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3730xl
Applied Biosystems 3730xl User Manual
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F
or Resear
ch Use Onl
y. Not for use in diagnostic pr
oc
edur
es.
3730xl DNA Anal
yzer
USER GUIDE
3730xl Data Coll
ection Softwar
e 5
Windows
™
10 Operating Sys
tem
Catal
og Number
A39079
Publication Number
100077621
Revision
A
2
Table of Contents
Default Chapter
3
Table of Contents
3
CHAPTER 1 Instrument and Software Description
10
Overview
11
Parts of the Instrument
12
Instrument Interior Components
13
Instrument Front Panel Indicators
14
Consumables and Usage Limits
16
Important Notice Regarding Use of Consumables that Exceed Supported Limits
16
Important Notice Regarding Use of Consumables that Exceed Supported
16
Limits
16
Computer and Software Requirements
17
Theory of Operation
17
Preparing Samples
17
Preparing the Instrument
18
During a Run
18
Results
18
Overview of the Software
19
Use the Instrument with Thermo Fisher Connect
22
Secondary Analysis Software
23
Data Collection Software Terminology
24
Workflow for a Typical Run
26
CHAPTER 2 Prepare the Instrument
27
Power on the Computer and the Instrument
27
Start the Software
28
Prepare Buffer and Fill the Reservoirs
29
Required Materials
29
Run Buffer Storage
29
When to Change the 1X Run Buffer
30
Prepare the 1X Run Buffer
30
Fill the Water and Buffer Reservoirs
30
Place Reservoirs into the Instrument
32
Fill the Anode Buffer Jar
33
Check the Polymer Level
34
Check for Bubbles in the Pump System
35
Check the Active Spectral Calibration
36
Prepare and Load Sample Plates
37
Default Injection Positions-48-Capillary Arrays
37
96-Well Plate, 48 Capillaries
37
384-Well Plate, 48 Capillaries
38
Default Injection Positions-96-Capillary Arrays
39
96-Well Plate, 96 Capillaries
39
384-Well Plate, 96 Capillaries
40
Seal and Assemble Plates
41
Seal and Prepare the Plate Assemblies
41
Prepare the Plate Assemblies
42
Important Heat Seal Recommendations
44
Place Plate Assemblies into the Instrument
44
CHAPTER 3 Use the Instrument with Thermo Fisher Connect
46
Thermo Fisher Connect Features
46
Register and Obtain a Thermo Fisher Connect Account
47
Connect the Instrument to Your Thermo Fisher Connect Account
47
Set up the Data Storage Location and Email Notifications
48
Monitor a Run from Instrumentconnect
49
Monitor a Run from a Mobile Device
50
View Notifications from the Instrument on the Cloud
51
For more Information on Using Instrumentconnect
52
Thermo Fisher Connect Administrators for an Instrument
52
First User Who Links Is Assigned Administrator Role
52
Instrument Administrator Functions
52
Manage the Users and Administrators of Your Instrument
53
Disconnect Individual Users from an Instrument
54
CHAPTER 4 Create Results Groups and Plate Records Using
55
Default Settings
55
Create a Results Group (Using Defaults)
55
Create a Plate Record
56
CHAPTER 5 Run the Instrument
59
Understanding Run Modes and Default Injection Positions
59
Manual and Auto Run Mode Features
59
Default Injection Order on Plates
59
Run the Instrument in Auto Mode
61
Run the Instrument in Manual Mode
61
Change Injection Order of Plate Quadrants
63
Move a Plate in the Input Stack During a Run
64
Controlling the Run
64
Monitor the Status of the Run
65
Add Reinjections to a Plate Record
66
Check Instrument Status
67
Events Box
67
Errors Box
67
View the Event Log
68
View Data from the Run
69
View Electropherogram Data
69
View Electrophoresis Conditions (EPT)
71
View Data from a Completed Run (Run History)
71
Check the Autoextraction Status and Manually Re-Extract
72
Autoextraction and Re-Extraction
72
Re-Extract Runs
72
CHAPTER 6 Create and Manage Plate Records and
74
Results Groups
74
Overview of Plate Records
74
Create and Manage Plate Records
76
Search for a Plate Record
77
Import a Plate Record
78
Overview of Results Groups
79
Create and Manage Results Group
80
Create a Results Group (Detailed Procedure)
80
Specify Custom Sample File Naming in a Results Group
82
CHAPTER 7 Create and Manage Instrument Protocols, Run
84
Modules, and Analysis Protocols
84
Create and Manage Instrument Protocols
84
Create an Instrument Protocol
85
Create Run Module
86
Run Module Parameters
87
Overview of Analysis Protocols (Sequence Analysis)
87
Create and Manage Analysis Protocols
88
Create an Analysis Protocol
89
Analysis Protocol Parameters
89
CHAPTER 8 Calibrate the Instrument
91
Perform Spatial Calibration
91
Spatial Calibration Description and Run Time
91
When to Perform a Spatial Calibration
91
Evaluate the Spatial Calibration Data
92
Examples of Passing and Failing Spatial Profiles
94
Magnify the Spatial Profile
96
Perform Spectral Calibration for Sequencing and Fragment Analysis
97
Spectral Calibration Definition and Run Time
97
When to Perform the Calibration
97
Supported Dye Sets and Calibration Standards
98
Required Materials
98
Prepare the Spectral Calibration Standard
99
Create a Spectral Instrument Protocol
99
Create a Spectral Calibration Plate
100
Run the Spectral Calibration Plate
101
Place Plate Assemblies into the Instrument
102
View the Pass/Fail Status after the Run
103
Evaluate the Spectral Calibration Data
105
Magnify the Spectral Profile
108
Examples of Passing Sequencing Spectral Calibrations
110
Example of a Passing Fragment Analysis Spectral Calibration
111
Select a Previous Calibration as the Active Spectral Calibration
111
CHAPTER 9 Maintenance
113
Maintenance Schedules
113
Daily Maintenance
113
Weekly Maintenance
114
Monthly Maintenance
115
As-Needed Maintenance
115
Wizards Types and Functions
116
Typical Conditions for Using Maintenance Wizards
117
Effects of the Instrument Door State on Wizard Tasks
118
Manual Control of Autosampler Content
118
Clean the Instrument
119
Replenish or Change Polymer Type
119
Before Using the Polymer
119
Replenish the Polymer
119
Change Polymer Type
120
Clean the Polymer Delivery Pump (PDP) and Lower Polymer Block
121
Parts of the Polymer Delivery Pump
121
Guidelines
121
Frequency
121
Clean the Polymer Delivery Pump Chamber, Channels, and Tubing
122
Flush the Water Seal Trap
122
Install the Capillary Array
123
Required Materials
123
Install a New or Used Capillary Array
123
Store a Capillary Array
124
Clean the Detection Cell
125
Perform a Short-Term Shutdown
126
Materials Required
126
Perform a Short-Term Shutdown
127
Maintain Adequate Space for Database and Sample Data Storage
130
Pre-Run Automatic Disk Space Checks
130
Full Database Error
131
Check Available Disk Space on E: Drive
131
Delete Data from the Database
132
Restart the Instrument and the Computer
134
APPENDIX A Troubleshooting
135
Display the Event Log
135
Review a Run Log File
135
Hi-DI ™ Formamide Preparation and Storage
136
Front Panel Status Light Troubleshooting
136
Instrument Run Troubleshooting
137
Re-Extraction Troubleshooting
137
Service Console Troubleshooting
138
Spatial Calibration Troubleshooting
138
Spectral Calibration Troubleshooting
139
General Troubleshooting
140
APPENDIX B Instrument Specifications
142
Instrument Specifications
142
Environmental Requirements
143
Electrical Requirements
144
Power and Communication Connections
145
APPENDIX C Run Modules
146
Fragment Analysis Run Times
146
Sequence Analysis Run Times
146
APPENDIX D Dye Sets: G5, G5-RCT, Any4Dye, Any4Dye-HDR
148
And Any5Dye
148
Supported Dye Sets and Calibration Standards
148
Dye Sets G5 and G5-RCT for Fragment Analysis
149
Fragment Analysis Using a 96-Capillary Array: Cross-Talk Peaks
149
Reduced Cross-Talk-Dyeset G5-RCT
149
When to Use RCT Dye Sets
149
APPENDIX E Catalog Numbers
150
Plates, Bases, Retainers, and Septa
150
Instrument Consumables
151
Sequencing and Fragment Analysis Calibration Standards
151
Fragment Analysis Size Standards
152
APPENDIX F Safety
153
Symbols on this Instrument
153
Safety Symbols
153
Location of Safety Labels
155
Control and Connection Symbols
156
Conformity Symbols
156
Safety Information for Instruments Not Manufactured by Thermo Fisher Scientific
157
Instrument Safety
157
General
157
Physical Injury
157
Electrical Safety
158
Cleaning and Decontamination
159
Instrument Component and Accessory Disposal
159
Laser Safety
160
Safety and Electromagnetic Compatibility (EMC) Standards
160
Safety Standards
161
EMC Standards
161
Environmental Design Standards
162
Chemical Safety
163
Biological Hazard Safety
164
Documentation and Support
165
Related Documentation
165
Customer and Technical Support
165
Limited Product Warranty
166
Index
167
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Applied Biosystems 3730xl Specifications
General
Brand
Applied Biosystems
Model
3730xl
Category
Measuring Instruments
Language
English
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