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Applied Biosystems 3730xl, User Manual

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Contents

■

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
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
1X 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

3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide

3

Summary of Contents for 3730xl

Page 1: ...search Use Only Not for use in diagnostic procedures 3730xl DNA Analyzer USER GUIDE 3730xl Data Collection Software 5 Windows 10 Operating System Catalog Number A39079 Publication Number 100077621 Revision A ...

Page 2: ...AL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT INCLUDING YOUR USE OF IT Revision history Pub No 100077621 Revision Date Description A 1 October 2018 New document Important Licensing Information These products may be covered by one or more Limited Use Label Licenses By use of these products you accept the terms and conditions of all applicable Limited Use Label Licenses TRADEMARKS All ...

Page 3: ...hermo 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 1X run buffer storage 29 When to change the 1X run buffer 30 Prepare the 1X run buffer 30 Fill the water and ...

Page 4: ...t 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 instru...

Page 5: ...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 modules and analysis protocols 84 Create and manage instrument protocols 84 Creat...

Page 6: ...ce 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 schedule...

Page 7: ...ull database error 131 Check available disk space on E drive 131 Delete data from the database 132 APPENDIX A Troubleshooting 134 Restart the instrument and the computer 134 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 ...

Page 8: ...tandards 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 1...

Page 9: ...mentation and support 165 Related documentation 165 Customer and technical support 165 Limited product warranty 166 Index 167 Contents 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide 9 ...

Page 10: ...ant notice regarding use of consumables that exceed supported limits 16 Computer and software requirements 17 Theory of operation 17 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 1 10 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide ...

Page 11: ...and for system qualification Computer workstation and monitor Integrated software for instrument control and data collection Optional secondary analysis software See Secondary analysis software on page 23 IMPORTANT The protection provided by the equipment may be impaired if any of the following conditions occur The instrument is operated outside the environment and use specifications The user prov...

Page 12: ...and capillary array are inside this compartment 3 Stacker automated plate handler 4 Stacker door indicator light 5 Power button and status lights 6 Tray button 7 Buffer water and waste reservoirs Chapter 1 Instrument and software description Parts of the instrument 1 12 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide ...

Page 13: ...ll behind door 3 Capillary array 1 2 3 6 7 4 5 Figure 3 Polymer delivery pump PDP 1 Pump block 2 Polymer supply tube 3 Polymer reservoir 4 Anode buffer jar 5 Capillary array 6 Interconnect tube 7 Lower polymer block Chapter 1 Instrument and software description Instrument interior components 1 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide 13 ...

Page 14: ...servoir or capillary array is not installed Flashing Yellow The instrument is performing diagnostics The instrument door or oven door is open An automated wizard operation is in progress with the instrument door open The instrument is downloading firmware Solid Red The instrument has detected a problem See Appendix A Troubleshooting Restart the instrument and computer See Power on the computer and...

Page 15: ...s in the In stack and Out Stack Empty no plates in stack Solid Red In Stack Empty no plates in stack and Out Stack Full remove plates before you can start another run Chapter 1 Instrument and software description Instrument front panel indicators 1 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide 15 ...

Page 16: ...hat have not exceeded supported limits The use of consumables beyond the supported limits may impact data quality or cause damage to the instrument or capillary array The cost of repairing such damage is NOT covered by any Life Technologies product warranty or service plan Customer use of expired consumables is at customer s own risk and without recourse to Life Technologies For example product wa...

Page 17: ...ation Operating system Operating system Windows 10 Enterprise 2016 LTSB 64 bit requires 5 partitions Consult with a Thermo Fisher Scientific representative before updating the Windows operating system or firewall settings Instrument firmware Instrument firmware is to be updated only by a Thermo Fisher Scientific representative Antivirus software requirements No antivirus software is provided with ...

Page 18: ...ll In the detection cell the dyes that are attached to DNA are excited by a narrow beam of laser light The laser light is directed into the plane of the capillaries from both the bottom and top A small amount of laser light is absorbed by the dyes and emitted as longer wavelength light in all directions CCD captures the fluorescent light on the instrument optics while blocking the laser light The ...

Page 19: ...ure allows you link the instrument to your Thermo Fisher Connect account and upload data Use the Navigation pane Figure 4 to set up your run view and interrogate results or to determine the amount of free space remaining in your database Figure 4 Navigation pane Chapter 1 Instrument and software description Overview of the software 1 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User ...

Page 20: ...e records using default settings and Create and manage plate records on page 76 5 Protocol Manager Create and manage instrument protocols which specify run modules dye sets capillary length polymer and chemistry type See Chapter 7 Create and manage instrument protocols run modules and analysis protocols 6 Module Manager Create and manage run modules which specify instrument settings See Chapter 7 ...

Page 21: ...n 5 Capillary Viewer View the signal intensity for individual capillaries 6 Array Viewer View the signal intensity for the entire array 7 Spectral Calibration Viewer View the spectral calibration from a specific run 8 Reextraction Check autoextraction success or failure and re analyze samples with different settings See Check the autoextraction status and manually re extract on page 72 Chapter 1 I...

Page 22: ...bration for sequencing and fragment analysis on page 97 7 Manual Control Send a manual command to adjust parameters for electrophoresis the laser autosampler polymer delivery pump oven or other system or miscellaneous parameters 8 Service Log View the service history Use the instrument with Thermo Fisher Connect The new Thermo Fisher Connect feature allows you to connect the instrument to your The...

Page 23: ...stems genetic analyzers Reports variants at genomic coordinates Allows export of variant calls in standard Variant Call Format Next generation Confirmation NGC module Confirms next generation sequencing NGS variants using CE technology Allows visualization of the variants that are detected by both NGS and CE platforms Allows export of confirmed variants in standard Variant Call Format Fragment ana...

Page 24: ...t you can perform after a run is complete See Autoextraction and re extraction on page 72 Batch Run All plates in the Input Stack list Database Internal database in the Data Collection Software that stores plate records results groups instrument protocols run modules analysis protocols and data that is collected on the instrument Data is autoextracted from the database to generate data files at th...

Page 25: ...late For example a 96 well plate on a 48 capillary instrument will require 2 runs injections to sample all wells on the plate Injection 1 Injection 2 Chapter 1 Instrument and software description Data Collection software terminology 1 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide 25 ...

Page 26: ...tional Link the instrument to Thermo Fisher Connect page46 Schedule runs Place plates in stacker in any order Place plates in stacker in run order Prepare plates page 37 Start run Create a results group page 55 Monitor run status page 65 Create a plate record page 55 View data from the run page 69 Review results in secondary analysis software on Thermo Fisher Connect or on desktop software page 23...

Page 27: ...ult injection positions 96 capillary arrays 39 Seal and assemble plates 41 Place plate assemblies into the instrument 44 IMPORTANT Before using this product read and understand the information in the Safety appendix in this document Power on the computer and the instrument 1 Power on the monitor and computer 2 In the Log On to Windows dialog box a In the User Name field enter your user name b In t...

Page 28: ... and services start Note If the dialog box is not displayed click the Service Console tab in the Windows task bar If all services do not display after 1 2 minutes see Service console troubleshooting on page 138 Chapter 2 Prepare the instrument Start the software 2 28 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide ...

Page 29: ... and fill the reservoirs Retainer buffer water waste Septa Reservoir caps Reservoir buffer water waste Plate base water waste Plate base buffer Water deionized 180 mL plus 160 mL for water and waste reservoirs 3730 Running Buffer 10X 20 mL Graduated cylinder 250 mL Gloves silicone free powder free 2 8 C for up to 1 month Room temperature for 1 week Required materials 1X run buffer storage Chapter ...

Page 30: ...g the autosampler to the forward position see Figure 1 3 Wait for the autosampler to stop moving and for the green status light to illuminate before you open the instrument door 4 Unplug the buffer reservoir Remove the buffer water and waste reservoir assemblies from the instrument 5 Disassemble each reservoir assembly then empty the contents of the reservoirs into an aqueous waste container 6 Cle...

Page 31: ...r to each reservoir 2 Assemble each reservoir assembly as shown below 1 2 3 4 5 1 Retainer 2 Septum 3 Reservoir cap 4 Reservoir 5 Plate base 9 To prevent damage to the capillary array inspect each reservoir for the following conditions Septa fit snugly and flush on the reservoir cap Rubber gasket surrounding the reservoir cap is seated correctly 1 1 Rubber gasket not seated correctly Chapter 2 Pre...

Page 32: ...reservoir plate base cable into the heater outlet inside the instrument 1 2 1 Heater outlet 2 Plate base cable 2 Move the cable out of the way of the autosampler Move the buffer reservoir to the Buffer position left 1 3 2 1 Buffer reservoir 2 Left reservoir position 3 Middle reservoir position Chapter 2 Prepare the instrument Place reservoirs into the instrument 2 32 3730xl DNA Analyzer with 3730x...

Page 33: ...duce polymer into the anode buffer jar When you replace the 1X run buffer do not add fresh buffer to old buffer Discard old buffer then add fresh buffer IMPORTANT Using old 1X buffer can lead to loss of resolution and data quality 1 Remove the anode buffer jar by pulling it down then twisting it slowly 2 Empty the anode buffer jar into an aqueous waste container 3 Rinse the anode buffer jar using ...

Page 34: ...he electrode is immersed in the buffer Check the polymer level Check the level of polymer then replenish if needed Replace polymer if it has been on the instrument for more than 1 week See Replenish or change polymer type on page 119 IMPORTANT Allow polymer to reach room temperature before installing on the instrument 2 1 1 Electrode 2 Meniscus Chapter 2 Prepare the instrument Check the polymer le...

Page 35: ...ble Remove Wizard For more information see Typical conditions for using maintenance wizards on page 117 IMPORTANT When this wizard runs it introduces polymer into the anode buffer jar Replace the anode jar buffer after you run this wizard See Fill the anode buffer jar on page 33 Chapter 2 Prepare the instrument Check for bubbles in the pump system 2 3730xl DNA Analyzer with 3730xl Data Collection ...

Page 36: ...04 Instrument name4 Spectral Viewer 1 2 1 Dye set for the run 2 Active spectral calibration 2 Select the dye set for the run 3 If the active spectral calibration is not appropriate for your application see Select a previous calibration as the active spectral calibration on page 111 Chapter 2 Prepare the instrument Check the active spectral calibration 2 36 3730xl DNA Analyzer with 3730xl Data Coll...

Page 37: ...s or are not located at the bottom of the well briefly centrifuge the plate remove the plate from the centrifuge and verify that each sample is positioned correctly in the bottom of its well 3 Store the plate on ice and protected from light until you prepare the plate assembly and load the plate in the instrument After you load samples in plates see Seal and assemble plates on page 41 Default inje...

Page 38: ... 2 3 4 Injection 1 Injection 2 No injection 1 Quadrant 1 2 Quadrant 2 3 Quadrant 3 4 Quadrant 4 384 Well plate 48 capillaries Chapter 2 Prepare the instrument Default injection positions 48 capillary arrays 2 38 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide ...

Page 39: ...itions 96 capillary arrays 1 injection 96 Well plate 96 capillaries Chapter 2 Prepare the instrument Default injection positions 96 capillary arrays 2 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide 39 ...

Page 40: ...ate 1 2 3 4 Injection 1 No injection 1 Quadrant 1 2 Quadrant 2 3 Quadrant 3 4 Quadrant 4 384 Well plate 96 capillaries Chapter 2 Prepare the instrument Default injection positions 96 capillary arrays 2 40 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide ...

Page 41: ...is seated and aligned see Figure 8 The septa lie flat against the plate You should not feel any lumps or raised edges The septa are inserted straight into the wells You should not see any bent or crooked duckbills when viewing the plate from above 1 2 3 4 Figure 8 Examples of bad and good septa alignment 1 Septum and well are not aligned 2 Septum and well are not aligned 3 Septum and well are not ...

Page 42: ... 3 5 1 2 3 4 1 Plate retainer 2 Plate septum 3 Septum sealed sample plate 4 Black plate base 5 Assembled components Prepare the plate assemblies Chapter 2 Prepare the instrument Seal and assemble plates 2 42 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide ...

Page 43: ...Amp Fast 96 Well Reaction Plates 0 1 mL use only dark green plate base and matching retainer 2 Verify that the holes of the plate retainer and the septa are aligned IMPORTANT The plate may damage the array if the retainer and the septum holes are not aligned 3 Make sure when you assemble a plate that the retainer clip is flush with the plate base A simple way to ensure that they are flush is to ru...

Page 44: ...ore the injection Place plate assemblies into the instrument 1 Open the stacker drawer 2 Open the door of the In Stack tower 3 Place the plate assemblies into the stacker Ensure that the notched corner of the plate assembly is at the rear right corner of the stacker IMPORTANT Do not place more than 16 plates in the stacker 1 Notched corner Important heat seal recommendations Chapter 2 Prepare the ...

Page 45: ... the metal In Stack tower door 5 Close the Stacker drawer Chapter 2 Prepare the instrument Place plate assemblies into the instrument 2 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide 45 ...

Page 46: ...nect features This option is not available if Access Control Administration is enabled in the AB Navigator Software If the instrument is connected to a network you can use the Thermo Fisher Connect feature Thermo Fisher Connect provides the following functions Automatically transfer data files from the instrument to your Thermo Fisher Connect account Receive instrument status email notifications V...

Page 47: ...eate account Connect the instrument to your Thermo Fisher Connect account 1 In the navigation pane of the Data Collection Software select GA Instruments4 ga37304 Thermo Fisher Connect Chapter 3 Use the instrument with Thermo Fisher Connect Register and obtain a Thermo Fisher Connect account 3 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide 47 ...

Page 48: ...ction Software select GA Instruments4 ga37304 Thermo Fisher Connect 2 In the middle of the screen click your User ID to connect the instrument to your Thermo Fisher Connect account 3 Select the Enable Destination checkbox then select the storage location in your Thermo Fisher Connect account When a run is complete the data is stored in the results group folder that is specified in the plate record...

Page 49: ...n Instrument function is not supported for the instrument See Connect the instrument to your Thermo Fisher Connect account on page 47 3 Click the instrument to display instrument status Chapter 3 Use the instrument with Thermo Fisher Connect Monitor a run from InstrumentConnect 3 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide 49 ...

Page 50: ...isher Connect account on page 47 1 On your mobile device download the InstrumentConnect from the Apple Store or from Google Play 2 On your mobile device launch InstrumentConnect 3 Touch the instrument to monitor Chapter 3 Use the instrument with Thermo Fisher Connect Monitor a run from a mobile device 3 50 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide ...

Page 51: ...isher Cloud click 2 Click a notification then click Dismiss or Dismiss all to dismiss the notification Chapter 3 Use the instrument with Thermo Fisher Connect View notifications from the instrument on the Cloud 3 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide 51 ...

Page 52: ...linking An administrator can perform the following tasks from InstrumentConnect Access the Manage users function to see a list of all accounts that are linked to the instrument Assign administrator role to one or more users Remove an account from an instrument Disconnect the instrument from InstrumentConnect Change the instrument name First user who links is assigned administrator role Instrument ...

Page 53: ...n to thermofisher com cloud 2 Click Connect Your Lab then click to access InstrumentConnect 3 Select the instrument Note The Manage users and other administrator functions are not enabled until you select an instrument 4 To assign the Admin role to a user or to remove a user click Manage users then perform the following tasks as needed To Do this Assign the Admin role to an additional user Select ...

Page 54: ... data for that instrument from InstrumentConnect You can remove a user from the instrument However doing so deletes the user data from the instrument For more information see Manage the users and administrators of your instrument on page 53 Disconnect individual users from an instrument Chapter 3 Use the instrument with Thermo Fisher Connect Thermo Fisher Connect administrators for an instrument 3...

Page 55: ...otocols Create a results group using defaults This procedure creates a results group that uses the default destination and naming conventions For more information on results groups see the following sections Overview of results groups on page 79 To define a custom destination or to specify custom naming conventions see Create a results group detailed procedure on page 80 1 In the navigation pane o...

Page 56: ... default order of injections for the plate quadrants 384 well plates or 96 well plates on 48 capillary instruments For more information see Default injection order on plates on page 59 Sample and run information Sample name type comment and the settings to use for the run described below 4 Enter a sample name in the Sample Name field then press Enter 5 Optional To add reinjections for a plate sele...

Page 57: ...ormation by using Fill Down commands or by copy pasting Fill Down Copy paste Select the entire row select Edit4Fill Down Special then select a fill down option For 48 capillary instruments select Fill down Special 48 Cap For 96 capillary instruments 96 well plate Select Fill Down 384 well plate Fill down Special 96 Cap If you copy multiple cells select the same number of corresponding target cells...

Page 58: ... 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 View the Event Log 68 View data from the run 69 Check the autoextraction status and manually re extract 72 5 58 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide ...

Page 59: ... which they are placed in the stacker bottom plate runs first Plates are run in the order in which they are placed in the stacker bottom plate runs first The currently running plate is listed in the Auto Sampler field The currently running plate is listed in the Auto Sampler field Completed plates are listed in the Output Stack list Completed plates are listed in the Output Stack list For plates t...

Page 60: ...well 1 Q1 injection 1 Well A1 Q1 injection 2 Well A2 48 384 well 1 Q1 injection 1 Well A1 Q1 injection 2 Well A3 2 Q2 injection 1 Well B1 Q2 injection 2 Well B3 3 Q3 injection 1 Well A2 Q3 injection 2 Well A4 4 Q4 injection 1 Well B2 Q4 injection 2 Well B4 Note With a 384 well plate and a 48 capillary array you can change the run order of the main quadrant bold numbers above but not the injection ...

Page 61: ...the autosampler plate barcodes are scanned and their plate records are used for the run IMPORTANT Ensure that barcodes have been scanned or manually entered for each plate If the plate barcode scanned by the instrument does not match a barcode in the plate record the plate will be put in the Output Stack During an auto run No plates are listed in the Input Stack The currently running plate is list...

Page 62: ...he name of the plate or scan the Plate ID then click Search You can also change the Type of Search to Advanced and enter more specific plate criteria to search for For more information see Search for a plate record on page 77 Chapter 5 Run the instrument Run the instrument in manual mode 5 62 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide ...

Page 63: ...field Completed plates are listed in the Output Stack For more information see Monitor the status of the run on page 65 Change injection order of plate quadrants You can change the run order of quadrants Changing the order of the quadrants overrides the setting in the plate record and is applied to all plates 1 Select GA Instruments4 ga37304Instrument name4 Run Scheduler 2 At the top of the screen...

Page 64: ...nt in manual mode change the order of the plate records in the Input Stack list The order must correspond to the plate order in the In Stack tower Controlling the run You can use the toolbar at the top of the Data Collection Software window to control the run To Click Start the run Stop the current run Stop after the current run Skip to next run stops the current run and begins next scheduled run ...

Page 65: ... page 39 Status Description Input stack Completed Run data for all injections in the plate record is added to the database and autoextraction of data files is starting Processed Data files for all injections in the plate record are autoextracted from the database to the location specified in the results group A processed plate cannot be run again To run the plate again add samples to the plate rec...

Page 66: ...trument is running flashing Check the Event Log See View the Event Log on page 68 or Display the Event Log on page 135 Instrument has stopped Add reinjections to a plate record To add a reinjection edit the plate record then run the plate again 1 In the navigation pane of the Data Collection Software double click GA Instruments4 ga37304 Plate Manager 2 Select a plate record then click Edit 3 Selec...

Page 67: ...lary passed or failed at the end of a spectral calibration Calibration data at the end of a spatial calibration Information for service engineers Displays errors that have occurred during the current run Some of the error messages provide information for service engineers A fatal error usually requires that you restart the Data Collection Software Events box Errors box Chapter 5 Run the instrument...

Page 68: ...e4 Instrument Status4 Event Log 1 1 Clear Errors 2 To delete error messages select all error messages then click Clear Errors Error messages are retained in the Runviewer event log files that are stored in The system status indicator flashes red until all errors are cleared Chapter 5 Run the instrument View the Event Log 5 68 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide ...

Page 69: ...opherogram is a graph of relative dye concentration as a function of time for each dye The displayed data has been corrected for spectral overlap multicomponented How to zoom To zoom an area of an electropherogram 1 Click drag the mouse over the area of interest 2 Release the mouse then click to expand the view 3 Click to return to full view Click individual colors to view or hide them View electr...

Page 70: ...lection Software select GA Instruments4 ga37304 Instrument name4 Array Viewer 1 2 1 Capillary 1 2 Capillary 48 or 96 How to zoom 1 To expand the view click drag the mouse over the area of interest 2 Click to return to full view Display or hide color Click individual colors in the color bar to view or hide the color in the Array View Chapter 5 Run the instrument View data from the run 5 70 3730xl D...

Page 71: ...lect GA Instruments4 ga37304 Run History 2 Search for the plate record of interest See Search for a plate record on page 77 3 Select the run of interest then select any of the icons that are listed below Run History views Icon EPT Viewer Spatial Calibration Viewer Capillary Viewer Array Viewer Spectral Calibration Viewer Reextraction View electrophoresis conditions EPT View data from a completed r...

Page 72: ... with different names or in different locations than autoextracted files extract with a different results group To save data files with different analysis settings than autoextracted files 1 In the navigation pane of the Data Collection Software select GA Instruments4 ga37304 Run History 2 Search for the plate record of interest See Search for a plate record on page 77 All completed runs from the ...

Page 73: ... analysis The ABIBasecaller does not assign a score 5 Select the checkboxes in the Extract column for the samples to re extract 6 As needed select different results group and other settings 7 Click Extract Reextraction creates a new sample file and does not replace the previously saved sample file For example if the first extracted file name is sample01 ab1 then the second first extracted file is ...

Page 74: ...Create results groups and plate records using default settings Overview of plate records A plate record is similar to a plate sample sheet or injection list that you may have used with other instruments The first screen in a plate record specifies the following information Plate attributes Barcode name owner operator number of wells and sealing option Scheduling injection order by plate quadrant A...

Page 75: ...age 79 The remaining fields that are listed are determined by the Application you select for the plate record These fields are imported from the secondary analysis software associated with the plate record Application All fields contain lists of available items that have been created in the secondary analysis software For information on these fields see the user documentation or software help prov...

Page 76: ...d Create and manage plate records 1 In the navigation pane of the Data Collection Software select GA Instruments4 ga37304 Plate Manager 2 Use the following functions if needed Function Description Search See Search for a plate record on page 77 New See Create a plate record on page 56 Edit Opens an existing plate record and allows changes Duplicate Copies information from an existing protocol to a...

Page 77: ...ed 1 From the Type of Search list select Advanced 2 Click the Condition field then select the relevant search condition The conditions that are displayed depends on the attribute that is selected equal less than greater than Not Equal Contains Starts With Ends With or Between 3 In the Value field enter the attributes of interest Value 2 is active only when the Between search condition is selected ...

Page 78: ...instrument protocol or results group name the entry must exactly match a name that currently exists in the Data Collection Software including capitalization If entries do not match exactly an error is displayed and the plate record is not imported 1 In the Plate Manager click Import then navigate to the plate record TXT file to import 2 Select the file of interest then click Open A progress screen...

Page 79: ...p Naming for run folders Default structure and naming convention is Instr Type Instr Name Run Name This string is appended to the directory specified in the location to save files where Run Name is the plate record name Table 6 Results group Analysis Type and settings that are applied to or saved with the data Sequencing Analysis SeqScape Computer name GeneMapper Computer name GeneMapper Generic A...

Page 80: ...s as an XML file in E Users username Documents 3 Click OK Create a results group detailed procedure 1 In the navigation pane of the Data Collection Software select GA Instruments4 Results Group 2 Click New 3 In the General tab enter a Results Group Name and an optional owner and comment 4 Click the Analysis tab then select the Analysis Type For more information see Overview of results groups on pa...

Page 81: ...e remote location to a local drive letter Map Network Drive feature in the Windows operating system You can specify a mapped drive as a destination IMPORTANT Do not specify C drive locations for data storage C drive is used for the operating system The software does not perform pre run disk space checks on C drive 6 Click the Naming tab You can use the default naming conventions for sample files a...

Page 82: ... Sample File Name Format If you do not the Example displays INVALID NAME Note Even if you create a custom run folder location a separate default run folder is generated that contains the log file The log file can be used for troubleshooting Field Description Example Interactively displays the attributes you select The ext attribute is determined by the Analysis Type you select in the Analysis tab ...

Page 83: ... the software Sample GUID Sample File Name Format only Sample Name Sample File Name Format only Time of Extraction Sample File Name Format only Time of Run Sample File Name Format only Unique Time Stamp Integer Sample File Name Format only Subfolder Delimiter Run File Name Format only User Name the user logged into the software if you are using the AB Navigator Software Well Position 4 Click OK Ch...

Page 84: ...he navigation pane of the Data Collection Software select GA Instruments4 ga37304 Protocol Manager 2 Use the following functions if needed Function Description New See Create an instrument protocol on page 85 Edit Opens an existing results group and allows changes Duplicate Copies information from an existing protocol to a new protocol Delete Deletes a saved protocol Import Imports an XML file Exp...

Page 85: ...ts Protocols section click New 3 Enter a protocol name and optional description 4 Select Regular in the Type dropdown list 5 Select the run module and dye set for the protocol see Appendix C Run modules Note If you will use BigDye XTerminator Purification Kit for sequencing reaction clean up select the run modules marked as BDx 6 Click OK Chapter 7 Create and manage instrument protocols run module...

Page 86: ...ware select GA Instruments4 ga37304 Module Manager 2 Click New 3 Enter a run module name and optional description 4 Select Regular in the Type dropdown list 5 In the Template dropdown list select a template module 6 Edit the settings as needed See Run module parameters on page 87 7 Click OK Chapter 7 Create and manage instrument protocols run modules and analysis protocols Create run module 7 86 3...

Page 87: ...ed electrophoresis current variation Current fluctuations above this value will be attributed to air bubbles in system and the voltage automatically powered off Ramp_Delay 1 1 1 800 seconds Delay During Voltage Ramp Data_Delay 1 1 800 seconds Time from the start of separation to the start of sample data collection Run_Time 300 14 000 seconds Run time during which data is collected after Ramp_Delay...

Page 88: ... page 89 Edit Opens an existing results group and allows changes Duplicate Copies information from an existing protocol to a new protocol Delete Deletes a saved protocol IMPORTANT Do not delete the analysis protocol during a run If deleted autoanalysis by Sequencing Analysis Software or SeqScape Software will not be performed Import Imports an XML file Export Saves as an XML file in E Users userna...

Page 89: ...file in other software ABI format that is used with Applied Biosystems software FASTA format that is used with other software Write Standard Chromatogram Format file SCF When selected the software creates a SCF file that can be used with other software The SCF extension is not appended to the file name Write Phred PHD 1 File When selected and the KB basecaller is used the software creates a PHD 1 ...

Page 90: ... a base to every position as well as the QV Assign N s to Basecalls with QV 15 When using the KB basecaller use this option to assign Ns to bases with QVs less than the set point The QV is still displayed Mixed Bases Note This function is active with the KB Basecaller only When enabled determines the secondary peak height ratio where the secondary peak is considered a potential mixed base Reaching...

Page 91: ...Move the instrument Move the array detection cell Note Failure to perform a new spatial calibration can result in poor data quality 1 In the navigation pane of the Data Collection Software select GA Instruments4 ga37304 Instrument name4 Spatial Run Scheduler 2 In the Spatial Run Scheduler view select one of the following options Protocol4SpatialNoFill if the capillaries contain fresh polymer Proto...

Page 92: ...es For additional information see Examples of passing and failing spatial profiles on page 94 A profile is not acceptable if the peak heights are irregular See Spatial calibration troubleshooting on page 138 2 Verify that an orange cross appears at the top of each peak in the profile Expand the profile if needed See Magnify the spatial profile on page 96 1 Figure 14 Peak that does not have orange ...

Page 93: ... 9 11 pixels for a 48 capillary array Note Higher values are acceptable if a corresponding gap in the capillaries in the detection cell are visible Examine every position for the capillary array 4 Click Accept or Reject Chapter 8 Calibrate the instrument Perform spatial calibration 8 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide 93 ...

Page 94: ... Typical passing profile Examples of passing and failing spatial profiles Chapter 8 Calibrate the instrument Perform spatial calibration 8 94 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide ...

Page 95: ...t the beginning and the end of the profile Figure 17 Passing profile with low signal at the beginning of the profile Chapter 8 Calibrate the instrument Perform spatial calibration 8 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide 95 ...

Page 96: ...19 Failing spectral profile 1 Click drag the cursor to create a box around the area of interest 2 Release the mouse button Magnify the spatial profile Chapter 8 Calibrate the instrument Perform spatial calibration 8 96 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide ...

Page 97: ...andard POP 7 36 cm Spect36_MtxStd_POP7 50 50 cm Spect50_MtxStd_POP7 60 1 The software may take up to 30 minutes to calculate the matrices after the run is complete For each dye set capillary array type capillary array length combination After the laser or CCD camera has been realigned replaced by a service engineer After the capillary array is changed or replaced If you see a decrease in spectral ...

Page 98: ... Signal intensity is reduced by approximately half relative to the standard dye sets along with a minimal reduction in the noise resulting in a very slight decrease in the signal noise ratio when compared to data generated using the standard dye sets 3 When using this dye set perform spectral calibrations each time the capillary array is replaced or moved within the detection cell 384 or 96 Well R...

Page 99: ...alysis protocols 2 In the Instrument Protocols pane click New 3 Select Spectral from the Run Module dropdown list 4 Select the dye set polymer and array length 5 Select the run module and the chemistry Calibration type Run Module for the installed capillary length Chemistry Matrix Spect36_MtxStd_1 Spect50_MtxStd_POP 7 _1 Matrix Standard Sequencing Spect36_SeqStd_1 Spect50_SeqStd Sequence Standard ...

Page 100: ...pplication dropdown list 4 In row A01 enter a sample name click the next cell then enter a comment if needed 5 In column 1 of row A01 select the instrument protocol you created for the spectral calibration Create a spectral calibration plate Chapter 8 Calibrate the instrument Perform spectral calibration for sequencing and fragment analysis 8 100 3730xl DNA Analyzer with 3730xl Data Collection Sof...

Page 101: ... within one protocol Note Use the Duplicate function in the Plate Manager to copy information from an existing protocol to a new protocol 7 Click OK 1 In the navigation pane of the Data Collection Software select GA Instruments4 ga37304 Instrument name4 Run Scheduler 2 In the Add Plate field type the Plate ID then press Enter or scan the bar code of a plate to add it to the input stack 3 Place the...

Page 102: ... in the Event Log See View the Event Log on page 68 5 When the run is finished remove the plate from the instrument 1 Open the stacker drawer 2 Open the door of the In Stack tower Place plate assemblies into the instrument Chapter 8 Calibrate the instrument Perform spectral calibration for sequencing and fragment analysis 8 102 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide ...

Page 103: ...r After the instrument completes the spectral calibration run the pass or fail status of each capillary is listed in the Event Log 1 In the navigation pane of the Data Collection Software select GA Instruments4 ga37304 Instrument name4 Instrument Status4 Event Log View the Pass Fail status after the run Chapter 8 Calibrate the instrument Perform spectral calibration for sequencing and fragment ana...

Page 104: ...peaks cause the true dye peak to be missed by the algorithm and can lead to a higher Quality Value than would be computed with the correct peak Therefore it is important to visually inspect the spectral calibration profile for each capillary Condition Number A Condition Number indicates the amount of overlap between the dye peaks in the fluorescence emission spectra of the dyes in the dye set If t...

Page 105: ...ane of the Data Collection Software select GA Instruments4 ga37304 Instrument name4 Spectral Viewer 1 2 3 1 Spectral profile 2 Raw data matrix standards 3 Rename or set the active calibration 2 In the Dye Set drop down list select the dye set Evaluate the spectral calibration data Chapter 8 Calibrate the instrument Perform spectral calibration for sequencing and fragment analysis 8 3730xl DNA Anal...

Page 106: ...elect a passing capillary from which to borrow the calibration 5 Evaluate the spectral calibration profile for each capillary Ensure that the profile meets the criteria listed in the following table See also Magnify the spatial profile on page 96 Attribute Acceptance criteria Example Order of the peaks in the spectral profile intensity vs pixel from left to right 4 dye blue green yellow red 5 dye ...

Page 107: ...le from left to right Fragment analysis 4 dye red yellow green blue 5 dye orange red yellow green blue Extraneous peaks in the raw data profile intensity vs scan None Note The E5 profile may include extraneous peaks outside the matrix peak region which can be ignored Chapter 8 Calibrate the instrument Perform spectral calibration for sequencing and fragment analysis 8 3730xl DNA Analyzer with 3730...

Page 108: ...o the right bottom may not be as rounded and symmetrical as the peak morphology for other dye sets shown above due to the effect of variable binning a feature that reduces signal variation between dyes of different fluorescent efficiencies 1 Click drag the cursor to create a box around the area of interest Magnify the spectral profile Chapter 8 Calibrate the instrument Perform spectral calibration...

Page 109: ...ouse button 3 Press R to reset the view Chapter 8 Calibrate the instrument Perform spectral calibration for sequencing and fragment analysis 8 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide 109 ...

Page 110: ...ted from a sequencing standard Examples of passing sequencing spectral calibrations Chapter 8 Calibrate the instrument Perform spectral calibration for sequencing and fragment analysis 8 110 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide ...

Page 111: ...the way the spectral calibration is generated it is specific to the capillary array used to generate the calibration 1 In the navigation pane of the Data Collection Software select GA Instruments4 ga37304 Instrument name4 Spectral Viewer Failed calibrations are marked with an asterisk 2 Select the dye set of interest 3 Click the List of Calibrations list in the lower right pane Example of a passin...

Page 112: ...5 Click Set to display the selected spectral calibration in the Active Calibration text box Chapter 8 Calibrate the instrument Perform spectral calibration for sequencing and fragment analysis 8 112 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide ...

Page 113: ... in this document Maintenance schedules Daily maintenance Task Frequency Ensure that adequate levels of liquid are in the buffer waste and water reservoirs Before each run 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 Make sure the retainer clips are flush with the sides of t...

Page 114: ...h run Check the loading end header of the capillary array Ensure that the capillary tips are not crushed or damaged Daily or before each run Check the level of polymer in the bottle to ensure that the volume is sufficient for runs Daily or before each run Clean the instrument surfaces Daily Check for leaks around the array knob interconnect tubing nuts and check valve Daily Weekly maintenance Task...

Page 115: ...ailable disk space on E drive on page 131 Monthly As Needed maintenance Task Frequency Clean the drip tray As needed Change the capillary array using the Install Array wizard see Typical conditions for using maintenance wizards on page 117 As needed Remove any dried polymer from the capillary tips Use a lint free wipe moistened with deionized water As needed Chapter 9 Maintenance Maintenance sched...

Page 116: ...e Remove To remove bubbles in the polymer delivery pump chamber channels array ferrule and tubing Water Wash To wash the polymer delivery pump chamber lower polymer block channels and tubing with water when the following conditions are met As part of a monthly maintenance protocol To remove any suspected contaminants in the polymer delivery pump To remove persistent bubbles followed by the Bubble ...

Page 117: ... is idle bubbles that previously did not move are often cleared by running the Bubble Remove wizard Many or large bubbles are present in the pump chamber Run the Water Wash wizard No bubbles are present in the array port during the monthly water wash procedure Perform the Flush Array Port procedure using the Water Wash wizard as part of monthly maintenance even if no bubbles are present Occasional...

Page 118: ... an automated procedure is in progress Leave the door in the starting state whether open or closed until the automated procedure is complete Begin an automated procedure Open The procedure continues when the door is closed and after the autosampler moves to initialize If you open the door again the procedure pauses until the door is closed Begin an automated procedure Closed The procedure pauses i...

Page 119: ...n the instrument for more than 1 week 1 Remove the polymer from 4 storage 2 Loosen the cap and bring the polymer to room temperature 3 To dissolve deposits tighten the cap and gently swirl the polymer IMPORTANT Wear gloves while handling polymer the capillary array septa or buffer reservoirs 1 In the navigation pane of the Data Collection Software select GA Instruments4 ga37304 Instrument name 2 A...

Page 120: ... 2 At the top of the screen select Wizards4Change Polymer Type wizard IMPORTANT When this wizard runs it introduces polymer into the anode buffer jar Replace the anode jar buffer after you run this wizard See Fill the anode buffer jar on page 33 Change polymer type Chapter 9 Maintenance Replenish or change polymer type 9 120 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide ...

Page 121: ...n the polymer blocks Clean the exterior 1 time per week when you replenish polymer Flush the polymer delivery pump water trap 1 time per week Clean the polymer delivery pump chamber channels and tubing 1 time per month Parts of the polymer delivery pump Guidelines Frequency Chapter 9 Maintenance Clean the polymer delivery pump PDP and lower polymer block 9 3730xl DNA Analyzer with 3730xl Data Coll...

Page 122: ...20 mL syringe from the Polymer Block Cleaning Kit Cat No 4335860 with distilled or deionized water Expel any bubbles from the syringe Note Do not use a syringe smaller than 20 mL A smaller syringe may generate excessive pressure within the trap 2 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 fi...

Page 123: ...h the other hand Install the capillary array Capillary array 96 or 48 capillary Lab wipes lint free Gloves IMPORTANT Wear gloves when you handle the capillary array Use the Install Array wizard when changing capillary arrays to properly fill the capillaries with polymer 1 In the navigation pane select GA Instruments4 ga37304 Instrument name 2 At the top of the screen select Wizards4Install Array w...

Page 124: ...on again 2 Place 80 mL of 1X run buffer in the capillary array header shipping cover 3 Lower the capillary tips of the array header into the shipping cover and lock the header onto the cover The tips of the capillaries should be immersed in buffer 4 Clip the detection cell window cover onto the detection cell 5 Attach the detection cell with cover to the storage post on the capillary array frame 1...

Page 125: ...els in the shipping cover and vial at least once a week replenish the buffer as necessary to keep both ends of the capillaries immersed in buffer Clean the detection cell 1 Open the instrument door and the oven door 2 Open the detection cell door by turning the door knob to the left then lowering the door 2 3 1 1 Detection cell door knob 2 Capillary array knob 3 Capillary array 3 Turn the capillar...

Page 126: ...uffer valve lever engages the buffer pin valve 9 Carefully place the detection cell into the detection block Secure it by rotating the cam knob 1 4 turn counterclockwise The pointer on the knob is pointed down 10 Close the detection cell door oven door and instrument door Perform a short term shutdown Perform the short term shutdown procedure if the instrument will be idle for 1week 1X run buffer ...

Page 127: ...tus lights 2 Tray button 4 Remove the buffer water and waste reservoir assemblies from the instrument 5 Disassemble each reservoir assembly and empty the contents of the reservoirs into an aqueous waste container 1 1 Aqueous waste 6 Rinse each reservoir using deionized water Perform a short term shutdown Chapter 9 Maintenance Perform a short term shutdown 9 3730xl DNA Analyzer with 3730xl Data Col...

Page 128: ...ervoir assemblies 1 Add 80 mL 1X run buffer to the Buffer reservoir 2 Assemble the reservoir assembly as shown below 1 2 3 4 5 6 1 Retainer 2 Septum 3 Reservoir cap 4 Reservoir 5 Heated plate base 6 Power cable 1 Add 80 mL high quality deionized water to each reservoir 2 Assemble each reservoir assembly as shown below 1 2 3 4 5 1 Retainer 2 Septum 3 Reservoir cap 4 Reservoir 5 Plate base Chapter 9...

Page 129: ... not aligned 10 Dry the reservoirs using lint free wipes 1 1 Lint free wipe 11 Connect the buffer reservoir plate base cable to the heater outlet inside the instrument IMPORTANT After installing the buffer reservoir make sure the cable is out of the way of the autosampler 1 2 1 Buffer reservoir 2 Buffer position 12 Place the water and waste reservoirs in the instrument Load the three reservoirs in...

Page 130: ...adequate space for database and sample data storage Before a run or batch of runs the Data Collection Software automatically checks free disk space If sufficient disk space is not available to store the run data the following occurs An error message is displayed in the Error Code pane in the Event Log The status bar displays a flashing Pre run automatic disk space checks Chapter 9 Maintenance Main...

Page 131: ...e Delete data from the database on page 132 1 1 Cleanup Processed Plates Check disk space monthly 1 In the navigation pane of the Data Collection Software select GA Instruments4 Database Manager Full database error Check available disk space on E drive Chapter 9 Maintenance Maintain adequate space for database and sample data storage 9 3730xl DNA Analyzer with 3730xl Data Collection Software 5 Use...

Page 132: ...All run data in the database that corresponds to the plate records Spectral calibration plate records Sequence analysis and fragment analysis plate records with a status of Completed Instrument protocols Result groups Analysis protocols IMPORTANT Do not delete spectral calibration plate records Doing so permanently deletes the spectral information from the database and prevents you from re extract...

Page 133: ...te It may take several minutes to clean up the database Chapter 9 Maintenance Maintain adequate space for database and sample data storage 9 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide 133 ...

Page 134: ...the end of spatial calibration if Accept Reject buttons are dimmed If maintenance wizards are taking longer than expected If software operations are taking longer than expected When you are instructed to restart the instrument and the computer 1 Exit the Data Collection Software 2 Power off the computer 3 Make sure the instrument door is closed then power off the instrument 4 When the computer is ...

Page 135: ...last message in the log file 3 Perform the required tasks to fix the problem Review a run log file Run log files are stored in the default directory not in the destination directory specified by the results group Navigate to E AppliedBiosystems UDC DataCollection Log Appendix A Troubleshooting Display the Event Log A 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide 135 ...

Page 136: ...pen Close the instrument door The oven door is open Close the oven door The buffer reservoir or capillary array are not installed Install the buffer reservoir or capillary array Status light is solid yellow The instrument cannot communicate with the computer 1 Ensure that the instrument door is closed 2 Ensure that the Ethernet cable is connected to the back of the instrument and to the computer A...

Page 137: ...atch the plate type Sealing type from instr is Heat Sealing and does not match set by user Septa message in Event Log The plate record specifies a sealing type that does not match the base in which the plate is loaded Edit the plate record to specify the sealing type that matches the base in which the plate is loaded Load the plate in the correct base See Prepare the plate assemblies on page 42 Er...

Page 138: ...ore help is available by typing NET HELPMSG 2182 Ignore message Ignore message Spatial calibration troubleshooting Observation Possible cause Recommended action Spatial calibration fails Bubbles are present in capillaries Run the Bubble Remove wizard Observe the array port area to ensure bubbles are removed Detection cell window is not clean Clean the detection cell see page 125 Problem with capil...

Page 139: ...r Action 1 for Cause 1 Insert paragraphs notes lists figures or tables as needed Replace the polymer with a fresh lot using the Change Polymer wizard Air bubbles especially in the polymer Refill the capillaries using the Bubble Remove wizard Properly bring the polymer to room temperature Replace expired polymer Possible contaminant in the polymer Replace the polymer using the Change Polymer wizard...

Page 140: ...g in the pump system Clean the pump See Clean the polymer delivery pump PDP and lower polymer block on page 121 Bubbles in the tubing or in the polymer block Use the Bubble Remove wizard Air bubbles in the pump Fittings may be loose Finger tighten all fittings Do not overtighten Run the Bubble Remove wizard For persistent bubbles replace the polymer with water then run the Bubble Remove wizard Rep...

Page 141: ... specify the sealing type that matches the base in which the plate is loaded Load the plate in the correct base See Prepare the plate assemblies on page 42 Plate sensor malfunction Contact Support Full database message Insufficient disk space See Maintain adequate space for database and sample data storage on page 130 Appendix A Troubleshooting General troubleshooting A 3730xl DNA Analyzer with 37...

Page 142: ...5 in 1 kg 0 2 lbs Access to all four sides of the instrument is required for servicing Do not block access to the rear of the instrument Minimum rear clearance is 30 5 cm 12 in If two instruments are placed back to back allow 61 cm 24 in of clearance between the instruments Table 10 Operating specifications Component Specification Laser Long life single line 505 nm solid state laser excitation sou...

Page 143: ...etic radiation for example unshielded intentional RF sources Strong electromagnetic radiation may interfere with the proper operation of the device Transient overvoltage category Installation categories II Vibration The instrument is not adjacent to strong vibration sources such as a centrifuge pump or compressor Excessive vibration will affect instrument performance Pollution degree II Install th...

Page 144: ...ely disconnect the main power supply to all the equipment Allow adequate space between the wall and the equipment so that the power cords can be disconnected in case of emergency Dedicated line and ground between the instrument and the main electrical service Maximum power dissipation 600 VA not including computer and monitor Mains AC line voltage tolerances must be up to 10 percent of nominal vol...

Page 145: ...Because of the Ethernet cable connection between the instrument and the computer the computer must be located within 9 feet of the instrument Appendix B Instrument specifications Power and communication connections B 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide 145 ...

Page 146: ...un Sequencing Run Modules Approximate Run Times 1 minutes KB Basecaller QV20 CRL Bases 2 POP 7 50 Extra long read XLRSeq50_POP7 180 900 BDx_XLRSeq50_POP7 3 50 Long read LongSeq50_POP7 120 850 BDx_LongSeq50_POP7 3 50 Fast read FastSeq50_POP7 60 700 BDx_FastSeq50_POP7 3 36 Standard read StdSeq36_POP7 60 700 BDx_StdSeq36_POP7 3 36 Rapid read RapidSeq36_POP7 35 550 BDx_RapidSeq36_POP7 36 Short read Ta...

Page 147: ...h 98 5 basecalling accuracy and less than 2 N s using pGEM 32f as template 3 Run the BDx utility after installation or after preventative maintenance is performed 4 Time stated for 400 bases Module can be customized to run 200 400 bases IMPORTANT Use BDX run modules only if you prepare samples with BigDye XTerminator Purification Kit Use non BDX run modules for samples purified with other methods ...

Page 148: ...matrix standards Dye Set Calibration Standards G5 DS 33 G5 RCT reduced cross talk 1 J6 DS 36 Any4Dye Any5Dye Custom Any4Dye HDR high dynamic range 2 3 Custom Any5Dye DS 02 for SNaPshot applications Custom 1 Use for fragment analysis applications on 96 capillary arrays 2 Signal intensity is reduced by approximately half relative to the standard dye sets along with a minimal reduction in the noise r...

Page 149: ... noise ratio Because of the decrease in overall signal intensity a higher dynamic range is available when using RCT dye sets The spectral calibration for an RCT dye set is specific to the capillary array on which is it run Do not ovveride spectral calibration when you use an RCT dye set Fragment analysis with a 96 capillary array Applications with a high dynamic range where the signal intensity of...

Page 150: ...L 96 well 4367472 Plate Base for 3730 septa seal Fast 0 1 mL 96 well 4367469 Plate Retainer heat seal for 3730 Systems Fast 0 1mL 96 well 4367474 Plate Base heat seal for 3730 Systems Fast 0 1 mL 96 well 4367473 384 well MicroAmp Optical 384 Well Reaction Plate with Barcode 4309849 Plate Septa 384 well 4315934 Plate Base septa seal for 3730 3730xl 384 well 4334874 Plate Base heat seal for 3730 373...

Page 151: ...ffer 10X 500 mL 4335613 Miscellaneous Hi Di Formamide 4311320 Polymer Block Cleaning Kit 4335860 SNaPshot Multiplex Kit 4323159 Sequencing and fragment analysis calibration standards Item Cat No Sequencing 3730 3730xl DNA Analyzer Sequencing Standards BigDye Terminator v3 1 4336943 3730 3730xl DNA Analyzer Sequencing Standards BigDye Terminator v1 1 4336799 Fragment analysis DS 33 Matrix Standard ...

Page 152: ...Installation Standards with GeneScan 600 LIZ Size Standard v2 0 4376911 GeneScan 120 LIZ Size Standard 4324287 GeneScan 500 ROX Size Standard 401734 GeneScan 600 LIZ Size Standard v2 0 4408399 GeneScan 1200 LIZ Size Standard 4379950 Appendix E Catalog numbers Fragment analysis size standards E 152 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide ...

Page 153: ...ntation and Support section in this document Symbols on this instrument 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 CAUTION Indicates a potentially hazardous situation that if not avoided may result in minor or moderate injury It may al...

Page 154: ... Consulter le manuel pour d autres renseignements de sécurité MISE EN GARDE Risque de choc électrique MISE EN GARDE Surface chaude MISE EN GARDE Danger biologique potentiel MISE EN GARDE Rayonnement ultraviolet Appendix F Safety Symbols on this instrument F 154 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide ...

Page 155: ... closed 1 Physical hazard 2 Electric shock 1 Figure 21 Safety symbols that are visible with the oven door open 1 Laser Location of safety labels Appendix F Safety Symbols on this instrument F 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Guide 155 ...

Page 156: ...current Both direct and alternating current Conformity mark Description Indicates conformity with safety requirements for Canada and U S A Indicates conformity with China RoHS requirements Indicates conformity with European Union requirements Control and connection symbols Conformity symbols Appendix F Safety Symbols on this instrument F 156 3730xl DNA Analyzer with 3730xl Data Collection Software...

Page 157: ...t system are not designed or built by Thermo Fisher Scientific Consult the manufacturer s documentation for the information needed for the safe use of these products Instrument safety CAUTION 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 shoc...

Page 158: ...e est déconnecté La continuité de la mise à la terre est impérative pour le fonctionnement de l instrument en toute sécurité WARNING Power Supply Line Cords Use properly configured and approved line cords for the power supply in your facility AVERTISSEMENT Cordons d alimentation électrique Utiliser des cordons d alimentation adaptés et approuvés pour raccorder l instrument au circuit électrique du...

Page 159: ... personne responsable est tenu d assurer le respect des exigences suivantes Ne pas utiliser d agents de nettoyage ou de décontamination susceptibles de réagir avec certaines parties de l appareil ou avec les matières qu il contient et de constituer de ce fait un DANGER L instrument doit être correctement décontaminé a si des substances dangereuses sont renversées sur ou à l intérieur de l équipeme...

Page 160: ... the instrument Alert DANGER Class 3B III visible and or invisible laser radiation present when open and interlocks defeated Avoid exposure to beam CAUTION 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 Alerte français DANGER Rayonnement laser v...

Page 161: ...as applicable 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 standards Reference Description EU Directive 2014 30 EU European Union EMC Directive EN 61326 1 IEC 61326 1 Electrical Equipment for Measurement Control and Laboratory Use EMC Requirements Part 1 Gener...

Page 162: ...rence by one or more of the following measures Reorient or relocate the receiving antenna Increase the separation between the equipment and receiver Connect the equipment into an outlet on a circuit different from that to which the receiver is connected Consult the dealer or an experienced radio TV technician for help Environmental design standards Reference Description Directive 2012 19 EU Europe...

Page 163: ...aste 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 AVERTISSEMENT PRÉCAUTIONS GÉNÉRALES EN CAS DE MANIPULA...

Page 164: ...des limitations peuvent s appliquer à leur élimination Biological hazard safety WARNING BIOHAZARD Biological samples such as tissues body fluids infectious agents and blood of humans and other animals have the potential to transmit infectious diseases Conduct all work in properly equipped facilities with the appropriate safety equipment for example physical containment devices Safety equipment can...

Page 165: ...related products Document Publication number AB Navigator Software Administrator Guide 4477853 BigDye XTerminator Purification Kit Protocol 4374408 SeqScape Software 3 User Guide 4474242 DNA Sequencing Analysis Software 6 4474239 GeneMapper Software v4 1 Quick Reference Guide 4403615 Customer and technical support Visit thermofisher com support for the latest service and support information Worldw...

Page 166: ...anty Life Technologies Corporation and or its affiliate s warrant their products as set forth in the Life Technologies General Terms and Conditions of Sale at www thermofisher com us en home global terms and conditions html If you have any questions please contact Life Technologies at www thermofisher com support Documentation and support Limited product warranty 166 3730xl DNA Analyzer with 3730x...

Page 167: ... 152 front panel indicators 14 G green indicator light 14 GS600 LIZ v2 0 size standard 152 I Index Term 26 159 instrument components 13 description 10 disconnect from Thermo Fisher Connect 53 during a run 18 remove user 53 restart 134 theory of operation 17 L laser specifications 142 limited product warranty 166 M matrix standard part numbers 152 mobile device monitor a run 50 view results 50 P pa...

Page 168: ...ity value 104 spectral calibration standard 99 support customer and technical 165 symbols conformity 156 control and connection 156 safety 153 system specifications 142 T terms and conditions 166 theory of operation 17 Thermo Fisher Connect disconnect instrument 53 ThermoFisher Connect analysis software 23 W warranty 166 Index 168 3730xl DNA Analyzer with 3730xl Data Collection Software 5 User Gui...

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Page 170: ...thermofisher com support thermofisher com askaquestion thermofisher com 1 October 2018 ...

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