise) left (counterclockwise)

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 1 Maintenance
Shutting Down the Instrument

Shutting Down the Instrument

Perform the appropriate shutdown procedure based on the information in the following table:

If the instrument will be unattended for ...
no more than 1 week with a full buffer reservoir
for more than 1 week

Perform this shutdown procedure ...
Short-term IMPORTANT! The key to a successful short-term shutdown is keeping the capillary array in 1X running buffer. This prevents the polymer from drying in the capillaries.
Long-term

Performing a Short-Term Shutdown

Fill the Capillary With Fresh Polymer Using Manual Control

1. Ensure the oven and instrument doors are closed.

2. Collect polymer waste:

a. Click GA Instruments > ga3130xl> instrument name> Manual Control.

ga3130 or

b. In the Send Defined Command drop-down menu, select Autosampler.

c. In the Command Name drop-down menu, select Move autosampler to site.

d. In the Value menu, select Waste.

e. Click Send Command. Wait for the autosampler to stop moving and Send Command becomes active, before proceeding.

3. Fill the capillaries:
a. In the Send Defined Command for dropdown menu, select Polymer Delivery Pump.

Notes
12

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

b. In the Command Name, select the appropriate Fill <length> cm capillary array length.
c. Click Send Command.The array fill is finished when Send Command becomes active.
d. Return the buffer reservoir to the capillaries.
Cleaning the Reservoirs
1. Press the Tray button to move the autosampler
forward.
2. Open the doors, then remove the:
� Plates � Cathode buffer reservoir and water
reservoirs
3. Dispose of remaining fluids and rinse out the
reservoirs with deionized water.
Note: Follow your company's waste disposal practices for appropriate disposal procedures.
4. Rinse the cathode reservoir with 1X running
buffer, and then fill to the line with 1X running buffer (about 16 mL).
5. Fill the three water reservoirs to the line with
quality deionized water (about 16 mL).
Ensure that the septa fit snugly and flush on the tops of the reservoirs to prevent damaging the capillary tips.
6. Place a clean reservoir septa on each reservoir,
and dry the outside of the reservoirs using a lint-free wipe.

GR1857b

Chapter 1 Maintenance
Shutting Down the Instrument
1
Fill line

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 1 Maintenance
Shutting Down the Instrument
7. Place the reservoirs into position on the
autosampler as shown below.
8. Close the instrument doors.
Note: Closing the doors returns the autosampler to the home position, placing the tips of the capillaries in buffer.
9. Shut down the computer and turn off the
instrument.
Performing a Long-Term Shutdown
Select Instrument Shutdown Wizard and follow the prompts.
IMPORTANT! Make sure all parts are completely dry before long-term storage.

Water reservoir (waste)

Water reservoir (rinse)

Cathode reservoir (1X running buffer)

Water reservoir (spare)

Home position

Notes
14

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 1 Maintenance
Wizards

Wizards

Accessing In the tree pane of the Data Collection software, click

Wizards

GA Instruments > ga3130 or ga3130xl > instrument name or any topic

name below instrument name to see Wizards in the menu bar.

The Wizards in the Data Collection software guide you through several maintenance procedures.

If plates are linked in the Run Scheduler and you complete a Wizard, the plates automatically unlink. You will get a warning dialog box. Click , and then relink the plate if applicable.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 1 Maintenance
Wizards

General Use Guidelines

The following table lists the Wizards and when to use them.

Wizard

Use to...

Install Array
Change Polymer Type Replenish Polymer
Bubble Remove Water Wash
Instrument Shutdown Autosampler Calibration Update Cap Array Info

� Install a capillary array: � On a new instrument � To reactivate an instrument that has been shut down
� Replace an installed capillary array with another capillary array
� Change to a different polymer type than the one presently being used
� Replenish the polymer supply � Replace the polymer in the PDP with polymer of the same or
different lot � Enter polymer information when Data Collection software is installed
or upgraded
Remove bubbles in the PDP chamber, channels, and tubing � Wash the PDP chamber, lower polymer blocka, channels, and tubing
with water: � As part of a monthly maintenance protocol � To remove any suspected contaminants in the PDP � To remove persistent bubbles (followed by the Bubble Remove
Wizard, if needed) � To replace old polymer in the PDP
Prepare the instrument for a period of disuse of greater than one week
Calibrate the autosampler positions
� Update the capillary array information and the serial number � Correct an entry mistake after using a Wizard

a The lower polymer block is cleaned on the instrument using this Wizard and should not be removed.

IMPORTANT! Use of CAP polymer requires a dedicated array. CAP polymer is not compatible with any other POP polymer. Even trace amounts of CAP polymer with other polymers will irreparably damage the array and pump and void any service contract or warranty for the instrument. It is important to dedicate a capillary array, polymer block, and syringe for CAP polymer use exclusively. Also, buffer and water reservoirs should be cleaned every time a different polymer is used.
After you use the Change Polymer Type Wizard, ensure that you choose a proper spectral calibration as the active spectral calibration, or that you run a new spectral calibration.

Notes
16

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 1 Maintenance
Flushing and Filling the Water Trap
Flushing and Filling the Water Trap
1
Overview
The PDP water trap should be flushed with either distilled or deionized water at least once per week to wash out any diluted polymer and to clear bubbles.
Leave the trap filled with either distilled or deionized
water.
To flush the water seal trap:
1. Fill the supplied 20 mL, all-plastic Luer lock
syringe (in the PDP Cleaning kit, Part no. 4359572) with distilled or deionized water. Expel any bubbles from the syringe.
2. Do not use a syringe smaller than 20 mL. Doing
so can generate excessive pressure within the trap.
3. Attach the syringe to the forward-facing Luer
fitting at the top of the pump block. Hold the fitting with one hand while threading the syringe onto the fitting with the other hand.
4. Open the Luer fitting by grasping the body of the
fitting and turning it and the attached syringe approximately one-half turn counterclockwise.
5. Open the exit fitting at the top left side of the
pump block by turning it approximately one-half turn counterclockwise.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 1 Maintenance
Flushing and Filling the Water Trap
6. Hold an empty tube or beaker under the exit
fitting to receive approximately 5 mL of waste. Flush the trap by pushing steadily on the syringe plunger.
IMPORTANT! DO NOT USE EXCESSIVE FORCE when you push the syringe plunger as this may damage the trap seals. Take approximately 30 seconds to flush 5 mL of either distilled or deionized water through the trap.
Note: Because the water trap volume is approximately 325 L, a relatively small volume of water is adequate for complete flushing. However, a larger volume only improves flushing as long as force and flow rate are kept within the limits given above.
7. Close the fittings in this order by turning each
clockwise until the fittings seal against the block: a. Luer fitting b. Exit fitting
IMPORTANT! Do not over-tighten the fittings. Very little pressure develops within the trap during pump operation, so the fittings require only enough tightening to prevent water leaks. Excessive tightening can damage the fittings.
c. Remove the syringe from the Luer fitting. Hold the fitting with one hand while turning the syringe counterclockwise with the other hand.

Notes
18

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 1 Maintenance
Fluids and Waste

Fluids and Waste

Scheduling the Buffer Change

CHEMICAL HAZARD. 10X Genetic Analyzer Buffer with EDTA may cause eye, skin, and respiratory tract irritation. Read the SDS, and follow the handling instructions. Wear appropriate protective eyewear, clothing, and gloves.

Change the buffer before each batch of runs or at least every 24 hours. Do not simply `top off' buffer. Full replacement is critical.
Making Buffer for a Single Run
To prepare 50 mL of 1X running buffer:
1. Add 5 mL of 10X Genetic Analyzer buffer into a
graduated cylinder.

2. Add deionized water to bring the total volume up
to 50 mL.

3. Mix well.

50 mL total

1
45 mL DI H2O

Storing the Buffer
The 1X running buffer can be stored at: � 2 to 8�C for up to 1 month � Room temperature for 1 week

50 mL graduated cylinder

5 mL 10X Genetic Analyzer buffer

Buffer Storage Conditions

Option A

Option B

2 to 8�C

20 to 25�C

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

1 month

7 days

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 1 Maintenance
Fluids and Waste
Polymer
Storing Polymer
Store any remaining POPTM polymer at 2 to 8�C until the expiration date printed on the jar.
Note: Warm ambient temperature will shorten the working life of the polymer.
When to Change the Polymer
Change the polymer weekly. The polymer is stable on the instrument for 7 days. (The specified ambient temperature for instrument operation is 15�30�C.)

POP-4� or POP-6TM Polymer Storage Conditions
Su M T W Th F S

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
CHEMICAL HAZARD. POPTM Polymers cause eye, skin, and respiratory tract irritation. Read the SDS, and follow the handling instructions. Wear appropriate protective eyewear, clothing, and gloves.
IMPORTANT! Wear gloves when you handle the polymer.

20 to 25�C

7 days

Notes
20

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

1. Click Wizards > Replenish Polymer Wizard.

Chapter 1 Maintenance
Fluids and Waste
1

2. Follow the directions given in the Wizard to load
fresh polymer on the instrument.
3. Relink plate(s), if applicable.
Changing to a Different Polymer Type
CHEMICAL HAZARD. POPTM Polymers cause eye, skin, and respiratory tract irritation. Read the SDS, and follow the handling instructions. Wear appropriate protective eyewear, clothing, and gloves.
IMPORTANT! Wear gloves when you handle the polymer.
1. Click Wizards > Change Polymer Type
Wizard.
2. Follow the Wizard prompts.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 1 Maintenance
Capillary Array

Capillary Array

When to Change A capillary array should last approximately 100 runs. a Capillary Array
The following problems may indicate that a new capillary array is required:
� Poor sizing precision or allele calling � Poor resolution and/or decreased signal intensity

Checking the

ELECTRICAL SHOCK/FIRE HAZARD. Do not leave liquid on

Cathode Bar the cathode header. This can lead to electric shock or even fire if not properly

maintained.

When placing a used array back on the instrument, be sure that the cathode bar is dry (see figure below). A wet bar can lead to arcing.

Back view: Ensure the cathode header is dry � especially in the center

GR2146

3130xl capillary array

3130 capillary array

Notes
22

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Installing, Removing, or Replacing a Capillary Array
IMPORTANT! Wear gloves when you handle the polymer blocks.

CHEMICAL HAZARD. POPTM polymers cause eye, skin, and respiratory tract irritation. Read the SDS, and follow the handling instructions. Wear appropriate protective eyewear, clothing, and gloves.

1. Close the oven and instrument doors, and then
press the Tray button.
2. Select Wizards > Install Array Wizard.
IMPORTANT! The capillary array length defined in the Wizard must match the array length you are using.

3. Open instrument and oven doors.

4. Follow the directions given in the Wizard to
install or replace an array.

5. Click

when done.

6. Close and lock the oven door, then close the
instrument doors.

IMPORTANT! If you installed or replaced an array that is a different length than the one you were using, you must reset the active spectral calibration or create a new spectral calibration for the dye set and array length combination (see "Activating a Spectral Calibration" in the Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide).

7. Relink plate(s), if applicable.

Chapter 1 Maintenance
Capillary Array
1

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 1 Maintenance
Capillary Array

Updating Capillary Array
Information

Use the Update Cap Array Info Wizard to: � Update the capillary array length and serial number information into the database � Correct an entry error after using another Wizard

IMPORTANT! The capillary array length defined in the Wizard must match the array length you are using.

Caring for the Capillary Array and Work Area

Follow these guidelines to properly care for the capillary array and area:
� Wear gloves and handle the capillary array gently. � Do not touch the detection cell. � Keep the ends of the capillary array wet at all times. � Do not overtighten the capillary array knob.
� Clean off any polymer buildup (crystals) on the instrument, including the capillary electrodes and the stripper plate, with deionized water and lint-free tissue.

Keep clean

CHEMICAL HAZARD. POP polymer causes eye, skin, and respiratory tract irritation. Read the SDS, and follow the handling instructions. Wear appropriate protective eyewear, clothing, and gloves.

Note: When cleaning the capillary electrodes, be careful not to bend them out of position. If the electrodes bend, follow the procedure "Storing Capillary Arrays" on page 25.

IMPORTANT! Never use organic solvents to clean the instrument.

Filling the Capillary Array Using Manual
Control

See "Fill the Capillary With Fresh Polymer Using Manual Control" on page 12.

Notes
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Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Storing Capillary Arrays
Storing a Capillary Array on the Instrument
Store the capillary array on the instrument only when the capillary array will be unused for less than 1 week. To store the capillary array on the instrument, follow the instructions to perform a short-term shutdown described on page 12.
Storing a Capillary Array off the Instrument
Store the capillary array off of the instrument when the capillary array will be unused for longer than 1 week.
IMPORTANT! Before storing the capillary array for long periods, fill the capillaries with fresh polymer.
IMPORTANT! Wear gloves while performing the following procedure, and any other time you handle the capillary array, septa, or buffer reservoirs.
CHEMICAL HAZARD. POP Polymer causes eye, skin, and respiratory tract irritation. Read the SDS, and follow the handling instructions. Wear appropriate protective eyewear, clothing, and gloves.
1. Remove the capillary array from the instrument
by selecting Install Array Wizard.
2. Select Store Array and follow the prompts.
3. Replace the cover over the detection cell.
4. Fill a buffer reservoir with fresh 1X running
buffer and cover with a septa strip. Insert the capillary tips into the buffer.
5. Fill the shipping vial with fresh 1X running
buffer and insert the detection end of the capillary array.
Notes

Chapter 1 Maintenance
Storing Capillary Arrays

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

1
25

Chapter 1 Maintenance
Storing Capillary Arrays
6. Store the capillary array upright.
7. Check the 1X running buffer level in the
reservoir and tube weekly and replenish the buffer as needed.
Removing Bubbles from the Polymer Blocks
Bubbles may be found in the polymer system, especially after a polymer change or array installation.
Remove the bubbles from all parts of the polymer system including the pump chamber, the pump block channel, polymer supply and interconnect tubing and the lower polymer block channel.
To clear bubbles:
1. Select Wizards > Bubble Remove Wizard to
clear bubbles.
IMPORTANT! Remove bubbles from the interconnect tubing and the channel of the lower polymer block. These areas are part of the electrophoresis current path. Absence of bubbles in the current path is important for problem-free electrophoresis.
2. Replace the buffer if excess polymer is expelled
into the anode buffer jar during bubble removal.

Notes
26

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Autosampler Calibration
When to Calibrate the Autosampler
Calibrate the autosampler only as needed. Symptoms of autosampler alignment problems may include:
� Poor injection for a small number of capillaries � Low signal strength � No evidence of sample
Calibrating the Autosampler 1. Close the oven and instrument doors. 2. Select Wizards > Autosampler Calibration
Wizard.
3. If plates are linked in the Run Scheduler, the
plates automatically are unlinked. In the Warning dialog box, click .

4. Follow the directions given in the Wizard to
calibrate the autosampler.

5. Click

and turn the instrument power off

for 10 sec then on.

Chapter 1 Maintenance
Autosampler Calibration
1

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 1 Maintenance
Manual Control

Manual Control

Note: Manual control is active only if the oven and instrument doors are closed.

Table of The following table displays the manual control options in the Data Collection software. Commands

Command Function Electrophoresis Laser
Oven Autosampler a

Command Options

Value

Turn On/Off power supply Set voltage Read voltage Read current Set laser state
Set laser power Read laser power setting Read laser power Read laser current Open/Close shutter
Set state
Set temperature Initialize autosampler Bring autosampler to forward position Initialize and return to previous position Move autosampler up/down Move autosampler to site

� On � Off A number between 0.0 and 15 kV N/A
� Idle � On � Off A number between 0 and 25 mW N/A
� Open � Closed � On � Off A number between 18 and 65�C N/A
A number between �500 and 500 steps
� Buffer (left, front for 1X running buffer), home position
� Water1 (left, rear for deionized water) � Water2 (right, front for deionized water) � Waste (right, rear for deionized water)

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Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 1 Maintenance
Manual Control

Command Function Command Options

Value

Polymer Deliver Pump Initialize polymer

N/A

delivery pump

Home piston

Read piston position

Move piston down 1 to 38,000 counts

Move piston up

1 to 38,000 counts

Fill capillary array

1 to 38,000 counts

Buffer Valve

Close/Open buffer valve

� Close � Open

Detection Cell Heater

Turn On/Off detection cell heater

� On � Off

Read detection cell N/A heater temperature

Oven

Turn On/Off oven

� On � Off

Set oven temperature

A number between 18 and 70�C

Read oven

N/A

temperature

a Use the manual control of the autosampler feature with care. Give attention to the autosampler position when you use Manual Control to move the autosampler. If the autosampler reaches its maximum travel position, a fatal instrument error is generated. The software needs to be re-started after this error.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 1 Maintenance
Manual Control
Using Manual Control
Note: Manual control functions cannot be used during a run.
1. In the tree pane of the Data Collection software,
click GA Instruments > ga3130 or ga3130xl> instrument name> Manual Control.

2. In the Send Defined Command For drop-down
list, select a function.
3. In the Command Name drop-down list, select a
command and enter a value, if required.
Note: The command names are filtered based the function selected in step 2.

4. Click

Notes
30

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 2
Computer Maintenance

Overview This chapter covers the following topics:

Computer Task Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

Working With Drives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

Hard Disk and Database Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Archiving Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Defragmenting the Computer Hard Drive . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

Deleting Records from the Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 2 Computer Maintenance
Computer Task Lists

Computer Task Lists
Weekly Tasks Perform this task at least once per week.
Maintenance Task Check database space. Delete plate records from the instrument database and archive sample files. Restart the computer and instrument.

Frequency Weekly

Working With Drives

Checking Available Space
on All Drives

Before a run or batch of runs, the Data Collection software checks the space on drives C, D, E, and F to ensure that there is sufficient space to store the newly created database and sample file data. The Data Collection software sends a warning message:
� Remove data� the drive is getting full � Clean up the database (when the database is getting full, ~70�75% of capacity)
Search for generated errors in the View the Errors pane's Instrument Status window and in the Event Log window. Check the status light in the bottom left corner of the data collection window to see if it flashes red.

Full Database To view the error messages, click GA Instruments > ga3130 or ga3130xl >

Error

instrument name > Instrument Status> Event Log.

"Database is full" error message

Notes
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Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 2 Computer Maintenance
Working With Drives

Disk Drive Full To view the error messages, click GA Instruments > ga3130 or ga3130xl >

Error

instrument name > Instrument Status > Event Log.

Status light

"Disk drive is full" error message Runs cannot start until data is removed from the drive and/or database is cleaned up.

Cleaning Drives

Ensure that you have sufficient drive space by regularly:
� Archiving data � Deleting unneeded files � Emptying the trash � Defragmenting the drives

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 2 Computer Maintenance
Hard Disk and Database Status
Hard Disk and Database Status
Manually Checking Available Disk Space on E Drive 1. In the tree pane of the Data Collection software,
click GA Instruments > Database Manager to open the Database Manager.
2. Check the Database Status section. The Data
Collection software will prompt you when it is 70�75% full. At 78% full, the software will not start a run.
3. If there is insufficient space:
a. Archive the sample files to a CD-RW (see page 35) or another volume.
b. Delete the sample file data from the E drive and empty the contents of the Recycle Bin.
IMPORTANT! Data Collection software might not recover data properly if the free disk space on the E: drive is less than 2 GB. To prevent this error, perform regular file system maintenance. Move files from the E:\ drive to archival locations regularly.

Check the Database Status section Check disk space status here

Notes
34

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 2 Computer Maintenance
Archiving Data

Archiving Data

A basic version of Roxio Easy CD CreatorTM 5 software is loaded on your DellTM computer. Use this software to archive data to a CD. The software is also part of the CD set you received with your Dell computer.

Creating a Data CD

1. Select Start > All Programs > Roxio Easy CD

Creator 5 > Applications > Easy CD Creator.

The Untitled - Easy CD Creator dialog box opens.

Optional: For help creating a data CD, select Help Topics> Contents tab.

2. In the left tree pane, select Making Data CDs
for Archiving and Sharing > Making a Data CD.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 2 Computer Maintenance
Archiving Data
3. Follow the instructions to create the CD.
Instructions for creating a data CD

Notes
36

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 2 Computer Maintenance
Defragmenting the Computer Hard Drive

Defragmenting the Computer Hard Drive

The fragmentation of files decreases the performance of both the Data Collection software and the computer operating system. Programs take a longer time to access files by performing multiple search operations of the fragments.

When to Defragment the Computer Hard

Drive

Defragment the computer hard drive:

� At least once every month. � Before fragmentation reaches 10%.

Defragmenting the Drives
1. In the Windows desktop, right-click
My Computer, then select Manage.

2. In the tree tab of the Computer Management
dialog box, click Computer Management (Local) > Disk Fragmenter.

3. Select the E drive.

4. Click

The computer displays the Defragmentation Complete dialog box after completing the defragmentation.

5. In the Defragmentation Complete dialog box,

click

6. In the Computer Management dialog box,
click .

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 2 Computer Maintenance
Deleting Records from the Database
Deleting Records from the Database
Deleting Processed Frame Data
The Cleanup Database utility deletes all run data and plate records in the database. Before running the utility, be sure that all runs have been extracted from the database.
1. In the tree pane of the Data Collection software,
click GA Instruments > Database Manager to view the Database Manager.

2. Click Cleanup Processed Plate.
The following dialog box opens.

3. Click

Note: The spatial and spectral calibrations are not deleted.

Note: It may take several minutes to clean up the database if it contains a lot of data or is full.

Notes
38

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 2 Computer Maintenance
Deleting Records from the Database

Deleting a Spectral Calibration

� Spectral calibrations can be deleted by deleting the spectral plate associated with the spectral calibration only after deleting all processed plates associated with the spectral plate.

Processed plates are associated with a spectral plate if the plates used the spectral plate's calibration as the active calibration when it was processed.

� Delete spectral plates that are not associated with

any processed plates directly in the Plate

Manager.

Option one: Delete a spectral plate after performing the Cleanup Processed Plate procedure.

Note: Use this option if you want to delete many spectral plates, and you don't mind deleting all processed plate data from the database.

1. Clean up all processed plates by using the
Database Manager. See "Deleting Processed Frame Data" on page 38.
2. Select the Plate Manager view.
3. Select the spectral plate that you want to delete.
4. Click Delete.
5. Repeat steps 3 and 4, as needed.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 2 Computer Maintenance
Deleting Records from the Database
Option two: Delete a spectral plate after manually deleting the associated processed plates.
Note: Use this option if you are trying to delete one or two spectral plates but do not want to delete all the processed plates in the database.
1. Select the Plate Manager view.
2. Search for and select a processed plate associated
with the spectral calibration you are trying delete.
3. Click Delete to delete the processed plate.
4. Repeat steps 2 and 3 until all associated
processed plates are deleted.
5. Search for and select the spectral plate that you
want to delete.
6. Click Delete.

Notes
40

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 3
Managing Software License for 3130 Series Data Collection Software 4

Overview This chapter covers the following topics:

Manage software licenses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

Obtain and activate a software license . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

Renew a software license . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 3 Managing Software License for 3130 Series Data Collection Software 4
Manage software licenses
Manage software licenses
The 3130 Series Data Collection Software 4 requires a license to run.
IMPORTANT! If you replace or add a network card in the computer running the software, or relocate the software to a new computer, contact Life Technologies to update your license for the new network card or computer.
Obtain and activate a software license
The 3130 Series Data Collection Software 4 Software Activation dialog box is displayed when you start the software if no license is installed and activated on your computer.
This task is typically performed by the Life Technologies service representative during installation of the instrument.
1. Ensure that all network cards in the computer are
enabled.
IMPORTANT! You can run the 3130 Series Data Collection Software 4 using only the network cards enabled when you activate the software license. For example, if you activate the software when your wireless network card is disabled, you will not be able to run the software when the wireless network card is enabled.

Notes
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Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 3 Managing Software License for 3130 Series Data Collection Software 4
Obtain and activate a software license
2. Display the Software Activation dialog box by
starting the 3130 Series Data Collection Software 4.
3

3. Obtain the license key. The license key is
provided on the 3130 Series Data Collection Software 4 CD case, or in an email from Life Technologies.
4. Request the software license file by performing
steps 1a, 1b, and 1c as listed on the activation screen.
IMPORTANT! Keep a record of the email address used to activate the software license. You must use the same email address to renew the software license when it expires.
5. Obtain the software license file from your email.
6. Make a copy of the software license file and keep
in a safe location.
7. Copy the software license file to the desktop of
the 3130 Series Data Collection Software 4 computer.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 3 Managing Software License for 3130 Series Data Collection Software 4
Renew a software license
8. If the Software Activation dialog box has closed,
start the 3130 Series Data Collection Software 4 to open it.
9. Click Browse, then navigate to the software
license file saved on your computer.
10. Click Install and Validate License. A message
is displayed when the license is installed and validated.
11. Click Close.
Renew a software license
1. Ensure that all network cards in the computer are
enabled.
2. Display the Software License Renewal dialog
box by doing either of the following: � Select Activate License Now in the Warning:
License Will Expire Soon dialog box that is displayed 8�30 days prior to expiration.

� Click Yes in the Critical Warning: License Will Expire Soon dialog box that is displayed within 7 days of expiration.

Notes
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Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 3 Managing Software License for 3130 Series Data Collection Software 4
Renew a software license
3. Choose Activate/Install License Now to display
page shown at right. Click Reinstall License in the lower-left Corner.
3

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 3 Managing Software License for 3130 Series Data Collection Software 4
Renew a software license
4. Complete the License Renewal dialog box as
described below:
5. Enter the email address used to activate the
software license.
IMPORTANT! You must use the same email address to activate and renew the software license. If you do not have the activation email address available, enter any email address, click the licensing link in the Software Renewal dialog box, then click Contact Support in the License Renewal web page displayed.
6. Request the renewed software license file by
performing step 1c as listed on the renewal screen.
7. Obtain the renewed software license file from
your email.
8. Copy the renewed software license file to the
desktop of this computer.
9. Click Browse, then navigate to the renewed
software license file saved on your computer.
10. Click Install and Validate License. A message
is displayed when the license is installed and validated.
11. Click Close.

Notes
46

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 4
Troubleshooting

Overview

This chapter includes troubleshooting the following topics:
Instrument Startup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 Instrument Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 Spatial Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 Spectral Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52 Plate Linking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 Run Performance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

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Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 4 Troubleshooting
Instrument Startup

Instrument Startup

Troubleshooting instrument startup (see also H1Heading1"Instrument Status" on page 49)

Observation

Possible Cause

Recommended Action

No communication between the instrument and the computer. The event viewer is blank.

Incorrect Ethernet configuration.

Check the configuration of the IP address.
1. Select Start > All Programs > Accessories > Command Prompt.
2. At the C:\ prompt, type IPconfig /all.
3. Press Enter. The command prompt window displays information on the network.
4. Ensure the IP address for Ethernet adapter 1 is set for the machine (i.e., the motherboard Ethernet connection). The correct IP address is: 192.168.0.1
Note: The local IT group should use Adapter 2 for networking.

Instrument red light is blinking. Incorrect start up procedure.

Start up in the following sequence: 1. Log out of the computer. 2. Turn off the instrument. 3. Boot up the computer. 4. After the computer has booted completely, turn
the instrument on. Wait for the green status light to come on. 5. Launch the Data Collection software.

Data Collection software will not launch.

Applications in the Service Console did not start properly.
(It takes several minutes before data collection software opens.)

Restart the computer.

Computer screen is frozen.

Communication error.

There will be no loss of data. However, if the instrument is in the middle of a run, wait for the run to stop. Then, exit the Data Collection software and restart as described above.

Autosampler does not move to the forward position.

Possible communication error.
Oven or instrument door is not closed.

Restart the system, and then press the Tray button.
1. Close and lock the oven door. 2. Close the instrument doors. 3. Press the Tray button.

Instrument does not respond to commands immediately after closing the doors.

Autosampler reinitializes its location.

Wait for the autosampler to home before continuing.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 4 Troubleshooting
Instrument Status

Instrument Status

Troubleshooting instrument status (see also H1Heading1"Instrument Startup" on page 48)

Observation

Possible Cause

Recommended Action

The yellow light in the LED panel on the bottom left corner of the instrument remains solid yellow.

A Power override is enabled.

Cycle power on the system in the following order:
a. Boot/Reboot the computer workstation. b. Log in to the computer workstation. c. Ensure that the buffer, water, and waste
reservoirs are in their appropriate stations. d. Close the oven door. e. Close the stacker drawer. f. Close the instrument doors. g. Cycle power on the Applied Biosystems
3130 Series Genetic Analyzer.

The account password for User 1. Boot/Reboot the instrument and computer

name "3130User" has changed

workstation.

or has been entered with the wrong case (the user name and

2. Log in, taking care to type 3130User with the capitalization shown here.

password are case-sensitive).

The account password for User name "3130User" is expired or corrupt.

Start up in the following sequence:
1. Log out of the computer and turn off the instrument.
2. Boot up the computer.
3. After the computer has booted completely, turn the instrument on. Wait for the green status light to come on.
IMPORTANT! Do not launch the Data Collection software.
4. Reset the account password: a. Right click "My Computer". b. Click "Manage". c. In the Computer Management window, click "Local Users and Groups", then click "User". d. On the right side of the window, right-click "3130User", then select "Set Password". e. Set the password to "3130User", confirm the password entry, then click "OK". f. In the Computer Management window, rightclick "3130User" and select "Properties". g. Confirm "User cannot change password" and "Password never expires" are selected. Click "OK" then exit out of the Computer Management window.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 4 Troubleshooting
Instrument Status

Troubleshooting instrument status (see also H1Heading1"Instrument Startup" on page 48) (continued)

Observation

Possible Cause

Recommended Action

The yellow light in the LED panel on the bottom left corner of the instrument remains solid yellow. (continued)

The original communication cable is loose, has been replaced with a standard cable or is improperly attached.

� Only the communication cable shipped with the instrument can be used as it is specifically designed for the instrument.
� Confirm that the original communication cable is attached snugly, with the "computer"-labeled end attached to computer and "instrument"labeled end attached to instrument.

Computer network configuration or access has changed.

Confirm the following are unchanged:
� The name of the computer workstation � The firewall/antiviral software on the computer
workstation � The original IP address of the
computer/network card � The computer configuration for network access � The Operating System/Service Pack � The 3130 Series Data Collection Software 4
runs on Windows 7 SP 1 professional 32-bit operating system

The instrument software cannot find the "3130calib.ini" file.

Confirm that the Instrument Data Collection Software "3130calib.ini" file is in the appropriate location:
C:/AppliedBiosystems/Firmware

If the problems persists, contact Applied Biosystems Technical Support or Technical Assistance Center.

Notes
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Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 4 Troubleshooting
Spatial Calibration

Spatial Calibration

Troubleshooting spatial calibration

Observation

Possible Cause

Recommended Action

Unusual peaks or a flat line for the spatial calibration.

The instrument may need more time to reach stability. An unstable instrument can cause a flat line with no peaks in the spatial view.

Repeat the spatial calibration.

Improper installation of the detection cell.

Reinstall the detection cell to reposition and make sure it fits in the proper position. If the calibration fails again: 1. Fill the capillaries with polymer. 2. Repeat the spatial calibration.

Persistently bad spatial calibration results.

Broken capillary resulting in a

Check for a broken capillary, particularly in the

bad array fill.

detection cell area. If necessary, replace the

capillary array using the Install Array Wizard.

Bad capillary array.

Replace the capillary array, and then repeat the calibration. Call Technical Support if the results do not improve.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 4 Troubleshooting
Spectral Calibration
Spectral Calibration
Tip: Magnifying the Spectral Profile or Raw Data 1. In the tree pane of the Data Collection
software, click GA Instruments > ga3130xl or
ga3130 > instrument 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 the r key to reset the view.

Magnified area of that spectral profile

Troubleshooting spectral calibration

Observation

Possible Cause

Recommended Action

No signal.

Incorrect preparation of sample.

Replace samples with fresh samples prepared with fresh Hi-DiTM formamide.
CHEMICAL HAZARD. Formamide causes eye, skin, and respiratory tract irritation. It is a possible reproductive and birth defect hazard. Read the SDS, and follow the handling instructions. Wear appropriate protective eyewear, clothing, and gloves.

Bubbles in sample tray.

Centrifuge samples to remove bubbles.

Autosampler not correctly aligned. The capillary tips may be hitting the bottom of the wells, or they may not be touching the samples.

Check the autosampler calibration. If necessary, recalibrate the autosampler using the Autosampler Calibration Wizard.

Notes
52

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 4 Troubleshooting
Spectral Calibration

Troubleshooting spectral calibration (continued)

Observation

Possible Cause

Recommended Action

If the spectral calibration fails, or if a message displays "No candidate spectral files found."

Blocked capillary.

Refill capillary array. You may have to install a fresh array or consider that capillary non-usable for purposes of planning your runs.

Incorrect chemistry file, dye set, and/or Correct the files and rerun the

run module selected.

calibration.

Insufficient filling of array.

Check for broken capillaries and refill the capillary array.

Expired matrix standards or old reagents.

Check the expiration date and storage conditions of the matrix standards and/or reagents. If necessary, replace with a fresh lot.

Data Error - One or more peaks fall

One or more peaks fall below the

Rerun the spectral standards, and if

below the minimum required amplitude minimum required amplitude of 750. necessary, increase the amount of

of 750.

spectral standard added.
4

Spikes in the data or "Bad dye order Expired polymer.

Replace the polymer with a fresh lot

detected" error message.

using the Replenish Polymer Wizard.

! WARNING CHEMICAL HAZARD.
POP-4, POP-6, and POP-7 polymers cause eye, skin, and respiratory tract irritation. Read the SDS, and follow the handling instructions. Wear appropriate protective eyewear, clothing, and gloves.

Bubbles in the polymer system.

Select the Bubble Remove Wizard to clear the bubbles.

Possible contaminant or crystal deposits in the polymer.

Properly bring the polymer to room temperature; do not heat to thaw rapidly. Swirl to dissolve any solids.
Replace the polymer if it has expired.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 4 Troubleshooting
Spectral Calibration

Troubleshooting failing capillaries
Failing Capillary assigned a spectral profile If a capillary fails, it is automatically assigned the spectral profile of its nearest passing capillary. For applications where pull-up and pull-down peaks cause critical errors, repeat the spectral calibration and use a unique spectral for each capillary array length and polymer type.

Manually Overriding a Spectral Profile To override a spectral calibration profile:
1. Review the data.
2. In the plate diagram, select the capillary spectral profile you want to override.
3. Click Override Spectral. The Override Spectral dialog box opens.

Capillary 10 selected

4. Select a new capillary value from the drop-down list. 5. Click OK.

6. Click Save.

7. In "Save the modified spectral calibration" dialog box, enter a new name, then click Save.
8. Select the just saved spectral calibration and click Set to activate the spectral calibration.

When a Calibration Fails
If the spectral calibration failed, or if you do not like the appearance of the passed calibration, try one or more of the following:
� Verify that the correct chemistry and run module were selected. If not, correct, and then repeat the run. � Verify the freshness of the reagents used.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 4 Troubleshooting
Spectral Calibration

Troubleshooting failing capillaries (continued)
If All Capillaries Fail If all capillaries fail, no spectral profiles are created. However, the raw data can still be viewed.
Viewing the Raw Data for a Failed Spectral Calibration 1. In the tree pane of the Data Collection software, click
GA Instruments > ga3130 or ga3130xl > instrument name > Spectral Viewer, then review the spectral data. You observe: � The window displays data from the previous passing spectral calibration. � This System Status is blinking red.
2. Click Instrument Status > Event Log to view the Event and Errors messages.

System failure, check Event Log

3. Click Spectral Viewer.
4. In the Dye Set drop-down list, select the dye set for the failed calibration.
5. In the List of Calibrations drop-down list, select the failing run. The failing run has an asterisk (*) next to its name.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 4 Troubleshooting
Spectral Calibration
Troubleshooting failing capillaries (continued) The window is updated with the information from the failed E5 spectral calibration.
No spectral profile
Raw data
Failed capillaries

6. Use the list of questions below when reviewing the raw data to determine the cause of the failure. � How many peaks?
� Any extraneous peaks?
� Peak order? � Peak shape and signal strength?
� Negative peaks?
� Additional peaks (positive or negative) under the main color peak?
Note: It is helpful to magnify the raw data for the review process (see THL-TableHeadLeft"Tip: Magnifying the Spectral Profile or Raw Data" on page 52).

Raw data

Magnified raw data

Notes
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Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 4 Troubleshooting
Plate Linking

Plate Linking

Troubleshooting plate linking

Plate does not link.

Spatial calibration was not performed.

1. Perform a spatial calibration.
2. Relink the plate(s) in the Run Scheduler.

The plates in the Run Scheduler were linked, but now are unlinked.

A Wizard was used after linking a plate, but before starting a run � automatically unlinking the plate.

Relink the plate(s) in the Run Scheduler.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 4 Troubleshooting
Plate Linking

Troubleshooting plate linking (continued)

The plate links, but System Status changes from green to red.

A different length capillary array was installed, and the appropriate active spectral calibration was not selected or does not exists.

1. View the error messages in the Event Log.
2. In the Spectral Calibration Viewer, set the active spectral calibration for the dye set and array length.
3. If one does not exist, create a new spectral calibration for the dye set and array length you are using, then set it as the active spectral calibration.
4. Relink the plate(s) in the Run Scheduler.

The capillary array length and/or polymer type selected in the Instrument Protocol does not match capillary array length and/or polymer type stored in the database.

Correct the Instrument Protocol, or
1. Use the Wizards to update the information in the database.
2. Set or create an active spectral calibration.
3. Relink the plate.

The database and/or E drive is full.

To check the available space:
1. View the error messages in the Event Log.
2. Proceed to H1aHeading1_anywhere"Hard Disk and Database Status" on page 34.
3. Make more space.
4. Relink the plate(s) in the Run Scheduler.

Notes
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Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Run Performance

Chapter 4 Troubleshooting
Run Performance

Troubleshooting using Run validation tests

Run Validation All validation tests must pass before the run starts.

The Test checks...

Look For

Corrective Action

The capillary array length and/or polymer type in the Instrument Protocol against the capillary array length and/or polymer type in the database.

1. System Status changes from green to red.

Correct the Instrument Protocol, or
1. Use the Wizards to update the information in the database.

2. Set or create an active spectral calibration.

3. Relink the plate, then click .

The available space in the database and 2. View the error messages in

E drive.

the Event Log.

To correct: 1. See H1a-Heading1_anywhere"Hard

Disk and Database Status" on page 34

to access information on databases

and sample data storage.

2. Make more space.

3. Click .

If a different length capillary array was installed, and the appropriate active spectral calibration was not selected or does not exist.

To correct:
1. In the Spectral Calibration Viewer, set the active spectral calibration for the dye set and array length you are using.
2. If one does not exist, create a new spectral calibration for the dye set and array length you are using, then set as the active spectral calibration.
3. Click .

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 4 Troubleshooting
Run Performance

Troubleshooting run performance

Observation

Possible Cause

Recommended Action

No peaks in any sample file. Bubbles in the system. No sample injection.

Visually inspect the polymer block for bubbles.
Remove bubbles using the Bubble Remove Wizard.
1. If bubbles persist, select the Water Wash Wizard.
2. If necessary, select the Replenish Polymer Wizard to install fresh polymer. ! WARNING CHEMICAL HAZARD. POP-4, POP-6 and POP-7 polymers cause eye, skin, and respiratory tract irritation. Read the SDS, and follow the handling instructions. Wear appropriate protective eyewear, clothing, and gloves.

Possible contaminant in the polymer path.

Select the Water Wash Wizard.

Possible contaminant or crystal deposits in the polymer bottle.

Bring the polymer to room temperature, swirl to dissolve any deposits.
Replace the polymer if it has expired.
! WARNING CHEMICAL HAZARD. POP-4, POP-6 and POP-7 polymers cause eye, skin, and respiratory tract irritation. Read the SDS, and follow the handling instructions. Wear appropriate protective eyewear, clothing, and gloves.

No signal.

Autosampler calibration is not optimal.

Check the injection with 20-�L samples.
� If the 20-�L samples have adequate signal level, then recalibrate the autosampler using the Autosampler Calibration Wizard.
IMPORTANT! You must power on the instrument to use the new values.
� If the 20-�L samples still have no signal then check the other possible causes.

Bubble at bottom of sample tube.

Centrifuge the sample tubes.

Bent capillary array tips.

Replace the capillary array and recalibrate the autosampler using the Autosampler Calibration Wizard.

Failed reaction.

Repeat reaction.

Cracked or broken capillary.

Visually inspect the capillary array, including the detector window area for signs of breakage.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 4 Troubleshooting
Run Performance

Troubleshooting run performance (continued)

Observation

Possible Cause

Recommended Action

No signal.

Blocked capillary.

Refill capillary array. You may have to install a fresh array or consider that capillary non-usable for purposes of planning your runs.

Signal too high.

Sample concentration is too high.

Dilute the sample.

Decrease the injection time.

Too much DNA added to the reaction, resulting in uneven signal distribution.

Optimize reaction conditions.

Low signal strength.

Degraded formamide.

Use a fresh aliquot of Hi-Di formamide.

CHEMICAL HAZARD. Formamide causes eye, skin, and respiratory

tract irritation. It is a possible reproductive and

birth defect hazard. Read the SDS, and follow

the handling instructions. Wear appropriate protective eyewear, clothing, and gloves.

Pipetting error; not enough sample.

Increase the amount of DNA added.

Recalibrate the pipets.

Sample has high salt concentration.

Dilute with distilled or deionized water.

Desalt using a column purification method.

Insufficient mixing.

Vortex the sample thoroughly, and then centrifuge the tube to condense the sample to the bottom of the tube.

Autosampler out of calibration.

Check the injection with 20-�L samples. If the 20-�L samples have adequate signal levels, then recalibrate the autosampler using the Autosampler Calibration Wizard.
Power off and on the instrument to use the new calibration values.

Weak amplification of DNA.

Reamplify the DNA.

Check DNA quality.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 4 Troubleshooting
Run Performance

Troubleshooting run performance (continued)

Observation

Possible Cause

Recommended Action

Elevated baseline.

Possible contaminant in the polymer path.

Select the Water Wash Wizard.

Possible contaminant or crystal deposits in the polymer.

Bring the polymer to room temperature, swirl to dissolve any deposits.
Replace the polymer if it has expired.
! WARNING CHEMICAL HAZARD. POP-4, POP-6, and POP-7 polymers cause eye, skin, and respiratory tract irritation. Read the SDS, and follow the handling instructions. Wear appropriate protective eyewear, clothing, and gloves.

Poor spectral calibration.

Perform new spectral calibration.

Loss of resolution.

Too much sample injected.

Dilute the sample and re-inject.

Poor quality water.

Use distilled or deionized water.

Poor quality or dilute running buffer.

Prepare fresh running buffer from 10X 3130 buffer with EDTA.
CHEMICAL HAZARD. 10X Genetic Analyzer Buffer with EDTA may cause eye, skin, and respiratory tract irritation. Read the SDS, and follow the handling instructions. Wear appropriate protective eyewear, clothing, and gloves.

Degraded polymer.

Use a fresh supply of polymer.

Capillary array used for more than 100 injections.

Replace with new capillary array.

Degraded formamide.

Prepare fresh Hi-Di formamide and re-prepare samples.
CHEMICAL HAZARD. Formamide causes eye, skin, and respiratory tract irritation. It is a possible reproductive and birth defect hazard. Read the SDS, and follow the handling instructions. Wear appropriate protective eyewear, clothing, and gloves.

High salt concentration in samples.

Use a recommended protocol for salt removal. Dilute salts with water.

Notes
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Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 4 Troubleshooting
Run Performance

Troubleshooting run performance (continued)

Observation

Possible Cause

Recommended Action

Poor resolution in some capillaries.

Insufficient filling of capillary array.

Refill the capillary array and look for polymer leakage. If problem persists contact Technical Support.

Re-inject the same samples.

Poor quality samples.

Check the sample preparation.

No current.

Water placed in buffer reservoir position 1.

Replace with fresh 1X running buffer.

Not enough buffer in anode reservoir.

Add buffer up to the fill line.

Buffer too dilute.

Prepare 1X running buffer.

Add 3 mL 10X Genetic Analyzer Buffer with EDTA to 27 mL deionized water.

CHEMICAL HAZARD.

10X Genetic Analyzer Buffer with EDTA may

cause eye, skin, and respiratory tract irritation.

Read the SDS, and follow the handling

instructions. Wear appropriate protective

eyewear, clothing, and gloves.

Bubble(s) present in the lower polymer block and/or the array and/or tubing.

Pause run and inspect for bubbles hidden in the tubing connectors.
Select the Bubble Remove Wizard to remove the bubbles.

Elevated current.

Degraded polymer.

Open fresh supply of polymer and use Replenish Polymer Wizard.

Incorrect buffer dilution.

Prepare 1X running buffer.
Add 3 mL 10X Genetic Analyzer Buffer with EDTA to 27 mL deionized water.
CHEMICAL HAZARD. 10X Genetic Analyzer Buffer with EDTA may cause eye, skin, and respiratory tract irritation. Read the SDS, and follow the handling instructions. Wear appropriate protective eyewear, clothing, and gloves.

Arcing in the lower polymer block.

Inspect the lower polymer block for discoloration or damage. Replace the lower polymer block if necessary.

Fluctuating current.

Bubble in polymer block.

Pause run and inspect for bubbles hidden in the tubing connectors.
Select Bubble Remove Wizard to remove the bubbles.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 4 Troubleshooting
Run Performance

Troubleshooting run performance (continued)

Observation

Possible Cause

A slow leak may be present in the system.

Incorrect buffer concentration.

Poor performance of capillary array used for fewer than 100 runs.

Not enough buffer in anode reservoir. Arcing.
Poor quality samples, possible cleanup problems. Poor quality formamide.

Incorrect buffer.

Migration time becomes progressively slower.

Leak in system.
Improper filling of the system with polymer.
Expired polymer.

Recommended Action
Check polymer blocks for leaks. Tighten all fittings.
Prepare 1X running buffer.
Add 3 mL 10X Genetic Analyzer Buffer with EDTA to 27 mL deionized water.
CHEMICAL HAZARD. 10X Genetic Analyzer Buffer with EDTA may cause eye, skin, and respiratory tract irritation. Read the SDS, and follow the handling instructions. Wear appropriate protective eyewear, clothing, and gloves.
Add buffer up to the fill line.
Check for moisture in and around the septa, the reservoirs, the oven, and the autosampler.
Desalt samples using a recommended purification protocol.
Prepare fresh Hi-Di formamide and re-prepare samples.
CHEMICAL HAZARD. Formamide causes eye, skin, and respiratory tract irritation. It is a possible reproductive and birth defect hazard. Read the SDS, and follow the handling instructions. Wear appropriate protective eyewear, clothing, and gloves.
Use 10X Genetic Analyzer Buffer with EDTA to prepare 1X running buffer.
CHEMICAL HAZARD. 10X Genetic Analyzer Buffer with EDTA may cause eye, skin, and respiratory tract irritation. Read the SDS, and follow the handling instructions. Wear appropriate protective eyewear, clothing, and gloves.
Tighten the tubing connectors and array knob.
Polymer delivery pump may need to be serviced. Call a service representative.
Check expiration of polymer. If necessary, change the lot.

Notes
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Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 4 Troubleshooting
Run Performance

Troubleshooting run performance (continued)

Observation

Possible Cause

Recommended Action

Migration time becomes progressively faster.

Water in polymer system, resulting in diluted polymer.

Use Bubble Remove Wizard to add polymer to system.

Buffer valve leakage

Check the buffer valve pin and see if it closes correctly.

Extra peaks in the electropherogram.

Data off scale. Possible contaminant in sample.

Dilute the sample and re-inject the sample. Re-amplify the DNA.

Sample renaturation.

Peaks exhibit a shoulder in GeneMapper software applications.

Sample renaturation.

Heat-denature the sample in good-quality formamide and immediately place on ice.

CHEMICAL HAZARD. Formamide causes eye, skin, and respiratory

tract irritation. It is a possible reproductive and

birth defect hazard. Read the SDS, and follow

the handling instructions. Wear appropriate protective eyewear, clothing, and gloves.

Heat-denature the sample in good-quality

formamide and immediately place on ice.

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

Error message, "Leak detected" appears. The run aborts.

Bubbles in the polymer system. Leak in the polymer system.

Select the Bubble Remove Wizard to clear bubbles.
Check for evidence of leaks. Tighten the tubing connectors and array knob.

Buffer valve leakage.

Check the buffer valve pin and see if it closes correctly.

Buffer jar overflows very quickly with polymer.

Bubbles in the polymer path.

Check for bubbles and remove if present.

(Overuse of the Bubble Remove Wizard)

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 4 Troubleshooting
Run Performance

Troubleshooting run performance (continued)

Observation

Possible Cause

Detection cell comes out while replacing the capillary array. Replacing the cell in the correct orientation is difficult.

Improperly placed detection cell.

Detection cell stuck. It is difficult to remove when changing the capillary array.

Recommended Action
Loosen the array knob. Close the detection block door. Retighten the array knob.
To loosen the detection cell: 1. Undo the array knob and pull the polymer
block towards you to first notch. 2. Hold both sides of the capillary array around
the detection cell area, and apply gentle pressure equally on both sides. 3. Remove the capillary comb from the holder in oven. 4. Release.

Notes
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Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 5

Data Collection Software Advanced Functions

Overview

This chapter covers the following topics:
Customizing Run Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68 Run Priority Scheduling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70 Edit > Fill Down Special Option for Plate Records . . . . . . . . . . . . . . . . . . . . . . . . . 73 Multi-application (Mixed) Plate Record . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 5 Data Collection Software Advanced Functions
Customizing Run Modules
Customizing Run Modules
You can modify default run modules to suit your particular needs.
1. Click GA Instruments > ga3130xl or
ga3130 > instrument name > Module Manager.

2. Click

. The Run Module Editor dialog

box opens.

3. Complete the Run Module Editor dialog box:

a. Enter a name for your new module.

b. In the Type drop-down list, select the type

of module (Regular, Spatial, or Spectral).

c. In the Template drop-down list, select a

template module as a basis for the new

module.

3e
Note: You cannot edit a default module installed with the 3130 Series Data Collection Software 4.

4. Optional: Enter a description of your new run
module.

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Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 5 Data Collection Software Advanced Functions
Customizing Run Modules

5. Change to the desired module parameters using allowable ranges shown in the table
below:

Name

Range

Comment

Oven_Temperature

18�65�C

Temperature setting for main oven throughout run.

Poly_Fill_Vol

variable to 38000 counts

Check for amount of polymer available in the PDP.

Current_Stability

0�2000 �Amp

Maximum current variation during electrophoresis

PreRun_Voltage

0�15 kV

Pre run voltage setting before sample injection.

PreRun_Time

1�1000 sec

Prerun voltage time.

Injection_Voltage

0�15 kV

Injection voltage setting for sample injection.

Injection_Time

1�600 sec

Sample injection time.

Run_Voltage

0�15 kV

Final run voltage.

Voltage_Number_Of_Steps 0�100 steps

Number of voltage ramp steps to reach Run_Voltage. Applied Biosystems recommends that you do not change this value.

Voltage_Step_Interval

0�60 sec

Dwell time at each voltage ramp step. We recommend that you do not change this value.

Data_Delay_Time Run_Time

1�3600 sec

Time from the start of separation to the start of data collection.

300�14000 sec Duration data is collected after

Data_Delay_Time.

6. Click OK.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 5 Data Collection Software Advanced Functions
Run Priority Scheduling

Run Priority Scheduling

Priority Values The user-definable run priority scheduling function allows you to schedule runs in
custom order providing flexibility when scheduling runs.
A default value of 100 is assigned to each sample in the plate record. Changing the value to a smaller number causes that set of 16 or 4 samples to run before the others in the injection list.

Scheduling Examples

Default Run Scheduling

Using a 96-well Plate and 16 Capillary Array
In this example, 100 is the priority value for all samples in the plate record and the default run priority schedule is used (see table below). Samples A07�H08 called out on the plate record, correspond to Run 4 as displayed in the Run Scheduler > Run View window.

Well Numbers Run Number Priority

A01�H02

A03�H04

A05�H06

Well Numbers Run Number Priority

A07�H08

A09�H10

A11�H12

Default run priority schedule, samples in wells A07�H08 are scheduled as Run 4.

Notes
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Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 5 Data Collection Software Advanced Functions
Run Priority Scheduling

User-definable Run Priority Scheduling

In this example, the priority value for sample G07 is arbitrarily set to 80, a lower number than 100, forcing the software to give the sample a higher run priority. All other samples remain 100. Sample well G07 is contained in the A07�H08 injection set. All 16 samples now correspond to Run 1, as displayed in the Run Scheduler > Run View window.
The table below shows the change in the run priority schedule.

Well Numbers A07�H08 A01�H02 A03�H04 A05�H06 A09�H10 A11�H12

Run Number Priority 1 2 3 4 5 6

5
User defined run priority schedule, samples in wells A07�H08 are scheduled as Run 1 due to G07 sample assigned a value of 80.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 5 Data Collection Software Advanced Functions
Run Priority Scheduling
The rest of the samples are run after the samples in wells A07�H08. Samples in wells A01�H02 are now scheduled as Run 2.
User defined run priority schedule, samples in wells A01�H02 are now scheduled as Run 2.

Notes
72

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 5 Data Collection Software Advanced Functions
Edit > Fill Down Special Option for Plate Records

Edit > Fill Down Special Option for Plate Records

Using Fill Down Special Option
Based on your plate type (96- or 384-well) and capillary array (16 or 4 capillaries), the software automatically fills in the appropriate well positions for a single run.
The Fill Down Special option works with all plate records (Spectral, Sequencing Analysis, GeneMapper�software, and Mixed plates).

Creating and Completing the Plate Record

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

2. Click

to open the New Plate Dialog

dialog box.

3. Complete the information in the New Plate

Dialog box, then click

to open the Plate

Editor.

4. Complete the columns for a single well position.

Note: You can start at any well position, the software automatically fills up or down based on

the default run scheduling patterns.

5. Highlight the entire row.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 5 Data Collection Software Advanced Functions
Edit > Fill Down Special Option for Plate Records
6. Select Edit > Fill Down Special.

7. Click

to save the plate record.

Notes
74

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 5 Data Collection Software Advanced Functions
Edit > Fill Down Special Option for Plate Records
Examples of Fill Examples of completed plate records and run scheduling for the 3130 and 3130xl Down Special instruments, and 96- and 384-well plates are shown below.

96-well plate on a 3130xl genetic analyzer
5

Notes

384-well plate on a 3130xl genetic analyzer

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 5 Data Collection Software Advanced Functions
Edit > Fill Down Special Option for Plate Records

96-well plate on a 3130 genetic analyzer

Notes
76

384-well plate on a 3130 genetic analyzer Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 5 Data Collection Software Advanced Functions
Multi-application (Mixed) Plate Record

Multi-application (Mixed) Plate Record

Protocols for a Mixed Plate Record

To run a mixed plate containing sequencing and fragment analysis samples, the following files are required:
� Sequencing analysis � Results Group � Instrument Protocol � Analysis Protocol
� Fragment analysis � Results Group � Instrument Protocol � Files created in GeneMapper software

Creating Spectral For every dye set and capillary array length combination you use, a separate spectral Calibrations calibration must be created.

Setting the Active Spectral
Calibration

If you changed the capillary array length to run multi-application samples, you must set the active spectral calibration for each dye set used. See the Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide (Part no. 4477796) on how to set
the active calibrations once calibrations are performed for each dye set on each capillary
length.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 5 Data Collection Software Advanced Functions
Multi-application (Mixed) Plate Record

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

2. Click

The New Plate Dialog dialog box opens.

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 Mixed in the Application drop-down

list.
3b
d. Select 96-well or 384-well in the Plate Type

drop-down list.
3c

e. Type a name for the owner and operator.

f. Click

3f
The Integrated Plate Dialog box opens.

Notes
78

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 5 Data Collection Software Advanced Functions
Multi-application (Mixed) Plate Record
4. In the Set Application pane:
4a
a. On the plate map, click a well position. The run of 16 or 4 capillaries is outlined.
b. In the Application drop-down list select the appropriate application.

c. Repeat the process for additional samples and applications.

4b
5

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 5 Data Collection Software Advanced Functions
Multi-application (Mixed) Plate Record

5. Create the Sequencing sample sheets (plate

record).

a. On the plate map, click a well position that represents a sequencing sample.

b. Click Sample Sheet.

5b
The Sequencing Analysis Plate editor opens.
c. Complete the plate record. Note: The well column contains only those wells that were designated as sequencing samples on the plate map.
d. Click . You are automatically returned to the Integrated Plate dialog box.

Notes
80

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 5 Data Collection Software Advanced Functions
Multi-application (Mixed) Plate Record

6. Create the GeneMapper software sample sheet
(plate record).

a. On the plate map, click a well position that

represents a GeneMapper software sample.

b. Click Sample Sheet to open the GeneMapper software Plate editor.

c. Complete the plate record.

d. Click OK.

7. Click Done.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 5 Data Collection Software Advanced Functions
Multi-application (Mixed) Plate Record

Notes
82

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 6
Reference Tables

Overview

This chapter covers the following topics:
Sequencing Summary Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84 Fragment Analysis Run Module Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89 Run Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 6 Reference Tables
Sequencing Summary Tables

Sequencing Summary Tables

Performance Sequencing Resolution Performance and Specification Table

Type of Run

Capillary Length
(cm)

Polymer Type

Run Modulea

Run Time (min)

24 hr Throughput (number of samples)

3130
Genetic Analyzer

3130xl
Genetic Analyzer

KBTM
Basecaller QV20 LORb c

Ultra rapid

POP-4� UltraSeq36_POP4

144

576

400

POP-7TM UltraSeq36_POP7

164

656

500

Rapid

POP-6TM RapidSeq36_POP6

384

500

POP-7TM RapidSeq36_POP7

384

600

Fast

POP-7TM FastSeq50_POP7

384

700

Standard

POP-4� StdSeq50_POP4

100

224

600

POP-6TM StdSeq50_POP6

150

144

600

POP-7TM StdSeq50_POP7

120

192

850

Long read

POP-4� LongSeq80_POP4

210

700

POP-7TM LongSeq80_POP7

170

128

950

a When using the BigDye� XTerminator Purification Kit, choose the BDx version of the Run Modules; for example, BDx_UltraSeq36_POP7.
b 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.
c 98.5% basecalling accuracy, less than 2% Ns.

Notes
84

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 6 Reference Tables
Sequencing Summary Tables

Calibration Sequencing Dye Sets, Calibration Standards, and Chemistry File Standard Table

Sequencing Chemistry

Dye Set

Spectral Calibration Standard

Chemistry File

� BigDye� Terminator v3.1 Cycle Sequencing Kit
� BigDye� Direct Cycle Sequencing Kit � dGTP BigDye� Terminator v 3.0 Cycle
Sequencing Ready Reaction Kita
� BigDye� Terminator v1.1 Cycle Sequencing Kit
� BigDye� Primer Cycle Sequencing Kits � dGTP BigDye� Terminator v1.0 Cycle
Sequencing Ready Reaction Kita
� dRhodamine Dye Terminator Cycle Sequencing Kit

Z_BigDyeV3

BigDye� v3.1 Matrix Standards
BigDye� v3.1 Terminator Sequencing Standard

Matrix Standard Sequence Standard

E_BigDyeV1

DS-01 Matrix Standards
BigDye� v1.1 Terminator Sequencing Standard

Matrix Standard Sequence Standard

dRhodamine Matrix Standards Kit Matrix Standard

a 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.

Dye Set and Run Sequencing Kits, Dye Sets, Polymer Type and Run Modules Modules

POP-4� Polymer

POP-6TM Polymer

POP-7TM Polymer

UltraSeq36 StdSeq50 LongSeq80 RapidSeq36 StdSeq50 UltraSeq36 RapidSeq36 FastSeq50 StdSeq50 LongSeq80

Sequencing Chemistry

Dye Set

BigDye� Terminator v3.1 Cycle Sequencing Kit Z_BigDye

BigDye� Direct Cycle Sequencing Kit

---------- --

dGTP BigDye� Terminator v3.0 Cycle Sequencing Ready Reaction Kit

--------------------

BigDye� Terminator v1.1 Cycle Sequencing Kit E_BigDye

dGTP BigDye� Terminator v1.0 Cycle

--------------------

Sequencing Ready Reaction Kit

dRhodamine Dye Terminator Cycle Sequencing Kit

----------

BigDye� Primer Cycle Sequencing Kits

------ ----------

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 6 Reference Tables
Sequencing Summary Tables

KB Basecaller Basecaller and DyeSet/Primer Files Using KB Basecalling Table

3130/3130xl Genetic Analyzer Basecaller and DyeSet/Primer Files Used with BigDye� Terminator Chemistry and KB Basecalling

DNA Sequencing Chemistry
BigDye� Terminator v1.1 Cycle Sequencing Kit
BigDye� Terminator v3.1 Cycle Sequencing Kit
BigDye� Direct Cycle Sequencing Chemistry

Polymer POP-4� POP-6TM POP-7TM
POP-4� POP-6TM POP-7TM
POP-7TM

KB Basecalling Run Module
UltraSeq36_POP4 StdSeq50_POP4 LongSeq80_POP4 RapidSeq36_POP6 StdSeq50_POP6 UltraSeq36_POP7 RapidSeq36_POP7 FastSeq50_POP7 StdSeq50_POP7 LongSeq80_POP7 UltraSeq36_POP4 StdSeq50_POP4 LongSeq80_POP4 RapidSeq36_POP6 StdSeq50_POP6 UltraSeq36_POP7 RapidSeq36_POP7 FastSeq50_POP7 StdSeq50_POP7 LongSeq80_POP7 UltraSeq36_POP7 RapidSeq36_POP7 FastSeq50_POP7 StdSeq50_POP7

DyeSet/Primer KB_3130_POP4_BDTv1.mob KB_3130_POP6_BDTv1.mob KB_3130_POP7_BDTv1.mob
KB_3130_POP4_BDTv3_.mob KB_3130_POP6_BDTv3.mob KB_3130_POP7_BDTv3.mob
KB_3130_POP7_BDTv3direct.mob

Basecaller KB.bcp

Notes
86

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 6 Reference Tables
Sequencing Summary Tables

ABI Basecaller Table and Dye Terminator Kits

Basecaller and DyeSet/Primer Files Using ABI Basecalling with Dye Terminator Chemistry

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

DNA Sequencing Chemistry
BigDye� Terminator v1.1 Kit
BigDye� Terminator v3.1 Cycle Sequencing Kit
dRhodamine Dye Terminator Cycle Sequencing Kit

Polymer POP-4� POP-6TM POP-4� POP-6TM POP-4� POP-6TM

ABI Basecalling Run Module

Basecaller

UltraSeq36_POP4 LongSeq80_POP4 RapidSeq36_POP6 StdSeq50_POP6 UltraSeq36_POP4 LongSeq80_POP4 RapidSeq36_POP6 StdSeq50_POP6 UltraSeq36_POP4 LongSeq80_POP4 RapidSeq36_POP6 StdSeq50_POP6

Basecaller3130POP4UR.bcp
Basecaller3130POP4_80cmv3.bcp
Basecaller3130POP6RRv2.bcp
Basecaller3130POP6SR.bcp
Basecaller3130POP4UR.bcp
Basecaller3130POP4_80cmv3.bcp
Basecaller3130POP6RRv2.bcp
Basecaller3130POP6SRv2.bcp
Basecaller3130APOP4UR.bcp
Basecaller3130POP4_80cmv3.bcp
Basecaller3130POP6RRv2.bcp
Basecaller3130POP6SR.bcp

DyeSet/Primer DT3130POP4LR{BD}v1.mob DT3130POP6{BD}v2.mob DT3130POP4{BDv3}v1.mob DT3130POP6{BDv3}v1.mob DT3130POP4{dRhod}v2.mob DT3130POP6{dRhod}v2.mob

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 6 Reference Tables
Sequencing Summary Tables

ABI Basecaller Table and Dye
Primer Kits

Basecaller and DyeSet/Primer Files Using ABI Basecalling with Dye Primer Chemistry

3130xl Basecaller and DyeSet/Primer Files Used for Dye Primer Chemistry

DNA Sequencing Chemistry
BigDye� Primer Cycle Sequencing Kit

Polymer

ABI Basecalling Run Module

Basecaller

DyeSet/Primer

POP-6TM RapidSeq36_POP6 StdSeq50_POP6

Basecaller3130POP6RRv2.bcp
Basecaller3130POP6SR.bcp

DP3130POP6{BD-21M13}v1.mob DP3130POP6{BD-21M13Rev}v1.mob

Notes
88

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 6 Reference Tables
Fragment Analysis Run Module Specifications

Fragment Analysis Run Module Specifications

Run Modules

Capillary Length
(cm)

Polymer Type

Run Time (min)

24 hr Throughput (GTb)

3130 Analyzer

3130xl Analyzer

High Throughput, Small Size Fragment Analysis

FragmentAnalysis22_POP4

POP-4� 20

SNP22_POP4

Standard Fragment Analysis

FragmentAnalysis36_POP4

POP-4� 45

HIDFragmentAnalysis36_POP4

SNP36_POP4

FragmentAnalysis36_POP7

POP-7TM 35

FragmentAnalysis50_POP4

POP-4� 65

FragmentAnalysis50_POP6

POP-6TM 90

FragmentAnalysis50_POP7

POP-7TM 50

Large Size Fragment Analysis

GS1200_36_POP7

POP-7TM 125

GS1200_50_POP7

POP-7TM 135

Fragment Analysis using Non-Denaturing Polymer

ConformationAnalysis36_CAP

CAP

5,760 5,760
2,560 2,560 3,840 3,290 1,760 1,200 2,300
880 800

23,040 23,040
10,240 10,240 15,360 13,170 7,040 4,800 9,220
3,520 3,200

a Run time depends on customized polymer formulation and run module. b 20 GT (Genotypes)/capillary/injection.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 6 Reference Tables
Fragment Analysis Run Module Specifications

Fragment Analysis
Application/Kit and Run Modules

The table below lists the Applied Biosystems kit types, with the available run module(s) and dye sets.

Module

Application/Kit

SNP22_POP4 SNP36_POP4 HTSNP36_POP7 FragmentAnalysis22_POP4 FragmentAnalysis36_POP4 FragmentAnalysis36_POP7 FragmentAnalysis50_POP4 FragmentAnalysis50_POP6 FragmentAnalysis50_POP7 HIDFragmentAnalysis36_POP4 ConformationAnalysis36_CAP

SNaPshot� Multiplex System

E5 E5

Custom oligos
Single Strand Conformation Polymorphism (SSCP) Analysis using non-denaturing Conformational Analysis Polymer (CAP) 4-Dye Stockmarks� Kits (bovine and canine) 5-Dye Stockmarks� Kit (equine) AFLP� Kits 4-Dye AmpFlSTR� Kits 5-Dye AmpFlSTR� Kits

D, F, D, F, D, F, D, F, D, F, D, F, G5 G5 G5 G5 G5 G5
G5a
F
G5 F
F G5

a Adjust Dye Set depending on dyes used. Use filter set G5 if using the GeneScan 600 LIZ Size Standard, along with the Matrix Standard Set DS-33. Use filter set D if using the Gene Scan 500 ROX Size Standard.

AmpFlSTR Kit Table

Kits
AmpFlSTR� COfiler� Kit AmpFlSTR� Profiler Plus� Kit AmpFlSTR� Profiler Plus� ID Kit AmpFlSTR� Profiler� Kit AmpFlSTR� SGM Plus� Kit Other 4-Dye AmpFlSTR� Kits

HIDFragmentAnalysis36_POP4 F

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 6 Reference Tables
Fragment Analysis Run Module Specifications

Kits

HIDFragmentAnalysis36_POP4

AmpFlSTR� SEfiler PlusTM Kit

AmpFlSTR� Identifiler� Kit

AmpFlSTR� YfilerTM Kit

AmpFlSTR� Identifiler� Plus Kit

AmpFlSTR� Identifiler� Direct Kit

AmpFlSTR� SinofilerTM Kit

AmpFlSTR� MiniFilerTM Kit

AmpFlSTR� NGMTM Kit

AmpFlSTR� NGM SelectTM Kit

Other 5-Dye AmpFlSTR� Kits

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 6 Reference Tables
Fragment Analysis Run Module Specifications

Calibration Fragment Analysis Dye Sets, Calibration Standards, and Chemistry File Standards Table

Fragment Analysis Chemistry

Dye Set Spectral Calibration Standard

Chemistry File

� Custom oligos
� Custom oligos
� AFLP� kits � Stockmarks� Kits 4-dye (bovine and canine) � AmpFlSTR� COfiler� Kit � AmpFlSTR� Profiler� Kit � AmpFlSTR� Profiler Plus� Kit � AmpFlSTR� Profiler Plus� ID Kit � AmpFlSTR� SGM Plus� Kit � Other 4-Dye AmpFlSTR Kits
� SNaPshot� Multiplex System
� Stockmarks� Kit 5-dye (equine) � Custom oligos � AmpFlSTR� SEfiler PlusTM Kit � AmpFlSTR� YfilerTM Kit � AmpFlSTR� Identifiler Direct� Kit � AmpFlSTR� Identifiler Plus� Kit � AmpFlSTR� MiniFiler Kit � AmpFlSTR� NGM Kit � AmpFlSTR� NGM Select� Kit � Other 5-Dye AmpFlSTR� Kits

DS-30 Matrix Standards

DS-31 Matrix Standards

DS-32 Matrix Standards

DS-02 Matrix Standards

DS-33 Matrix Standards

Matrix Standard

Notes
92

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 6 Reference Tables
Run Modules

Run Modules

Spectral Run Modules

Polymer Type
POP-4�

Capillary Array Length
(cm)
22
36

POP-6TM

POP-7TM

CAP

Run Module
Spect22_POP4 Spect36_POP4 SpectSQ36_POP4 Spect50_POP4 Spect80_POP4 Spect36_POP6 Spect50_POP6 Spect36_POP7 Spect50_POP7 Spect80_POP7 Spect36_CAP

Sequencing Run Modules

Polymer

Capillary Array Length
(cm)

Run Modulea

POP-4�

UltraSeq36_POP4

StdSeq50_POP4

LongSeq80_POP4

POP-6TM

RapidSeq36_POP6

StdSeq50_POP6

POP-7TM

UltraSeq36_POP7

RapidSeq36_POP7

FastSeq50_POP7

StdSeq50_POP7

LongSeq80_POP7

a When using the BigDye� XTerminator Purification Kit, choose the BDx version of the Run Modules; for example, BDx_UltraSeq36_POP7.

Notes

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Chapter 6 Reference Tables
Run Modules
Fragment Analysis Run Modules See "Fragment Analysis Run Module Specifications" on page 89 and "Fragment Analysis Application/Kit and Run Modules" on page 90 for available fragment analysis run modules.

Notes
94

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Appendix A
Parts List

Capillary Arrays
22-cm capillary array 36-cm capillary array 50-cm capillary array 80-cm capillary array
22-cm capillary array 36-cm capillary array 50-cm capillary array 80-cm capillary array

Description 3130 Genetic Analyzer
3130xl Genetic Analyzer

Reagents and Standards
Notes

Description
10X Genetic Analyzer Buffer with EDTA 31xx BigDye� Terminator v1.1 Matrix Standards 31xx BigDye� Terminator v3.1 Matrix Standards BigDye� Terminator v1.1 Cycle Sequencing Kit (100 Reactions) BigDye� Terminator v3.1 Cycle Sequencing Kit (100 Reactions) BigDye� Direct Cycle Sequencing Kit (100 Reactions) BigDye� Terminator v1.1 Sequencing Standard BigDye� Terminator v3.1 Sequencing Standard GeneScanTM 120 LIZ� Size Standard GeneScanTM 500 LIZ Size Standard GeneScanTM 600 LIZ Size Standard GeneScanTM 500 ROX Size Standard GeneScanTM HD400 ROX Size Standard Hi-DiTM Formamide Matrix Standard DS-01

Part Number
4333463 4333464 4333466 4333465
4319898 4315931 4315930 4319899
Part Number 402824 4336824 4336974 4337450 4337455 4458687 4336791 4336935 4324287 4322682 4366589 401734 402985 4311320 4315974

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Appendix A Parts List

Description
Matrix Standard DS-02 Matrix Standard DS-30 (Dye Set D) Matrix Standard DS-31 (Dye Set D) Matrix Standard DS-32 (Dye Set F) Matrix Standard DS-33 (Dye Set G5) Performance Optimized Polymer 4 (POP-4� Polymer) Performance Optimized Polymer 6 (POP-6TM Polymer) Performance Optimized Polymer 7 (POP-7TM Polymer) POP Conformational Analysis Polymer (CAP)

Spare Parts

Description Array comb holders Array port plug Buffer reservoir, 16 mL Buffer/water/waste reservoir Ferrule knob Ferrule sleeves Polymer bottle Polymer tubing assembly Septa strip, buffer reservoir

Part Number 4323014 4345827 4345829 4345831 4345833 4316355 4352757 4352759 4340379
Part Number 628-0164 628-3776 4358351 628-0163 628-3730 628-0165 4362387 628-3732 4315932

Notes
96

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Documentation and Support

Related Documentation

The following related documents are shipped with the system:

Document title
Applied Biosystems� 3130/3130xl Genetic Analyzer Getting Started Guide Applied Biosystems� 3130/3130xl Genetic Analyzer Quick Reference Card Applied Biosystems� 3730/3730xl DNA Analyzer and 3130/3130xl Genetic Analyzers AB Navigator Software Administrator Guide

Pub. Part no.
4477796 4477795 4477853

Portable document format (PDF) versions of this guide and the documents listed above are also available on the Applied Biosystems� 3130 Series Data Collection Software 4 CD.
Note: To open the user documentation included on the Applied Biosystems� 3130 Series Data Collection Software 4 CD, use the Adobe� Reader� software available from www.adobe.com. Note: For additional documentation, see "Obtaining Support" on page 98.

Obtaining SDSs
Safety Data Sheets (SDSs) are available from www.lifetechnologies.com/support. Note: For the SDSs of chemicals not distributed by Life Technologies Corporation, contact the chemical manufacturer.

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Documentation and Support
Obtaining Support
Obtaining Support
For the latest services and support information for all locations, go to:
www.lifetechnologies.com/support
At the website, you can: � Access worldwide telephone and fax numbers to contact Technical Support and Sales facilities � Search through frequently asked questions (FAQs) � Submit a question directly to Technical Support � Search for user documents, SDSs, vector maps and sequences, application notes, formulations, handbooks, certificates of analysis, citations, and other product support documents � Obtain information about customer training � Download software updates and patches
Computer Configuration
Life Technologies Corporation supplies or recommends certain configurations of computer hardware, software, and peripherals for use with its instrumentation. Life Technologies Corporation reserves the right to decline support for or impose extra charges for supporting nonstandard computer configurations or components that have not been supplied or recommended by Life Technologies Corporation. Life Technologies Corporation also reserves the right to require that computer hardware and software be restored to the standard configuration prior to providing service or technical support. For systems that have built-in computers or processing units, installing unauthorized hardware or software may void the Warranty or Service Plan.
Limited Product Warranty
Life Technologies and/or its affiliate(s) warrant their products as set forth in the Life Technologies' General Terms and Conditions of Sale found on Life Technologies Corporation' website at www.lifetechnologies.com/termsandconditions. If you have any questions, please contact Life Technologies Corporation at www.lifetechnologies.com/support.
If for any reason it becomes necessary to return material to Life Technologies, contact Life Technologies Technical Support or your nearest Life Technologies subsidiary or distributor for a return authorization (RA) number and forwarding address. Place the RA number in a prominent location on the outside of the shipping container, and return the material to the address designated by the Life Technologies representative.

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Safety

GENERAL SAFETY. Using this product in a manner not specified in the user documentation may result in personal injury or damage to the instrument or device. Ensure that anyone using this product has received instructions in general safety practices for laboratories and the safety information provided in this document. � Before using an instrument or device, read and understand the safety information
provided in the user documentation provided by the manufacturer of the instrument or device. � Before handling chemicals, read and understand all applicable Safety Data Sheets (SDSs) and use appropriate personal protective equipment (gloves, gowns, eye protection, etc). To obtain SDSs, see "Obtaining Support" on page 98". � All testing should be performed in accordance with local, regional and national acceptable laboratory accreditation standards and/or regulations.

Symbols on instruments

Symbols may be found on the instrument to warn against potential hazards or convey important safety information. In this document, the hazard symbol is used along with one of the following user attention words described:
� 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.

Symbol

English

Caution, risk of danger
Consult the manual for further safety information.
Caution, hot surface

Fran�ais
Attention, risque de danger Consulter le manuel pour d'autres renseignements de s�curit�. Attention, surface chaude

Caution, risk of electrical shock

Attention, risque de choc �lectrique

Laser radiation

Rayonnement laser

Caution, piercing hazard

Attention, danger de perforation

Applied Biosystems 3130/3130xl Genetic Analyzers Maintenance, Troubleshooting, and Reference Guide

Safety
Safety alerts on this instrument

Symbol

English

Potential biohazard

Fran�ais Danger biologique potentiel

Ultraviolet light On

Rayonnement ultraviolet On (marche)

Off

Off (arr�t)

On/Off

On/Off (marche/arr�t)

Protective conductor terminal (main ground)
Terminal that can receive or supply alternating current or voltage
Terminal that can receive or supply alternating or direct current or voltage
Do not dispose of this product in unsorted municipal waste. Follow local municipal waste ordinances for proper disposal provisions to reduce the environmental impact of waste electrical and electronic equipment (WEEE).
To minimize negative environmental impact from disposal of electronic waste, do not dispose of electronic waste in unsorted municipal waste. Follow local municipal waste ordinances for proper disposal provision and contact customer service for information about responsible disposal options.

Borne de conducteur de protection (mise � la terre principale)
Borne pouvant recevoir ou envoyer une tension ou un courant de type alternatif
Borne pouvant recevoir ou envoyer une tension ou un courant continu ou alternatif
Ne pas �liminer ce produit avec les d�chets usuels non soumis au tri s�lectif.
Pour minimiser les cons�quences n�gatives sur l'environnement � la suite de l'�limination de d�chets �lectroniques, ne pas �liminer ce d�chet �lectronique avec les d�chets usuels non soumis au tri s�lectif. Se conformer aux ordonnances locales sur les d�chets municipaux pour les dispositions d'�limination et communiquer avec le service � la client�le pour des renseignements sur les options d'�limination responsable.

Conformity mark

Description Indicates conformity with safety requirements for Canada and U.S.A.

Safety alerts on this instrument
The following table shows the location of safety alerts found on the instrument. See "Symbols on instruments" on page 99 for more information.

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Safety
Instrument safety

English
Class 3B (III) visible and/or invisible laser radiation present when open and interlocks defeated. Avoid exposure to beam.

French translation
DANGER! Rayonnement laser visible ou invisible de classe 3B (III) pr�sent en position ouverte et avec les dispositifs de s�curit� non enclench�s. �viter toute exposition au faisceau.

Location on Instrument Detection cell cover

Instrument safety
General
Do not remove instrument protective covers. If you remove the protective instrument panels or disable interlock devices, you may be exposed to serious hazards including, but not limited to, severe electrical shock, laser exposure, crushing, or chemical exposure.

Physical injury

Moving and Lifting Injury. The instrument is to be moved and positioned only by the personnel or vendor specified in the applicable site preparation guide. Improper lifting can cause painful and permanent back injury. Things to consider before lifting or moving the instrument or accessories: � Depending on the weight, moving or lifting may require two or more persons. � If you decide to lift or move the instrument after it has been installed, do not attempt
to do so without the assistance of others, the use of appropriate moving equipment, and proper lifting techniques. � Ensure you have a secure, comfortable grip on the instrument or accessory. � 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. � For smaller packages, rather than lifting the object from the packing box, carefully tilt the box on its side and hold it stationary while someone else slides the contents out of

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Instrument safety

the box.

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

Electrical

Fuse Installation. Before installing the instrument, verify that the fuses are properly installed and the fuse voltage matches the supply voltage. Replace fuses only with the type and rating specified for the unit. Improper fuses can damage the instrument wiring system and cause a fire.

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.

Voltage Selector Switch. Before installing the instrument, verify that the voltage selector switch is set for the supply voltage. This will prevent damage to the instrument, reduce risk of fire, and enable proper operation.

Ensure appropriate electrical supply. For safe operation of the instrument: � Plug the system into a properly grounded receptacle with adequate current capacity. � Ensure the electrical supply is of suitable voltage. � Never operate the instrument with the ground disconnected. Grounding continuity is
required for safe operation of the instrument.

Power Supply Line Cords. Use properly configured and approved line cords for the power supply in your facility.

Disconnecting Power. To fully disconnect power either detach or unplug the power cord, positioning the instrument such that the power cord is accessible.

Overvoltage Rating
The Applied Biosystems 3130/3130xl Genetic Analyzers have an installation (overvoltage) category of II, and is classified as portable equipment.

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Instrument safety

Laser

LASER HAZARD. Under normal operating conditions, the Applied Biosystems 3130/3130xl Genetic Analyzers are categorized as a Class I laser product. However, removing the protective covers and (when applicable) defeating the interlock(s) may result in exposure to the internal Class 3B laser. Lasers can burn the retina, causing permanent blind spots. Use of controls or adjustments or performance of procedures other than those specified herein may result in hazardous radiation exposure. To ensure safe laser operation: � Never look directly into the laser beam. � Do not remove safety labels, instrument protective panels, or defeat safety interlocks. � The system must be installed and maintained by an Applied Biosystems Technical
Representative. Applied Biosystems Technical Representatives are instructed to: � Remove jewelry and other items that can reflect a laser beam into your eyes or those
of others � Wear proper eye protection and post a laser warning sign at the entrance to the
laboratory if the laser protection is defeated for servicing. DO NOT operate the laser when it cannot be cooled by its cooling fan; an overheated laser can cause severe burns on contact. Note the laser warnings provided in "Safety alerts on this instrument" on page 100.

LASER HAZARD, Bar Code Scanner. The bar code scanner included with the instrument system is a Class 2 laser. To avoid damage to eyes, do not stare directly into the beam or point into another person's eyes.

Laser Classification
The Applied Biosystems 3130/3130xl Genetic Analyzers use an Argon laser. Under 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 have been tested to and comply with 21 CFR, 1040.10 and 1040.11, as applicable.
The Applied Biosystems 3130/3130xl Genetic Analyzers have been tested to and comply with standard EN60825-1, "Radiation Safety of Laser Products, Equipment Classification, Requirements, and User's Guide."

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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 The instrument design and manufacture complies with the standards and requirements for safety and electromagnetic compatibility as noted in the following table:

Safety

Reference
21 CFR 1040.10 and 1040.11 except for deviations pursuant to Laser Notice No.50, dated June 24, 2007, as applicable

Description
U.S. FDA Health and Human Services (HHS) "Radiological health performance standards for laser products" and "Radiological health performance standards for specific purpose laser products"

EMC

Reference FCC Part 18 (47 CFR)

Description
U.S. Standard "Industrial, Scientific, and Medical Equipment"

U.S. and Canadian Safety Standards
This instrument has been tested to and complies with standard UL 61010-2:2001, "Safety Requirements for Electrical Equipment for Laboratory Use, Part 1: General Requirements."
This instrument has been tested to and complies with standard CSA C22.2 No. 61010-1, "Safety Requirements for Electrical Equipment for Measurement, Control, and Laboratory Use, Part 1: General Requirements."
This instrument has been tested to and complies with standard UL 61010-2-010, "Particular requirements for Laboratory Equipment for the Heating of Materials".
This instrument has been tested to and complies with standard UL 61010-2-081, "Particular requirements for Automatic and Semi0-Automatic Laboratory Equipment for analysis and other purposes".

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Chemical safety
Canadian EMC Standard
This instrument has been tested to and complies with ICES-001, Issue 3: Industrial, Scientific, and Medical Radio Frequency Generators.
European Safety and EMC Standards
Safety This instrument meets European requirements for safety (Low Voltage Directive 2006/95/EC). This instrument has been tested to and complies with standards EN 610101:2001, "Safety Requirements for Electrical Equipment for Measurement, Control and Laboratory Use, Part 1: General Requirements", EN 61010-2-010, "Particular Requirements for Laboratory Equipment for the Heating of Materials, EN 61010-2081:2003, "Particular requirements for Automatic and Semi0-Automatic Laboratory Equipment for analysis and other purposes", and EN 60825:2002, "Radiation safety of laser products, equipment classification, requirements and user's guide."
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."
Australian EMC Standards
This instrument has been tested to and complies with standard AS/NZS 2064, "Limits and Methods Measurement of Electromagnetic Disturbance Characteristics of Industrial, Scientific, and Medical (ISM) Radio-frequency Equipment."

Chemical safety

GENERAL CHEMICAL HANDLING. To minimize hazards, ensure laboratory personnel read and practice the general safety guidelines for chemical usage, storage, and waste provided below, and consult the relevant SDS for specific precautions and instructions: � Read and understand the Safety Data Sheets (SDSs) provided by the chemical
manufacturer before you store, handle, or work with any chemicals or hazardous materials. To obtain SDSs, see the "Documentation and Support" section in this document. � Minimize contact with chemicals. Wear appropriate personal protective equipment when handling chemicals (for example, safety glasses, gloves, or protective clothing). � Minimize the inhalation of chemicals. Do not leave chemical containers open. Use only with adequate ventilation (for example, fume hood). � Check regularly for chemical leaks or spills. If a leak or spill occurs, follow the manufacturer's cleanup procedures as recommended in the SDS. � Handle chemical wastes in a fume hood.

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Chemical safety
� Ensure use of 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.)
� After emptying a waste container, seal it with the cap provided. � Characterize (by analysis if necessary) the waste generated by the particular
applications, reagents, and substrates used in your laboratory. � Ensure that the 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.
HAZARDOUS WASTE (from instruments). Waste produced by the instrument is potentially hazardous. Follow the guidelines noted in the preceding General Chemical Handling warning.
4L Reagent and Waste Bottle Safety. Four-liter reagent and waste bottles can crack and leak. Each 4-liter bottle should be secured in a low-density polyethylene safety container with the cover fastened and the handles locked in the upright position.
Cleaning and decontamination
Cleaning and Decontamination. Using a cleaning or decontamination method not specified by the manufacturer may result in damage to the equipment. For the protection of others, ensure the instrument is properly decontaminated prior to having the instrument serviced at your facility or before sending the instrument for repair, maintenance, trade-in, disposal, or termination of a loan. Decontamination forms may be requested from customer service.

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Biological hazard safety
Biological hazard safety
BIOHAZARD. Biological samples such as tissues, body fluids, infectious agents, and blood of humans and other animals have the potential to transmit infectious diseases. Follow all applicable local, state/provincial, and/or national regulations. Wear appropriate protective equipment, which includes but is not limited to: protective eyewear, face shield, clothing/lab coat, and gloves. All work should be conducted in properly equipped facilities using the appropriate safety equipment (for example, physical containment devices). Individuals should be trained according to applicable regulatory and company/institution requirements before working with potentially infectious materials. Read and follow the applicable guidelines and/or regulatory requirements in the following: In the U.S.: � U.S. Department of Health and Human Services guidelines published in Biosafety in
Microbiological and Biomedical Laboratories found at: www.cdc.gov/biosafety � Occupational Safety and Health Standards, Bloodborne Pathogens
(29 CFR�1910.1030), found at: www.access.gpo.gov/nara/cfr/waisidx_01/ 29cfr1910a_01.html � Your company's/institution's Biosafety Program protocols for working with/handling potentially infectious materials. � Additional information about biohazard guidelines is available at: www.cdc.gov In the EU: � Check local guidelines and legislation on biohazard and biosafety precaution and refer to the best practices published in the World Health Organization (WHO) Laboratory Biosafety Manual, third edition, found at: www.who.int/ csr/resources/publications/biosafety/WHO_CDS_CSR_LYO_2004_11/en/

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 CAUTION Hazardous chemicals. Read the Safety Data Sheets (SDSs) before handling.
CAUTION Hazardous waste. Read the waste profile (if any) in the site preparation guide for this instrument before handling or disposal. CAUTION Hazardous waste. Refer to SDS(s) and local regulations for handling and disposal.
WARNING Hot lamp. WARNING Hot. Replace lamp with an Applied Biosystems lamp.
CAUTION Hot surface.

Francais
ATTENTION Produits chimiques dangeureux. Lire les fiches techniques de s�ret� de mat�riels avant la manipulation des produits.
ATTENTION D�chets dangereux. Lire les renseignements sur les d�chets avant de les manipuler ou de les �liminer.
ATTENTION D�chets dangereux. Lire les fiches techniques de s�ret� de mat�riels et la r�gulation locale associ�es � la manipulation et l'�limination des d�chets.
AVERTISSEMENT Lampe br�lante.
AVERTISSEMENT Composants br�lants. Remplacer la lampe par une lampe Applied Biosystems.
ATTENTION Surface br�lante.

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Workstation Safety

English DANGER High voltage. WARNING To reduce the chance of electrical shock, do not remove covers that require tool access. No user-serviceable parts are inside. Refer servicing to Applied Biosystems qualified service personnel.
DANGER Class 3B laser radiation present when open and interlock defeated. Avoid direct exposure to laser beam.
DANGER Class 3B laser radiation when open. Avoid direct exposure to laser beam.
DANGER Class 2(II) laser radiation present when open and interlock defeated. Do not stare directly into the beam
DANGER Class 2(II) laser radiation present when open. Do not stare directly into the beam. DANGER Class 2(II) LED when open and interlock defeated. Do not stare directly into the beam.
DANGER Class 2(II) LED when open. Do not stare directly into the beam.
CAUTION Moving parts.

Francais
DANGER Haute tension.
AVERTISSEMENT Pour �viter les risques d'�lectrocution, ne pas retirer les capots dont l'ouverture n�cessite l'utilisation d'outils. L'instrument ne contient aucune pi�ce r�parable par l'utilisateur. Toute intervention doit �tre effectu�e par le personnel de service qualifi� de Applied Biosystems.
DANGER Class 3B rayonnement laser en cas d'ouverture et d'une neutralisation des dispositifs de s�curit�. Eviter toute exposition directe avec le faisceau.
DANGER Class 3B rayonnement laser en cas d'ouverture. Eviter toute exposition directe avec le faisceau.
DANGER de Class 2(II) rayonnement laser en cas d'ouverture et d'une neutralisation des dispositifs de securite. Eviter toute exposition directe avec le faisceau.
DANGER de Class 2(II) rayonnement laser en cas d'ouverture. Eviter toute exposition directe avec le faisceau.
DANGER de Class 2(II) LED en cas d'ouverture et d'une neutralisation des dispositifs de securite. Eviter toute exposition directe avec le faisceau.
DANGER de Class 2(II) LED en cas d'ouverture. Eviter toute exposition directe avec le faisceau.
ATTENTION Parties mobiles.

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 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 postures.

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Index

Numerics
3130 basecaller and DyeSet/Primer files 87, 88 3130 series software license 42 3130calib.ini 50
A
account password, see password AmpFlSTR kits
matrix standard 92 table of dye sets, filter, modules 90 array port, illustration of 6 autosampler 14 calibrating 27 controlling. See manual control commands non-optimal calibration 60 will not move forward 48 Autosampler Calibration Wizard calibration, autosampler 27
B
basecaller and DyeSet/Primer files 86 basecaller files 86, 87, 88 basecaller, and ABI basecalling 87 BigDye� Direct Cycle Sequencing Kit
table, dye sets and standard 85 BigDye� Primer Cycle Sequencing Kits
table, dye sets and standard 85 BigDye� Terminator chemistry, information tables 86 BigDye� Terminator v1.1 Cycle Sequencing Kit
table, dye sets and standard 85 BigDye� Terminator v3.1 Cycle Sequencing Kit
table, dye set and standard 85 biohazard safety 107 Bubble Remove Wizard 26 bubbles, clearing 26 buffer fill-line 6 buffer jar, illustration of 6 buffer valve pin, illustration of 6 buffer, making and storing 19

C
calibration standards types, fragment analysis 92
CAP polymer fragment analysis application/kit and run modules, SSCP 90 fragment analysis run module specifications 89 POP Conformational Analysis Polymer part number 96 run modules 93
capillary array care 24 failing 54 illustration of 6 manually filling 12 poor performance 64 storing off the instrument 25 storing on the instrument 25 when to change 22
capillary array knob and tip, illustration of 6
cathode bar 22
CD, creating a data 35
Change Polymer Type Wizard 21
check valve diagram of 6
chemical safety 105
cleaning instrument, routine 9
cleaning safety 106
Cleanup Database utility 38
communication cable must be original 50 replacing 50
computer checking hard drive space 34 configuration requirement 98 frozen 48 technical support for altered configuration 98
current, troubleshooting 63
customizing 68
D
data archiving 35 none in capillaries 60

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Data Collection software will not launch 48
Data Explorer software 3130calib.ini file 50
database checking disk space 34 deleting records 38 error messages 32
decontamination safety 106 defragmenting hard drive 37 dGTP BigDye� Terminator Cycle Sequencing Kit
table, dye sets and standard 85 dGTP BigDye� Terminator v 3.0 Cycle Sequencing
Ready Reaction Kit table of dye set and standards 85 double-tapered ferrule, illustration of 6 dRhodamine Terminator Cycle Sequencing Kit table, dye sets and standard 85 drive checking available space 32 cleaning 33 defragmenting 37 dye primer chemistry, information table 88 dye set fragment analysis 92 dye set G5-RCT recommendations for use 42 Dye Terminator chemistry, files 86, 87 DyeSet/Primer files 86, 87, 88
E
E dye set, sequencing kit table 85 electrical safety 102 electrode, illustration of 6 elevated baseline 62 error messages 32
viewing 33 event log, accessing 33 event viewer, blank 48
F
failing capillaries 54 fill down special option 73 filter set
fragment analysis 90 flushing, water trap 17 fragment analysis
filter set 90 kit types 90 run modules 93

H
hard drive space, checking 34 hard drive, defragmenting 37
I
Install Array Wizard 23 instrument
cleaning, routine 9 moving and leveling 11 resetting 9 shutdown 12 instrument safety 101 instrument status, troubleshooting 49 interconnect tube 6
K
KB basecalling run modules 86
L
laser controlling. See manual control commands
laser safety 103 leaks, troubleshooting 65 LED, instrument status 49 length of read, definition 84 leveling , after moving instrument 11 LOR definition 84 loss of resolution 62 low signal strength 61 lower polymer block, illustration of 6 Luer fitting, illustration of 6
M
maintenance tasks 7 computer 32 routine 9
Managing Software License for 3130 Series Data Collection Software 4 41
manual control accessing 30 filling capillary array 12 options, table 28
manual control commands 28 manually filling capillary array 12 matrix standard
fragment analysis 92 migration time, too fast or too slow 65 modules 68
fragment analysis 89, 90

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KB basecalling 86 run module tables 93 run parameters 69 sequencing 84 mounting pin, illustration of 6 moving the instrument 11
N
"No candidate spectral files found" 53
O
O-ring, illustration of 6 oven, controlling. See manual control commands overflow hole, illustration of 6
P
password case-sensitive 49 changing 49 expired or corrupt 49 troubleshooting 49
PDP motor cover, illustration of 6 peaks, troubleshooting 65 physical injury safety 101 piston, illustration of 6 plate linking, relinking 57 plate record
creating multi-application 77 fill down special option 73 polymer cleaning off 9 storing 20 polymer blocks bubbles 26 polymer delivery pump (PDP) illustration 6 water trap 17 polymer supply bottle cap with hole, illustration of 6 polymer supply bottle, illustration of 6 polymer supply tube, illustration of 6 power override enabled 49 triggers 49 troubleshooting 49 priority scheduling 70 pump block, illustration of 6 pump chamber, illustration of 6
R
RA number. See return authorization number

red status light 48
removing bubbles 26
Replenish Polymer Wizard 21
reservoirs cleaning 14 positions on the autosampler 14
resetting the instrument 9
resolution fragment analysis 89
resolution, loss 62
return authorization (RA) number 98
Roxio Easy CD, accessing 35
run elevated baseline 62 elevated current 63 fast migration time 65 fluctuating current 63 high signal 61 loss of resolution 62 low signal 61 no current 63 no signal 60, 61 parameter ranges 69 priority scheduling 70 slow migration time 64
run module 93 customizing 68 tables 93
run time fragment analysis 89
Run validation tests 59
S
safety alerts on instrument 100 biohazard 107 chemical 105 cleaning and decontamination 106 electrical 102 instrument 101 laser 103 physical injury 101 symbols on instrument 99
scheduling, run priority 70
sequencing run modules 93 specifications 84
shut down 12
shutdown 14
signal too high 61
software license manage 42 obtain and activate 42

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renew 44
spatial calibration persistently bad results 51 troubleshooting 51 unusual peaks 51
specifications fragment analysis 89 sequencing 84
spectral calibration deleting a 39 if a capillary fails 54 if all capillaries fail 55 no signal 52 override capillaries 54 troubleshooting 52
spectral calibration standard, types 85
symbols, on instrument 99

Replenish Polymer Wizard 21 Update Cap Array Info 24
Y
yellow status light, instrument 49
Z
Z dye set, sequencing kit table 85

T
technical support, for computers with altered configuration 98
tests, validation 59
troubleshooting failing capillaries 54 instrument startup 48, 49 instrument status 49 leaks 65 password 49 plate linking 57 power override 49 run performance 60 spatial calibration 51 spectral calibration 52 using validation tests 59 yellow status light, instrument 49

U
Update Cap Array Info wizard 24

W
warranty for computers with altered configuration 98
water seal, illustration of 6
water trap filling 17 flushing and filling 17 illustration of 6
wizards accessing and overview 15 Autosampler Calibration 27 Bubble Remove Wizard 26 Change Polymer Type Wizard 21 Install Array Wizard 23 Instrument Shutdown 14

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Headquarters 5791 Van Allen Way | Carlsbad, CA 92008 USA | Phone +1 760 603 7200 | Toll Free in USA 800 955 6288 For support visit www.lifetechnologies.com/support or email techsupport@lifetech.com www.lifetechnologies.com
May 2012