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Thermo Scientific Applied Biosystems SeqStudio Genetic Analyzer, User Manual

The Thermo Scientific Applied Biosystems SeqStudio Genetic Analyzer is a cutting-edge genetic analysis system designed to deliver accurate and reliable results. To help users get started, we provide an informative "Getting Started Manual" that you can easily download for free from our website. Explore the possibilities of genetic analysis with confidence.

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Create your own local instrument profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
Change your own local instrument profile PIN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153

Manage storage space . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153

Automatic file cleanup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
Export or delete a plate setup (PSM file) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
Export results from the instrument (sample data files and QC reports) . . . . . . . . . . 154
Delete a run history . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
Back up user data (plates and results) (administrator only) . . . . . . . . . . . . . . . . . . . . 155

■

CHAPTER 11    

Maintain the instrument  .............................. 156

Regular maintenance tasks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156

Check the cathode buffer fill level . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156
Clean the instrument exterior and touchscreen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
Clean the autosampler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157

Manage the cartridge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158

Cartridge storage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158
Set cartridge storage mode (administrator only) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
Check or export the Instrument-cartridge history  . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
Check or export the cartridge history . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
Fill the capillary array and refresh the polymer delivery system . . . . . . . . . . . . . . . . 161
Remove the cartridge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
Insert the cartridge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
Store the cartridge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
SeqStudio

™

 Integrated Capillary Protector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164

Long-term on-instrument cartridge storage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165

Install cathode buffer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166

SeqStudio

™

 Genetic Analyzer Cathode Buffer Container storage . . . . . . . . . . . . . . . . 166

Remove the SeqStudio

™

 Genetic Analyzer Cathode Buffer Container . . . . . . . . . . . . 166

Assemble the SeqStudio

™

 Genetic Analyzer Cathode Buffer Container (CBC) . . . . . 166

Insert the Cathode Buffer Container . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167

■

APPENDIX A    

Troubleshooting ........................................ 169

Troubleshooting resources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
Troubleshooting workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
Export log files for plates, install runs, injections, and instrument . . . . . . . . . . . . . . . . . . . 170
View the raw data and the EPT plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
Data quality alerts  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
Sizecalling and basecalling quality alerts  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
Check size standard quality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
Instrument troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
Cartridge troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
Sample and data troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
EPT data  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180

Contents

8

SeqStudio

™

 Genetic Analyzer Instrument and Software User Guide

Summary of Contents for Applied Biosystems SeqStudio Genetic Analyzer

Page 1: ...ftware USER GUIDE for use with SeqStudio Data Collection Software v1 2 SeqStudio Plate Manager SeqStudio Remote Monitoring App SAE Administrator Console v2 0 SeqStudio Genetic Analyzer Cartridge Cat No A33671 SeqStudio Genetic Analyzer Cartridge v2 Cat No A41331 Publication Number MAN0018646 Revision A 0 ...

Page 2: ...t notice DISCLAIMER TO THE EXTENT ALLOWED BY LAW THERMO FISHER SCIENTIFIC INC AND OR ITS AFFILIATE S WILL NOT BE LIABLE FOR SPECIAL INCIDENTAL INDIRECT PUNITIVE MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT INCLUDING YOUR USE OF IT Revision history Pub No MAN0018646 Revision Date Description A 0 4 November 2019 New user guide for SeqStudio Data Collection Softw...

Page 3: ...g system options 25 Recommended browsers 25 SeqStudio Remote Monitoring App overview 26 Network connection options 27 Network and password security requirements 27 Network configuration and security 27 Password security 27 Experiment types 28 Data output 29 Secondary analysis software 29 Workflow Connect cloud based platform or desktop 31 Workflow instrument 32 CHAPTER 2 Prepare the samples and th...

Page 4: ...ions 48 Assign instrument administrator role to other users 48 Manage the users and administrators of your instrument 49 Disconnect individual users from an instrument 50 Register and obtain a Connect cloud based platform account 50 Link the instrument to your Connect cloud based platform account 51 Change your own Connect cloud based platform instrument profile PIN 52 Set up email notifications f...

Page 5: ...gs 75 Modify the default file name convention 75 Hide or share a plate Plate setup security 76 Define custom fields 76 CHAPTER 6 Create or modify a plate setup from the instrument 77 PSM and CSV plate setup files for import into the instrument 78 Shared public hidden my plates and guest plate setup files 79 Overview of plate setup settings 79 Optional Set up for auto export of sample data files AB...

Page 6: ...s 106 View results when the run is completed 107 Unload the plate or the tube assembly 109 CHAPTER 8 View and analyze results 110 View results in the Remote Monitoring App on the Connect cloud based platform 110 View results on the instrument 111 View results when the run is completed 111 Fragment HID analysis results 113 Sequence analysis results 115 EPT plot 117 View results for a previously run...

Page 7: ...tform account 136 Lock the touchscreen 137 Manage plate setups 138 Export or delete a plate setup PSM file 138 Import a plate setup from a CSV or PSM file 139 Manage run settings instrument 139 Manage run modules 139 Manage size standard definitions 142 Manage analysis settings 142 Modify the default file name convention 146 Manage instrument settings 147 Display instrument hardware and software i...

Page 8: ...resh the polymer delivery system 161 Remove the cartridge 161 Insert the cartridge 161 Store the cartridge 163 SeqStudio Integrated Capillary Protector 164 Long term on instrument cartridge storage 165 Install cathode buffer 166 SeqStudio Genetic Analyzer Cathode Buffer Container storage 166 Remove the SeqStudio Genetic Analyzer Cathode Buffer Container 166 Assemble the SeqStudio Genetic Analyzer ...

Page 9: ...e set and custom dye set calibration 192 System versus custom dyes 192 Factory auto and manual calibration 193 Determine if manual calibration is required 193 Perform a system dye calibration 195 Perform a custom dye calibration 197 View the dye calibration history 201 Import or export a custom dye set 202 Perform an install run 203 Overview of install checks 203 Perform an install run 204 View in...

Page 10: ...y equipment 226 APPENDIX H Safety 227 Symbols on this instrument 227 Conformity symbols 228 Safety alerts on this instrument 229 Safety information for instruments not manufactured by Thermo Fisher Scientific 230 Instrument safety 230 General 230 Physical injury 230 Electrical safety 230 Cleaning and decontamination 231 Instrument component and accessory disposal 231 Laser 231 Safety and electroma...

Page 11: ...Documentation and support 236 Related documentation 236 Customer and technical support 236 Limited product warranty 237 Index 238 Contents SeqStudio Genetic Analyzer Instrument and Software User Guide 11 ...

Page 12: ...e Manager overview 24 SeqStudio Remote Monitoring App overview 26 Network connection options 27 Network and password security requirements 27 Experiment types 28 Data output 29 Secondary analysis software 29 Workflow Connect cloud based platform or desktop 31 Workflow instrument 32 1 12 SeqStudio Genetic Analyzer Instrument and Software User Guide ...

Page 13: ...e a cartridge is inserted Performs an automatic spectral calibration adjustment auto calibration for each sample to correct for spectral overlap The instrument is compatible with 96 well Standard plates and 8 strip Standard tubes The SeqStudio Genetic Analyzer is a stand alone instrument It is run directly from the touchscreen with SeqStudio Data Collection Software and does not require a computer...

Page 14: ...the cathode buffer and sample plate or tubes 4 USB port 2 4 5 3 1 Figure 2 Interior of the instrument 1 Cartridge rails 2 Cartridge 3 Cathode buffer located inside the autosampler 4 Autosampler contains the plate or tube holder and the cathode buffer 5 Plate or tube holder Chapter 1 Product information Parts of the instrument 1 14 SeqStudio Genetic Analyzer Instrument and Software User Guide ...

Page 15: ...alyzer Cartridge A33671 1 cartridge with an optical cover and a SeqStudio Integrated Capillary Protector attached for shipment and storage See Table 1 on page 18 SeqStudio Genetic Analyzer Cartridge v2 A41331 1 cartridge with an optical cover and a SeqStudio Integrated Capillary Protector attached for shipment and storage See Table 2 on page 19 SeqStudio Genetic Analyzer Cathode Buffer Container A...

Page 16: ...tector See Figure 6 Has a radio frequency identification RFID tag which is used by the instrument to track remaining usage and expiration 1 2 3 4 5 6 Figure 4 Parts of the cartridge 1 Universal polymer Supplies polymer to the polymer delivery pump 2 Polymer delivery system Pumps polymer into the capillary array 3 Anode buffer reservoir Genetic Analysis running buffer to support electrophoresis 4 O...

Page 17: ...illary Protector 1 Optical cover 2 Optical cover hand hold for removing the optical cover 3 Integrated Capillary Protector 4 Cartridge hand hold IMPORTANT Remove the Integrated Capillary Protector before installing the cartridge into the instrument Installing the cartridge with the ICP in place can damage the capillary array Chapter 1 Product information SeqStudio Genetic Analyzer consumables 1 Se...

Page 18: ... instrument does not maintain the correct temperature conditions for the cartridge when it is powered off Avoid cartridge exposure to ambient temperature Off instrument storage For intermittent use can be stored off instrument until the expiry date on the label or up to 4 months after first use Store upright at 2 8 C with an integrated capillary protector ICP and optical cover installed see Store ...

Page 19: ...ent does not maintain the correct temperature conditions for the cartridge when it is powered off Avoid cartridge exposure to ambient temperature Off instrument storage For intermittent use can be stored off instrument until the expiry date on the label or up to 6 months after first use Store upright at 2 8 C with an integrated capillary protector ICP and optical cover installed see Store the cart...

Page 20: ...he autosampler 3 Fill line replace the CBC when the buffer is at the fill line 4 Cathode buffer compartment 5 Waste and wash compartment 1 4 2 3 Figure 8 Autosampler 1 Location of plate or tubes 2 Release button 3 Location of Cathode Buffer Container 4 Location to position the Cathode Buffer Container notch The cartridge and cathode buffer have radio frequency identification RFID tags The instrume...

Page 21: ... 250 injections Cathode buffer When the autosampler initializes When a plate is retracted The first time a new CBC is loaded on an instrument the installation date is recorded on the CBC After each injection the injection count is updated Every 8 hours and or before each run 1 When the CBC is within 2 days of expiry date When the number of injections is approaching the limit of 125 injections 1 If...

Page 22: ...ta Collection Software The touch screen allows scrolling and zooming by pinch Plates can be set up and saved on a computer using the SeqStudio Plate Manager running on a desktop or on the Connect cloud based platform These plate setups can be saved to and accessed from the instrument from A network drive A USB drive The Connect cloud based platform You can monitor runs directly from the instrument...

Page 23: ...jection options Create custom dye set to import open a plate setup containing a custom dye set to import open a plate setup containing a custom dye set Edit during a run or after a run is complete Monitor run Pause or cancel a run Edit injection parameters and re inject samples View results View run result details View PUP score View trace score sequence analysis only View size quality fragment HI...

Page 24: ...er overview The SeqStudio Plate Manager is a stand alone software It allows you to set up and save plates that you can open and run on the instrument The SeqStudio Plate Manager is available On the Connect cloud based platform as an app with access to the SeqStudio Remote Monitoring App At thermofisher com for download and installation on a computer On a USB for installation on a computer Install ...

Page 25: ...ozilla Firefox Version 32 0 3 Google Chrome Version 38 02 Apple Safari Version 7 Microsoft Edge 10 Windows 10 Microsoft Internet Explorer 11 Windows 7 The use of other browsers or other versions can result in reduced functionality and improper display of information Computer and operating system options Recommended browsers Chapter 1 Product information SeqStudio Plate Manager overview 1 SeqStudio...

Page 26: ... an app on the Connect cloud based platform with direct access from the Plate Manager or the InstrumentConnect At thermofisher com for download and installation on a mobile device Figure 10 Remote Monitoring App on the Connect cloud based platform Chapter 1 Product information SeqStudio Remote Monitoring App overview 1 26 SeqStudio Genetic Analyzer Instrument and Software User Guide ...

Page 27: ...software it is the responsibility of your IT personnel to ensure that such drives are configured and secured correctly to prevent data corruption or loss It is the responsibility of your facility administrator IT and security personnel to prevent the use of any unsecured ports such as USB Ethernet and ensure that the system security is maintained Thermo Fisher Scientific strongly recommends that y...

Page 28: ...Fragment HID analysis is the determination of the size of fragments It uses the size standard in each sample to create a standard curve for each sample It then determines the relative size of each dye labeled fragment in the sample by comparing fragments with the standard curve for that specific sample For more information see DNA Fragment Analysis by Capillary Electrophoresis User Guide Pub No 44...

Page 29: ...onnect for the latest available secondary analysis applications Note Data from the SeqStudio Genetic Analyzer may be labeled as 3200 in secondary analysis software Secondary analysis apps on the Connect cloud based platform Analysis App Description Sequencing Quality Check QC module Automatically checks sequence trace quality Provides a results summary that is based on quality parameter settings A...

Page 30: ... software cannot analyze data files generated by the SeqStudio Genetic Analyzer Contact Support for information on obtaining the latest versions of software Analysis Software Minimum version required Sequencing Sequencing Analysis Software 6 2 SeqScape Software 3 2 Variant Reporter Software 2 2 Minor Variant Finder Software 1 2 Fragment analysis GeneMapper Software 5 1 HID analysis GeneMapper ID X...

Page 31: ...nt Load the plate or the tube assembly page 92 Select a plate setup and start a run page 93 Monitor a run from the Connect cloud based platform page 95 Monitor a run from a mobile device page 103 Monitor a run from the instrument page 105 View and analyze results View results in the Remote Monitoring App on the Connect cloud based platform page 99 View results on the instrument page 111 Export res...

Page 32: ...om fields page 86 Start and monitor a run On the instrument Load the plate or the tube assembly page 92 Select a plate setup and start a run page 93 Monitor a run from the instrument page 105 View and analyze results View results on the instrument page 111 Export results from the instrument sample data files and QC reports page 121 Analyze data in a secondary analysis software application Chapter ...

Page 33: ...over There are no components inside the instrument that you can safely service yourself If you suspect a problem contact technical support CAUTION Moving parts CAUTION FIRE HAZARD For continued protection against the risk of fire replace fuses only with listed and certified fuses of the same type and rating as those currently in the instrument CAUTION Hot surface CAUTION Piercing hazard CAUTION Po...

Page 34: ...t is powered off Avoid cartridge exposure to ambient temperature 1 On Off switch Sign in 1 If another user is signed in touch in the home screen then touch Sign out 2 In the Sign in screen touch the down arrow 3 Touch your instrument profile then enter your PIN Note If the instrument is left unattended for 120 minutes the instrument profile is signed out Chapter 2 Prepare the samples and the instr...

Page 35: ...utton No PIN is required Sign out In the home screen 1 Touch 2 Touch Sign out Note If a run is in progress Lock the instrument is displayed instead of Sign out 3 Touch Yes to confirm Chapter 2 Prepare the samples and the instrument Sign in with the Guest instrument profile 2 SeqStudio Genetic Analyzer Instrument and Software User Guide 35 ...

Page 36: ... See Check the consumables status on page 39 7 Current user 8 Connectivity icons Connectivity icon Status or The instrument is connected to a wired or wireless network The instrument is connected to network drive The current instrument profile is linked to the Connect cloud based platform Chapter 2 Prepare the samples and the instrument Parts of the home screen 2 36 SeqStudio Genetic Analyzer Inst...

Page 37: ...tation spin columns or the BigDye XTerminator Purification Kit If ethanol precipitation or spin columns are used dry the samples in a vacuum centrifuge without heat or at low heat for 10 15 minutes or until dry Note Do not over dry the samples Resuspend in 10 20 µL of Hi Di Formamide Use a 65 µL or 130 µL sample volume for samples that are prepared with the BigDye XTerminator Purification Kit See ...

Page 38: ...col then pipet the sample into the plate 2 Place a septum onto the plate a Align the holes of the septa with the wells b Press gently until the septum is inserted into position in each well 3 Centrifuge the plate assembly briefly to collect the contents at the bottom of each well Centrifuge the plate assembly again if the contents are not at the bottom of the wells 4 Heat denature as required 5 Pl...

Page 39: ...tents are not at the bottom of the tubes 5 Heat denature as required 6 Place the tube assembly on ice for 3 minutes Load the tube assembly onto the instrument immediately or keep the tubes on ice and protected from light until they are loaded onto the instrument Prepare the instrument 1 Touch Settings4Consumable status 2 Ensure that Sufficient consumables are installed for the run Installed consum...

Page 40: ...d The cartridge has expired No injections remain for the capillary array or It has exceeded the manufacturer s expiry date or It has exceeded the maximum number of days allowed on the instrument 1 The buffer has expired No injections remain for the cathode buffer or It has exceeded the manufacturer s expiry date or It has been installed on the instrument for 14 days 1 The maximum number of days al...

Page 41: ...mpler to open the lid then remove the CBC 2 1 1 Release button 2 Location of CBC 3 Check the buffer fill level a Remove the CBC b Ensure that the level of buffer is above the fill line If the buffer is at or below the fill line see Assemble the SeqStudio Genetic Analyzer Cathode Buffer Container CBC on page 166 and Insert the Cathode Buffer Container on page 167 If the buffer is above the fill lin...

Page 42: ...prompted 7 Touch Eject cartridge then open the instrument door when prompted 8 Hold the cartridge at the hand hold above the capillaries then pull to remove it from the instrument 9 Insert a new cartridge see Insert the cartridge on page 161 10 Close the instrument door Chapter 2 Prepare the samples and the instrument Prepare the instrument 2 42 SeqStudio Genetic Analyzer Instrument and Software U...

Page 43: ...a Connect button in another location you touch a Link button Both actions do the same thing Connect the instrument to the InstrumentConnect on the Connect cloud based platform and Link your local instrument profile to your Connect cloud based platform account The first user who links the instrument to the Connect cloud based platform is automatically assigned the Connect platform administrator rol...

Page 44: ...t occur Before you link You enter your local instrument profile name in the Sign In screen Your local instrument profile UserABC is displayed in the home screen of the instrument All plates and results that you create are accessible only when you are signed in with your local instrument profile When you link You use an option described in Link the instrument to your Connect cloud based platform ac...

Page 45: ...re saved under local instrument profile and can be copied to the Connect platform see Export results from the instrument sample data files and QC reports on page 121 Your local instrument profile name UserABC is available for selection in the Sign In screen In this scenario your local instrument profile name is created automatically on the instrument before you link The same user name is used for ...

Page 46: ...nt profile Your Connect platform instrument profile name User G is available for selection in the Sign In screen If your Connect platform account is unlinked Your local instrument profile User G is displayed in the home screen of the instrument Plates and results that were saved under your Connect platform instrument profile are accessible under your local instrument profile New plates and results...

Page 47: ... instrument Assign the Connect platform administrator role to one or more users Remove a user from an instrument Disconnect the instrument from InstrumentConnect Change the instrument name 1 The first user who links their local instrument profile to their Connect platform account is assigned a Connect platform profile with administrator role In the top left of the screen you are viewing in the Con...

Page 48: ...sers Remove a user from an instrument Disconnect the instrument from InstrumentConnect Change the instrument name A Connect cloud based platform administrator for an instrument can assign instrument administrator role to other users 1 Sign in to thermofisher com connect 2 Click to access InstrumentConnect 3 Select the instrument Note The Manage users and other administrator functions are not displ...

Page 49: ...nect cloud based platform accounts Removes the instrument from InstrumentConnect 1 Sign in to apps thermofisher com 2 Click to access InstrumentConnect 3 Select the instrument Note The Manage users and other administrator functions are not displayed until you select an instrument 4 To assign the Admin role to a user or to remove a user click Manage users then To Do this Assign the Admin role to an...

Page 50: ...o deletes the user data from the instrument For more information see Manage the users and administrators of your instrument on page 49 Register and obtain a Connect cloud based platform account 1 Go to www thermofisher com 2 On the home page select Sign In4 Register 3 Fill in all information then click Create account Disconnect individual users from an instrument Chapter 3 Use the instrument with ...

Page 51: ...ct cloud based platform account detailed instructions 1 If a user is signed in touch then touch Sign out 2 In the Sign In screen touch Get started4Connect 3 In the Connect to the Cloud screen touch a connection option Chapter 3 Use the instrument with the Connect cloud based platform Link the instrument to your Connect cloud based platform account 3 SeqStudio Genetic Analyzer Instrument and Softwa...

Page 52: ...reen a link code is displayed On a computer 1 Access the Connect platform 2 Access InstrumentConnect 3 Click Add instrument 4 Select SeqStudio 5 Enter the link code Change your own Connect cloud based platform instrument profile PIN 1 Sign in to thermofisher com connect 2 Click to access InstrumentConnect 3 Click Update PIN number Chapter 3 Use the instrument with the Connect cloud based platform ...

Page 53: ...your Connect platform instrument profile and PIN 2 In the home screen of the instrument touch Settings4Instrument settings4Email notifications Note If you are signed in with a local instrument profile instead of a Connect platform instrument profile the Email notifications button is not displayed on the Instrument Settings screen Chapter 3 Use the instrument with the Connect cloud based platform S...

Page 54: ...he options for which you want to receive email notifications then touch Done Chapter 3 Use the instrument with the Connect cloud based platform Set up email notifications from the instrument 3 54 SeqStudio Genetic Analyzer Instrument and Software User Guide ...

Page 55: ...inistrator only 59 Disable SAE administrator only 59 Sign in with SAE enabled 60 Specify audit reasons 61 E signature requirements when you start a run 61 Sign a plate setup 63 View E signature records for a plate setup 63 Sign a dye calibration or an install run 64 View E signature records for a dye calibration or an install run 64 Signing in after automatic screen locking 64 Use the instrument w...

Page 56: ...ignature SAE v2 0 module provides the following SAE functionality on the instrument System security Controls user sign in and access to functions Auditing Tracks changes and actions performed by users E signature Allows users to provide an electronic signature user name and password when performing certain functions Depending on the way that your SAE administrator configures these features Some of...

Page 57: ...allows you to enter your password to allow the action Configuring the SAE module For information on configuration see SAE Administrator Console v2 0 User Guide Pub No MAN0017468 Chapter 4 Use the instrument with the Security Auditing and E signature SAE v2 0 module Configuring the SAE module 4 SeqStudio Genetic Analyzer Instrument and Software User Guide 57 ...

Page 58: ... Local instrument administrator Sign in is limited to users with local instrument profiles Auditing and E signature functions are not performed Connect cloud based platform and remote monitoring functions are enabled Connect the instrument to an SAE server administrator only Before you connect install the SAE Administrator Console on a computer with a static IP address 1 Touch Settings4SAE setting...

Page 59: ... SAE administrator account username and password then touch Enable SAE Disable SAE administrator only This procedure requires a local administrator profile or an SAE administrator account If you are signed in to the instrument as an SAE administrator a In the home screen touch Settings4SAE4Disable SAE b Enter your SAE administrator account username and password If you are not signed in to the inst...

Page 60: ...ch in the home screen then touch Sign out 2 In the Sign in screen touch Sign In then enter your SAE username and password To access Touch Sign in under All instrument functions allowed by your SAE account SAE Administrator access to functions on the Settings screen Local requires an administrator instrument profile The home screen is displayed Chapter 4 Use the instrument with the Security Auditin...

Page 61: ...uire users to select a reason E signature requirements when you start a run Depending on the way your SAE administrator has configured your instrument E signatures may be required when you start a run If starting a run is configured to require signatures a message is displayed when you start a run Touch View Details to show the pending signatures Chapter 4 Use the instrument with the Security Audi...

Page 62: ...omplete and 3 signatures are pending 2 administrator signatures for dye calibration dye set name is listed two times 1 signature that specifies the Reviewed and approved E signature meaning complete because 1 signature is required Signatures Required 1 and 1 signature has been logged Current 1 1 signature that specifies the Checked consumables meaning incomplete 1 administrator signature for the p...

Page 63: ...ouch Sign View E signature records for a plate setup 1 Open a plate setup 2 In the Plate Properties tab touch More Options then touch the Signing records Status Meaning Current The plate has not been modified after the plate was signed Obsolete The plate has been modified after the plate was signed Chapter 4 Use the instrument with the Security Auditing and E signature SAE v2 0 module Sign a plate...

Page 64: ...h a dye set or install run to view the data 4 Touch Select to sign then select an item 5 Touch the to display all signature records for the item Signing in after automatic screen locking Depending on the way your SAE administrator has configured your instrument the instrument touchscreen may automatically lock after a specified duration The users who can sign in when the screen is locked are deter...

Page 65: ...e Password Auditing of imported plate setups If you import a plate setup the following auditing occurs Note You can import only one plate setup at a time If the file was created on And your instrument has SAE enabled and is configured to Then the following occurs A different instrument with SAE enabled The plate is imported Auditing is restarted A different instrument with SAE disabled Open files ...

Page 66: ...e SAE Administrator Console is installed or a problem with the network Troubleshoot computer or network problems The computer on which the SAE Administrator Console has a dynamic IP address that is disconnecting the server when the computer is restarted Set a static IP address on the computer Incomplete audit trail when you import a plate setup There is a gap in the audit trail For example the pla...

Page 67: ...he next time that you open or create a hidden plate The analysis settings will not be available to other system users Shared plates The analysis settings are saved with the plate setup and are used the next time that you open or create a shared plate The analysis settings will be available to other system users User created analysis settings Users can name and save analysis settings If you create ...

Page 68: ...nager Connect cloud based platform the modules will not be available to other users Well Sample name Fragment HID analysis only Sample type Sequencing only Specimen and amplicon Custom fields 1 5 Specimen and Amplicon fields are useful in secondary analysis software applications that organize sample data files based on amplicon and specimen information Custom fields are text fields in which you ca...

Page 69: ...e setup that you created in Plate Manager on your Connect cloud based platform account Open from local drive Open a plate setup that you created in Plate Manager on your computer PSM file or in another application CSV file If you are running the Plate Manager on the desktop Click To New Create a new plate setup or to create a plate setup from a template Open Open a plate setup that you created in ...

Page 70: ...her system users 3 Select the Application type Sequencing Fragment analysis HID or Mixed plate sequencing fragment A mixed plate allows you to specify fragment analysis and sequence analysis settings on the same plate 4 Select the analysis settings If needed edit the settings see Edit analysis settings on page 75 5 Optional for Sequencing or Mixed plate Select the I am analyzing my data with Sange...

Page 71: ...ion group shift click or click drag to select multiple injection groups Each set of 4 wells on the plate is referred to as an injection group The default injection order is A1 D1 E1 H1 A2 D2 E2 H2 A12 D12 E12 H12 2 If you are creating a mixed plate select the Application type for the selected injection groups 3 Optional Edit the default Sample name well for each well Note If multiple injection gro...

Page 72: ...te setup in the Plate Manager on page 73 Keyboard shortcuts for the sample table Keys Action Navigation Arrow keys Move to the cell above below to the right or to the left of the current cell Tab Move to the cell to the right of the current cell Shift Tab Move to the cell to the left of the current cell Home Move to the first cell in the row End Move to the last cell in the row Ctrl Home Move to t...

Page 73: ...elected cells with edited cell s value Select a range of cells then press F2 to edit the first cell in the selection Type a value then press Ctrl Enter to fill all selected cells with the value Ctrl Z Undo Ctrl Y Redo After you assign wells to a plate setup 1 In the Save the plate setup dialog box modify any settings as needed Save a plate setup in the Plate Manager Chapter 5 Create or modify a pl...

Page 74: ...Additional plate settings Plate Manager In the Plate screen 1 Select Actions4Add injection 2 Select one or more injection groups then select a run module for the replicate injections You can add up to 5 replicate injections for a total of 6 injections Run module 1 is used for the first injection you specify Additional run module fields are added for replicate injections To remove a replicate injec...

Page 75: ...r FSA associated with a plate are named The default file name convention is Application Default settings Fragment HID analysis well _ sample name _ sample type _ date and timestamp fsa Sequence analysis well _ sample name _ date and timestamp ab1 Sequence analysis with the Sanger variant analysis option selected well _ sample name _ amplicon _ specimen _ date and timestamp ab1 To change the defaul...

Page 76: ...tings are saved with the plate setup and are used the next time that you open or create a shared plate Your analysis settings will be available to other system users Custom fields are text fields in which you can include additional sample attributes or identifiers Custom fields can be used by some secondary analysis applications In the Plate tab 1 Select Action4Add custom field You can add up to 5...

Page 77: ...d public hidden my plates and guest plate setup files 79 Overview of plate setup settings 79 Optional Set up for auto export of sample data files AB1 and FSA 80 Set up a plate using default settings instrument 81 Set optional plate settings instrument 87 6 SeqStudio Genetic Analyzer Instrument and Software User Guide 77 ...

Page 78: ...nloading a template from the SeqStudio Plate Manager desktop or Connect cloud based platform Size standard names only Dye set name only Run module names only All remaining plate setup field settings Well ID Sample name Application type and so on To update properties of the plate setup such as sample name after the size standard dye set and run module for the plate setup have been created or import...

Page 79: ...aved with plate setup Last settings specified by the signed in user not saved with plate setup Overview of plate setup settings Category Setting Notes Plate Plate properties Plate set up security Shared or Hidden File name convention Analysis settings The analysis settings are saved with the plate setup as follows Hidden plates The analysis settings are saved with the plate setup and are used the ...

Page 80: ... in which you can include additional sample attributes or identifiers Custom fields can be used by some secondary analysis applications Optional Set up for auto export of sample data files AB1 and FSA By default sample data files AB1 and FSA are saved to the instrument When you create a plate setup you can also set the Save location to Cloud Network Drive and or USB 1 1 Save location When the plat...

Page 81: ... to select 1 shared plates that were created by any user or 2 any plates that were created by a Guest user For more information see Shared public hidden my plates and guest plate setup files on page 79 Import a plate setup 1 Touch Cloud USB or Network Drive 2 Select PSM file CSV file For more information see PSM and CSV plate setup files for import into the instrument on page 78 Create or import a...

Page 82: ... plate setup The plate setup is always saved to the instrument In addition you can save the plate to the Connect cloud based platform a network or a USB which will auto export the sample data files IMPORTANT To view analyzed data in the Remote Monitoring App on the Connect platform you must save the plate setup to the Connect platform Note Sequencing and Fragment analysis If you save a plate setup...

Page 83: ... Modify the default file name convention on page 88 This feature is useful in secondary analysis software applications that organize files based on amplicon and specimen information Connect cloud based platform applications Variant Analysis VA module Next generation Confirmation NGC module desktop applications SeqScape Software Variant Reporter Software Minor Variant Finder Software Chapter 6 Crea...

Page 84: ...y the first well in the set of 4 for example Injection Group A1 contains wells A1 D1 The default injection order is A1 D1 E1 H1 A2 D2 E2 H2 A12 D12 E12 H12 2 Select injection groups then touch Edit Touch a well to select a single injection group Touch and drag to select multiple injection groups or the entire plate Assign wells run module size standard dye set and kit Chapter 6 Create or modify a ...

Page 85: ...odules read lengths size ranges and run times on page 140 5 Fragment HID analysis only Touch Size standard then select a size standard for the injection group 6 Swipe up to display the rest of the screen 7 Touch Dye set then select a dye set for the selected injection groups 8 HID analysis only Touch Kit then select a kit for the selected injection groups 9 Touch Done Chapter 6 Create or modify a ...

Page 86: ...tom fields Text fields to include additional sample attributes or identifiers that can be used by secondary analysis applications Sequencing only Amplicon and Specimen Amplicon and Specimen names for Sanger Sequence analysis if you selected the option in the Plate Properties screen Assign wells sample name sample type and custom fields Chapter 6 Create or modify a plate setup from the instrument S...

Page 87: ...ist 3 Optional Modify Run module Injection time Injection voltage Run time or Run voltage for the injections IMPORTANT The changes to the run conditions apply only to the replicate injection The changes are not saved to the run module 4 Touch Done In the Properties tab of the Plate properties screen 1 Touch More options4Analysis settings 2 Select a setting See Manage analysis settings on page 142 ...

Page 88: ...tamp ab1 1 Access the File name convention screen From Action Plate properties screen Select the Properties tab then touch More options4File name convention Home screen Touch Settings4Run settings 4File name convention 2 Touch Attributes 3 Select the attributes to include in the data file name For information on creating custom fields to include in file name conventions see Define custom fields on...

Page 89: ...re saved with the plate setup and are used the next time that you open or create a shared plate Your analysis settings will be available to other system users 3 Touch Done then touch Save Custom fields are text fields in which you can include additional sample attributes or identifiers Custom fields can be used by some secondary analysis applications In the Plate tab of the Plate properties screen...

Page 90: ...1 Touch the sample name field 3 Touch a custom field then enter the definition for the selected wells 4 Click Done Chapter 6 Create or modify a plate setup from the instrument Set optional plate settings instrument 6 90 SeqStudio Genetic Analyzer Instrument and Software User Guide ...

Page 91: ... or Run voltage for these injections Note Replicate indicates a duplicate the replicate has the same parameters as the original injection Re injection indicates a copy of the injection but with user modified parameters Note The changes to the run conditions apply only to the replicate or re injection The changes are not saved to the run module 3 Touch Done Optional View the injection list change i...

Page 92: ...en prompted 2 Press the release button on the autosampler to open the lid 3 Check the buffer fill level a Remove the CBC b Ensure that the level of buffer is above the fill line If the buffer is at or below the fill line see Assemble the SeqStudio Genetic Analyzer Cathode Buffer Container CBC on page 166 and Insert the Cathode Buffer Container on page 167 If the buffer is above the fill line reins...

Page 93: ...touch Setup run 2 Select the location of your plate setup then select the plate setup For information on plate setup files see PSM and CSV plate setup files for import into the instrument on page 78 and Shared public hidden my plates and guest plate setup files on page 79 3 Verify that settings are as needed The Save location must specify Cloud if you want to view analyzed data when you monitor th...

Page 94: ...trument on page 105 Before starting a run the instrument calculates the total amount of storage space required to save the run to the instrument If the required storage space is not available the instrument deletes files associated with the oldest exported plates until sufficient space is available Note Only complete plates that have been auto exported saved to Connect cloud based platform network...

Page 95: ... in progress Sign out is displayed instead of Lock instrument Monitor a run from the Connect cloud based platform A run is accessible from InstrumentConnect for 24 hours after the run is complete or until another run is started 1 Sign in to thermofisher com connect 2 Click to access InstrumentConnect 3 Click the run status dial to display the Remote Monitoring App Open the Remote Monitoring App fr...

Page 96: ...Figure 11 Remote Monitoring App Chapter 7 Start and monitor a run Monitor a run from the Connect cloud based platform 7 96 SeqStudio Genetic Analyzer Instrument and Software User Guide ...

Page 97: ...or at a later time In the Plate Manager on the Connect cloud based platform To open the Remote Monitoring App immediately after you save a plate setup and start the run click Monitor my run Open the Remote Monitoring App from the Plate Manager Chapter 7 Start and monitor a run Monitor a run from the Connect cloud based platform 7 SeqStudio Genetic Analyzer Instrument and Software User Guide 97 ...

Page 98: ... or click to access InstrumentConnect 1 1 Select an instrument or click to access InstrumentConnect Figure 12 Remote Monitoring App Chapter 7 Start and monitor a run Monitor a run from the Connect cloud based platform 7 98 SeqStudio Genetic Analyzer Instrument and Software User Guide ...

Page 99: ...d tab is disabled if the Save location for the plate setup is not set to Cloud or if the injection group has not finished running 3 In the Quality alerts screen click the Raw EPT or Analyzed tab to view data 4 As needed select Actions4Re inject group select the Run module and settings then click Inject Pause or cancel an injection in the Remote Monitoring App Select Actions4Pause plate to pause th...

Page 100: ...e setup Save location does not specify Cloud In the Remote Monitor screen Select Actions4QC Report A PDF of the plate QC report is generated Remote Monitoring App raw trace 1 2 3 4 5 6 Figure 13 Fragment analysis raw trace 1 Zoom in out 2 Raw trace 3 Thumbnail trace Click drag to view another region of the trace 4 Lock unlock trace zooming for all traces in the injection group 5 View Options Selec...

Page 101: ...asecalls to display set vertical scaling Remote Monitoring App EPT trace The EPT view ElectroPhoresis Telemetry shows instrument data conditions currents temperatures electrophoresis voltage as a function of time Chapter 7 Start and monitor a run Monitor a run from the Connect cloud based platform 7 SeqStudio Genetic Analyzer Instrument and Software User Guide 101 ...

Page 102: ...utside trace 7 Size standard curve red line 8 Actions Select commands to pause and cancel injections 1 4 5 6 2 3 Figure 16 Sequence analysis analyzed trace 1 Zoom in out 2 Analyzed trace 3 Thumbnail trace Click drag to view another region of the trace 4 Lock unlock trace zooming for all traces in the injection group 5 View Options Select the basecalls to display show hide quality bars and values s...

Page 103: ...mobile device on page 185 1 On your mobile device launch InstrumentConnect 2 Touch the instrument to monitor 3 Swipe left to view consumable status Chapter 7 Start and monitor a run Monitor a run from a mobile device 7 SeqStudio Genetic Analyzer Instrument and Software User Guide 103 ...

Page 104: ...oup to display quality alerts then touch View raw plot to view the data Swipe left to view the entire trace Pinch zoom to expand the trace Chapter 7 Start and monitor a run Monitor a run from a mobile device 7 104 SeqStudio Genetic Analyzer Instrument and Software User Guide ...

Page 105: ...o the run conditions apply only to the replicate or re injection The changes are not saved to the run module 3 Touch Done During a run the run status screen is displayed View the run time information and the status dial for each capillary The status dials are color coded for quality alerts All QC tests passed At least 1 warning quality alert was triggered At least 1 failing quality alert was trigg...

Page 106: ...ed At least 1 warning quality alert was triggered At least 1 failing quality alert was triggered For information on quality alerts see Data quality alerts on page 119 Sizecalling and basecalling quality alerts on page 119 1 In the run status screen touch Actions View real time results Pause a plate or cancel or stop injections Chapter 7 Start and monitor a run Monitor a run from the instrument 7 1...

Page 107: ... injection list edit run module information and or reinject samples View results for the plate when the run is completed all injections are finished 1 Touch Results to view the run results Arrows o use in this SVG ed callouts or arrows Callout Arrow_Libary and unused elements epository as needed 1 1 2 Touch List view Each injection group displays a QC color for each capillary All QC tests passed A...

Page 108: ...ce below the trace to scroll left or right 7 Optional Adjust the graphical view see Adjust the trace display on page 108 8 Touch or to scroll to the raw data or EPT Plot ElectroPhoresis Telemetry See EPT plot on page 117 Adjust the trace display See View results when the run is completed on page 107 to access results Drag one finger to pan to the left or right Zoom in and out by pinching and expan...

Page 109: ...id 3 Remove the plate or tube assembly 4 Close the autosampler lid Press down on the center of the lid or press down on both sides of the lid with equal pressure until the lid clicks shut 5 Touch Retract plate then close the instrument door when prompted Chapter 7 Start and monitor a run Unload the plate or the tube assembly 7 SeqStudio Genetic Analyzer Instrument and Software User Guide 109 ...

Page 110: ...ew The status dials are color coded for quality alerts All QC tests passed At least 1 warning quality alert was triggered At least 1 failing quality alert was triggered For information on quality alerts see Data quality alerts on page 119 Sizecalling and basecalling quality alerts on page 119 Note The Analyzed tab is disabled if the Save location for the plate setup is not set to Cloud or if the i...

Page 111: ...n the Run Result Details screen or touch for well details See Fragment HID analysis results on page 113 or Sequence analysis results on page 115 for detailed information 5 Touch a sample file name If the data triggered any quality alerts a QC alerts screen is displayed See Data quality alerts on page 119 and Sizecalling and basecalling quality alerts on page 119 for detailed information Touch View...

Page 112: ...ft or right Zoom in and out by pinching and expanding with two fingers Touch on the left border of the trace then touch a dye to deselect Touch on the right border of the trace then touch Zoom In Zoom Out or Fit to screen to adjust the display Drag the center of the pane in thumbnail view to scroll left or right Drag the right or left handle of the pane to zoom horizontally Chapter 8 View and anal...

Page 113: ... of the pane to zoom horizontally 5 Basepair or scan display selection 6 Zoom tools Touch to open 7 Next trace tool Touch to view the raw trace or EPT for the well Fragment HID analysis results Setting Description Quality QC flags All QC tests passed At least 1 warning quality alert was triggered At least 1 failing quality alert was triggered Fragment HID analysis results Chapter 8 View and analyz...

Page 114: ... actual distribution of size standard peaks in the sample calculates an interim SQ a value between 0 and 1 Exported The sample has been auto exported saved to the Connect cloud based platform network or USB or manually exported using Settings4Run History4plate name4Export Well details see below Well details Sample file name QC flag sample name sample type settings used to acquire the data size sta...

Page 115: ... 3 Trace color hide show Touch to open then touch a color to hide or show 4 Analyzed trace 5 Thumbnail trace Drag the center of the pane in the thumbnail trace to display another trace area in the top pane Drag the right or left handle of the pane to zoom horizontally 6 Zoom tools Touch to open 7 Next trace tool Touch to view the raw trace or EPT for the well Sequencing results Result Description ...

Page 116: ...secall Quality Value QV of bases in the clear range sequence of a trace The clear range is the region of the sequence that remains after excluding the low quality or error prone sequence at the 5 and 3 ends The clear range is calculated by the KB basecaller using QVs Median PUP pull up peak A measure of noise or pull up that is determined by taking the mean of the ratios of signal strength calcula...

Page 117: ... of 20 Review all mixed base calls Quality values QV and probability of error Pe QV Pe QV Pe 1 79 0 30 0 10 5 32 0 35 0 032 10 10 0 40 0 010 15 3 2 45 0 0032 20 1 0 50 0 0010 25 0 32 60 0 00010 The EPT view ElectroPhoresis Telemetry shows instrument data conditions currents temperatures electrophoresis voltage as a function of time Touch on the left border of the plot to display the legend EPT plo...

Page 118: ... Touch a sample file name 4 View the results in the Run history screen or touch to view well details See Fragment HID analysis results on page 113 or Sequence analysis results on page 115 for information View results for a previously run plate run history Chapter 8 View and analyze results View results on the instrument 8 118 SeqStudio Genetic Analyzer Instrument and Software User Guide ...

Page 119: ...e user manual Troubleshoot upstream PCR and sequencing steps Sizecalling and basecalling quality alerts Table 5 Sizecalling quality alerts Quality alert Description Action Sizing quality value is low due to poor size standard peak quality Peak height uniformity is low or the fitting quality in sizing is poor Low resolution or poor quality data is present Re inject the sample If the problem persist...

Page 120: ... and drag an injection group to a new location in the injection list Touch Inject first Moves the selected injection group to the top of the injection list Touch Edit and re inject Adds replicates or re injections to the injection list You can also modify Run module Injection time Injection voltage Run time or Run voltage for these injections 3 Touch Done Note The changes are not applied until you...

Page 121: ...ct Export only an FSA or AB1 file for each analyzed sample is exported Analyze data 1 Export results see Export results from the instrument sample data files and QC reports on page 121 or use auto exported data 2 Use an appropriate fragment analysis or sequencing application to analyze the data Note Data from the SeqStudio Genetic Analyzer may be labeled as 3200 in secondary analysis software For ...

Page 122: ...ent 1 Open a plate setup that specifies the custom dye set of interest 2 Export a plate setup that specifies the custom dye 3 Open the exported plate setup in the Plate Manager The custom dye is imported and is available for selection when you create new plates Download a plate setup template as a CSV file 1 Click to display the home screen 2 Click New select Create from template then click Downlo...

Page 123: ...p template Note You cannot add templates to the list of templates you select when you create a plate setup However you can create a plate setup with Template suffix then use it as a starting point for creating new plate setups 1 Click New select Create from template then click Download for the template of interest 2 Modify the CSV file as needed 3 Save the plate setup with a Template suffix exampl...

Page 124: ... can save PSM files in any location Connect cloud based platform Click in the Connect platform then use DataConnect to delete PSM files Manage email notifications in the Connect cloud based platform 1 In any screen in the Connect cloud based platform click Chapter 9 Manage the software Plate Manager Delete plate setups 9 124 SeqStudio Genetic Analyzer Instrument and Software User Guide ...

Page 125: ... 3 As needed select a run module of interest then click Edit or Delete user created run modules only Manage size standards This function manages the list of size standard definitions that you can select from during plate set up To assign a size standard definition to a plate see Assign wells Sample and run information on page 71 A size standard defines the sizes in basepairs of known fragments It ...

Page 126: ... Edit or Delete user created settings only Setting Description Size calling method Local Southern default Determines the fragment sizes using the reciprocal relationship between fragment length and electrophoretic mobility Global Southern Compensates for standard fragments with anomalous electrophoretic mobility similar to least squares methods 2nd LSQ 2nd Order Least Squares Uses regression analy...

Page 127: ...hold are not detected For example if you use the default values of 175 RFU peaks with heights equal to or greater than 175 RFU are detected Peaks with heights below 175 RFU are still displayed in the electropherogram plots but are not detected or labeled Note Use the same peak amplitude thresholds in secondary analysis software Primer peak If the primer peaks in your application obscure peaks of i...

Page 128: ... peak detector calculates the first derivative of a polynomial curve fitted to the data within a window that is centered on each data point in the analysis range Using curves with larger polynomial degree values allows the curve to more closely approximate the signal and therefore captures more of the peak structure in the electropherogram Slope Thresholds Peak Start and End Peak Start The peak st...

Page 129: ...te If you have PCR products with sequences that end while data is still being collected select the At PCR Stop checkbox Mixed bases threshold When enabled determines the secondary peak height ratio where the secondary peak is considered a potential mixed base Reaching the threshold is a necessary but not sufficient condition for the basecalling algorithm to call a mixed base Clear range methods Us...

Page 130: ...t settings 147 Manage instrument profiles on the instrument 151 Manage storage space 153 Connect the instrument to a network drive On the destination computer 1 In the Windows desktop click 2 In the search field at the bottom of the pane type command prompt then press Enter 3 At the command prompt type ipconfig then press Enter 10 Determine IP address for a computer on a network 130 SeqStudio Gene...

Page 131: ...Right click on a folder then select Sharing4Advanced or Share with4Advanced sharing 4 Select the Sharing tab 5 Click Advanced sharing 6 Select Share this folder 7 Click Permissions then select Full Control or Read Write and Delete options IMPORTANT Without these permissions the instrument cannot autoexport results when a run is complete 8 Click OK click OK then click Close Create folders and enabl...

Page 132: ...page 130 3 If necessary touch the appropriate fields to enter a domain name username and password 4 Touch Connect Before you begin create a plate setup PSM file or CSV file in the Connect cloud based platform location that you want to set as the default location To set the default location you must select a plate setup 1 In the home screen of the instrument touch Setup run then touch Cloud The Set...

Page 133: ...creen is displayed How to proceed Is not connected to a network drive Connect 1 In the Network Destination field enter the IP address of the computer followed by the folder names you created Example 10 43 32 82 SharedData Results 2 If required by your network enter Domain User Name and Password to access the shared location 3 Touch Connect The Setup Run screen is displayed Is connected to a networ...

Page 134: ...etwork Destination field If your instrument profile This screen is displayed How to proceed Is not connected to a network drive Connect 1 In the Network Destination field enter the IP address of the computer followed by the folder names you created Example 10 43 32 82 SharedData Resu lts 2 If required by your network enter Domain User Name and Password to access the shared location 3 Touch Connect...

Page 135: ...s folder Select the directory shown at the top of the screen 1 2 Figure 18 Select Directory screen example 1 Example IP address and folder locations 2 List of folders 6 In the Save Destination screen touch Done Chapter 10 Manage the software instrument Connect the instrument to a network drive 10 SeqStudio Genetic Analyzer Instrument and Software User Guide 135 ...

Page 136: ... your Connect cloud based platform account detailed instructions 1 If a user is signed in touch then touch Sign out 2 In the Sign In screen touch Get started4Connect 3 In the Connect to the Cloud screen touch a connection option Chapter 10 Manage the software instrument Link the instrument to your Connect cloud based platform account 10 136 SeqStudio Genetic Analyzer Instrument and Software User G...

Page 137: ...qStudio 5 Enter the link code Instrument In the Connect to the Cloud screen enter your account information then click Link account Lock the touchscreen During a run you can lock the touchscreen to prevent other users from using the instrument This feature is not available to Guest users Only the user who locked the touchscreen or an administrator can sign in to the instrument if the touchscreen is...

Page 138: ...a plate then touch Export or Delete 4 If you touched Export select a storage location then touch Export Delete then touch Yes to delete the plate setup Export or delete a plate setup PSM file Chapter 10 Manage the software instrument Manage plate setups 10 138 SeqStudio Genetic Analyzer Instrument and Software User Guide ...

Page 139: ...wells run module size standard dye set and kit on page 84 Factory installed items cannot be edited or deleted To create a new item from a factory installed item copy edit then save the new item Run modules are accessible only to the user who creates them For more information see Run modules read lengths size ranges and run times on page 140 1 Access the Manage run modules screen From Action Plate ...

Page 140: ... injection Prerun time seconds Prerun time Injection voltage Volts Voltage for sample injection Injection time seconds Sample injection time Run voltage Volts Final sample electrophoresis separation run voltage Run ramp duration seconds Time required to reach the Run voltage Note Data collection does not start until this time elapses Run time seconds Length of time that data is collected after the...

Page 141: ...ng interval divided by the peak width at half max in a GS600 or GS1200 LIZ size standard sample sized with a third order fit is 1 The table shows the resolution range in 90 of samples 2 Load a maximum of 48 samples per plate if you use a long run module Table 9 HID run modules Run module Resolution range Approximate run time Sizing precision Compatible size standards HIDAnalysis 60 470 bp 1 39 min...

Page 142: ... needed touch any of the following then touch Done Note To change an existing value add a new value then delete the original value One or more fragment size values then touch Delete Add to add a value 3 As needed touch a size standard of interest then touch Edit or View Edit fragment HID analysis settings Factory installed items cannot be edited or deleted To create a new item from a factory insta...

Page 143: ...d analysis settings then touch Copy b Enter a name and edit settings as needed see Sequencing settings base calling on page 129 c As needed touch View or Delete user created settings only 3 Touch Done Fragment HID analysis settings size calling Setting Description Size calling method Local Southern default Determines the fragment sizes using the reciprocal relationship between fragment length and ...

Page 144: ...d are not detected For example if you use the default values of 175 RFU peaks with heights equal to or greater than 175 RFU are detected Peaks with heights below 175 RFU are still displayed in the electropherogram plots but are not detected or labeled Note Use the same peak amplitude thresholds in secondary analysis software Primer peak If the primer peaks in your application obscure peaks of inte...

Page 145: ...ak detector calculates the first derivative of a polynomial curve fitted to the data within a window that is centered on each data point in the analysis range Using curves with larger polynomial degree values allows the curve to more closely approximate the signal and therefore captures more of the peak structure in the electropherogram Slope Thresholds Peak Start and End Peak Start The peak start...

Page 146: ...dary peak is considered a potential mixed base Reaching the threshold is a necessary but not sufficient condition for the basecalling algorithm to call a mixed base Clear range methods Use quality values Sets a window with a specified number of allowed low quality bases by removing bases until there are X number of bases per Z number of bases with QV Y Use base positions Specifies the first and la...

Page 147: ...n page 89 Note The timestamp attribute cannot be deselected it is always included in the data file name 4 Touch Done 5 Touch and drag attributes up or down in the list 6 Touch Done Manage instrument settings In the home screen 1 Touch Settings4Instrument settings 4About to access the instrument information Model name Ethernet IP address Ethernet MAC address Wireless IP address Wireless MAC address...

Page 148: ...l features of the system and provides simulated real time data and results You cannot save plates or settings in Demo mode In the home screen 1 Touch Settings4Instrument settings4Turn Demo mode on 2 Touch OK to allow the instrument to restart The instrument automatically restarts in Demo mode In the home screen 1 Touch Settings4Instrument settings4Date and Time 2 Slide the control to select a time...

Page 149: ...d c Click Join d Click OK when the authentication is completed 4 Optional Edit the Wired network settings a Select DHCP or Static IP An IP address is automatically assigned if DHCP is selected b Static IP only Enter an IP address Subnet mask Default gateway Primary DNS server and Secondary DNS server For more information see Determine IP address for a computer on a network on page 130 5 Touch OK M...

Page 150: ...to recognize the USB 3 Touch Update if an update is available Cancel if there is no update available A message is displayed during the software updated then the instrument automatically restarts Check for software updates administrator only Chapter 10 Manage the software instrument Manage instrument settings 10 150 SeqStudio Genetic Analyzer Instrument and Software User Guide ...

Page 151: ...n the home screen and the instrument is listed in the InstrumentConnect Guest Local All standard user functions except Cannot link to the Connect cloud based platform Cannot modify a public plate setup Note Standard instrument profiles cannot access Guest instrument profile plate setups unless the Plate Setup Security is set to Shared 1 The first user who signs in to the instrument is assigned a l...

Page 152: ...and results administrator only on page 155 In the home screen 1 Touch 2 Touch All accounts 3 Touch the instrument profile to delete 4 Touch Delete account 5 Touch Yes to confirm 6 Touch Done Local administrators and Connect cloud based platform administrators can delete the PIN for a local instrument profile In the home screen 1 Touch 2 Touch All accounts 3 Touch the instrument profile of interest...

Page 153: ...N then touch Enter 6 Touch Done Manage storage space Before starting a run the instrument calculates the total amount of storage space required to save the run to the instrument If the required storage space is not available the instrument deletes files associated with the oldest exported plates until sufficient space is available Note Only complete plates that have been auto exported saved to Con...

Page 154: ...ch Export 4 Select a storage location The following data is exported for the plate Fragment HID analysis FSA file for each sample Sequencing AB1 file for each sample Plate QC report in CSV and PDF format Note If you select a plate select View then select Export only an FSA or AB1 file for each analyzed sample is exported Export or delete a plate setup PSM file Export results from the instrument sa...

Page 155: ...ch the instrument profiles for which you want to back up plate and result information 4 Touch Backup 5 Specify a storage location then touch Export A folder containing plate setup and sample data file is backed up to the specified location Optional After backing up you can Delete the plates see Delete a run history on page 155 Open the CSV files in the folder on another instrument or in the Plate ...

Page 156: ...se In the home screen 1 Touch touch Eject plate then open the instrument door when prompted 2 Press the release button on the autosampler to open the lid then remove the CBC 2 1 1 Release button 2 CBC 3 Ensure that the level of buffer is above the fill line If the buffer is at or below the fill line see Assemble the SeqStudio Genetic Analyzer Cathode Buffer Container CBC on page 166 and Insert the...

Page 157: ...through the door Wipe the touchscreen with a lint free cloth and glass cleaner The autosampler is attached to the instrument Clean spills to prevent a build up of crystallized polymer or dried salt from the buffers Power off the instrument before cleaning the autosampler 1 Wipe the exterior of the autosampler with a lint free cloth and deionized water IMPORTANT Do not pour liquid directly on to th...

Page 158: ...re IMPORTANT The instrument does not maintain the correct temperature conditions for the cartridge when it is powered off Avoid cartridge exposure to ambient temperature Off instrument storage For intermittent use can be stored off instrument until the expiry date on the label or up to 4 months after first use Store upright at 2 8 C with an integrated capillary protector ICP and optical cover inst...

Page 159: ...abel or up to 6 months after first use Store upright at 2 8 C with an integrated capillary protector ICP and optical cover installed see Store the cartridge on page 163 Note After you remove the cartridge from the instrument install an ICP within a few minutes Avoid cartridge exposure to ambient temperature Reuse Can be removed from an instrument then inserted again on the same instrument or a dif...

Page 160: ...ment 1 Touch Settings4Cartridge4Instrument cartridge history 2 Optional Touch Export This function lists the instruments on which the cartridge has been installed Touch Settings4Consumables status then touch Cartridge history Check or export the Instrument cartridge history Check or export the cartridge history Chapter 11 Maintain the instrument Manage the cartridge 11 160 SeqStudio Genetic Analyz...

Page 161: ...ng tables For the SeqStudio Genetic Analyzer Cartridge see Table 1 on page 18 For the SeqStudio Genetic Analyzer Cartridge v2 see Table 2 on page 19 1 Touch touch Eject cartridge then open the instrument door when prompted 2 Hold the cartridge at the hand hold above the capillaries then pull to remove it from the instrument 3 Close the instrument door For more information see Store the cartridge o...

Page 162: ...e storage Avoid touching the capillaries that are protected by the optical cover c Pinch the clamp on the SeqStudio Integrated Capillary Protector then pull down Discard the SeqStudio Integrated Capillary Protector The SeqStudio Integrated Capillary Protector is single use Use a new SeqStudio Integrated Capillary Protector if you store the cartridge 1 1 Optical cover Chapter 11 Maintain the instru...

Page 163: ... the Consumables Status screen is displayed The cartridge is initialized 1 Touch touch Eject cartridge then open the instrument door when prompted 2 Hold the cartridge at the hand holds above the capillaries then pull to remove it from the instrument 3 Close the instrument door 4 Carefully place the optical cover on the cartridge to avoid damage to the capillaries 2 1 1 Insertion rails 2 Embossed ...

Page 164: ...ents the capillary array from drying out during off instrument storage of the cartridge and is removed before insertion of the cartridge into the SeqStudio Genetic Analyzer Each cartridge is supplied with an ICP for shipping and one additional ICP for off instrument cartridge storage 1 Figure 19 SeqStudio Integrated Capillary Protector 1 Clamp mechanism for attaching to cartridge IMPORTANT Remove ...

Page 165: ...C is installed Replace the CBC every 2 weeks IMPORTANT If the instrument will be idle for longer than the shelf life of the cartridge components remove the cartridge and cathode buffer then power off the instrument Table 12 Cartridge storage Cartridge Storage SeqStudio Genetic Analyzer Cartridge Cat No A33671 See Table 1 on page 18 SeqStudio Genetic Analyzer Cartridge v2 Cat No A41331 See Table 2 ...

Page 166: ...ary to remove the CBC after each run 1 Touch touch Eject plate then open the instrument door when prompted 2 Press the release button on the autosampler to open the lid 3 Lift the CBC out of the autosampler Equilibrate the CBC to room temperature 15 minutes to overnight before assembling On a clean and level surface 1 Ensure that the buffer is above the fill line 2 Carefully peel off the seal 3 Wi...

Page 167: ... line Install the CBC before you install the cartridge See Figure 2 on page 14 for the position of the cathode buffer on the instrument 1 Touch touch Eject plate then open the instrument door when prompted 2 Press the release button on the autosampler to open the lid 2 1 1 Release button 2 Location of CBC 3 Insert the cathode buffer in the autosampler with the notch positioned in the back right Se...

Page 168: ...utosampler lid until it clicks shut 5 Touch Retract plate then close the instrument door Chapter 11 Maintain the instrument Install cathode buffer 11 168 SeqStudio Genetic Analyzer Instrument and Software User Guide ...

Page 169: ...72 Instrument troubleshooting 173 Cartridge troubleshooting 174 Sample and data troubleshooting 175 EPT data 180 Software troubleshooting 181 Service tools 183 Troubleshooting resources Document Pub No Troubleshooting Sanger sequencing data User Bulletin MAN0014435 DNA Sequencing by Capillary Electrophoresis Chemistry Guide Second Edition 4305080 DNA Fragment Analysis by Capillary Electrophoresis ...

Page 170: ...rt log files if directed to do so by Technical Support In the home screen 1 Touch Settings4Maintenance and Service4Export logs 2 Select one of the following options Export logs for the last injection Includes all run types analysis run install run and calibration run Export logs for the last current plate Includes all run types Export logs for selected plates Includes options to export logs for re...

Page 171: ...jection voltage or time Dilute the sample No sample was detected Poor signal to noise ratio with low signal detected Verify that the sample volume follows recommendations in the user manual Troubleshoot upstream PCR and sequencing steps Sizecalling and basecalling quality alerts Table 13 Sizecalling quality alerts Quality alert Description Action Sizing quality value is low due to poor size standa...

Page 172: ...sample Various causes Analyze the data in a secondary analysis software with a corrected analysis range Re inject the sample Table 14 Basecalling quality alerts Quality alert Description Action Basecalling failed due to poor quality data Poor quality data is present Re inject the sample If the problem persists prepare fresh sample Troubleshoot upstream PCR and sequencing steps Check size standard ...

Page 173: ...at the labels are present and not visibly damaged Ensure that the consumables are installed correctly The Cathode Buffer Container should be firmly seated in the autosampler The cartridge will click into place when it is installed correctly The RFID reader is malfunctioning Insert consumables that have previously had RFID tags read Contact technical support if the RFID tags are not read The run st...

Page 174: ...lary array Small amounts of leakage around the cartridge capillary array are normal No action is required There are crystals on the cartridge polymer delivery system There is a leak in the polymer delivery system Run a control sample to determine if the cartridge function is affected Replace the cartridge if the leak affects the cartridge function Poor quality data is observed after prolonged dryi...

Page 175: ...page 37 The sample concentration was too low Re inject the samples with adjusted injection conditions Injection time voltage or a combination of these conditions can be adjusted There were bubbles in the sample wells Centrifuge the sample plate or tubes to remove the bubbles before loading onto the instrument If the samples have been run centrifuge the plate or tubes then set up a re injection The...

Page 176: ...damage There was poor resolution poor size quality or a poor sequencing result The samples degraded over time while on the instrument Analyze a maximum of 48 samples on a plate for long run modules Additional samples will take more than 24 hours and the samples can degrade Note Thermal breakdown of samples is normal Samples are stable for 16 24 hours on the instrument Use Hi Di Formamide to prepar...

Page 177: ...illary Electrophoresis User Guide Pub No 4474504 There was too much sample injected Dilute the sample and re inject it Spikes are present in raw and or analyzed fluorescence data Trace impurities passed the detector For fragment analysis increasing the Minimum peak half width setting in the analysis settings under Common settings can reduce the identification of spikes as peaks Note Secondary sequ...

Page 178: ...rimer and or a sufficient concentration of primer There is a heterozygous insertion deletion het indel that is causing multiple peaks to appear at the same basecall position The sequence can appear clean for some number of bases until the het indel is encountered Examine the analyzed trace A het indel typically has single peaks at the 5 end then part way through the trace two peaks appear in almos...

Page 179: ... the amplification temperature You accidentally contaminated the DNA and are sequencing two templates at the same time The analyzed trace shows extra peaks throughout the entire length of the trace Repeat the amplification and sequencing reactions with uncontaminated DNA There were impure or contaminated primers Primer stocks may have inadvertently had other primer solution introduced For best res...

Page 180: ...was selected in the Plate setup Correct the dye set and repeat the injection Select from the following E_BigDye Terminator v1 1 Z_BigDye Terminator v3 1 Z_BigDye Direct Reanalyze the data in the Sequencing Analysis Software using the correct mobility file Fragment analysis peaks are sized differently than previously observed Aging of the polymer in the cartridge which can cause small 0 5 bp change...

Page 181: ...reating the items manually Import CSV fails but import PSM with same settings imports with no errors The size standard dye set or run module specified in the CSV file does not exist on the instrument The CSV file contains the names only of the size standard dye set or run module it does not contain the settings The PSM file contains the names and settings of the size standard dye set or run module...

Page 182: ...t You selected Cloud in the Set up run screen or in the Save location field in the Plate properties screen then typed in your Cloud account email and password Return to Sign in screen touch touch Sign out then select your local profile from the Sign in list The Notifications button is not displayed in Instrument Settings You are signed in to the instrument with a local instrument profile Sign in t...

Page 183: ... of the unexpected error See Export log files for plates install runs injections and instrument on page 170 Restart the system using the On Off switch on the rear panel See Power on the instrument on page 34 Service tools The Service tools function is password protected and for service use only Appendix A Troubleshooting Service tools A SeqStudio Genetic Analyzer Instrument and Software User Guide...

Page 184: ...Connect cloud based platform account in any of the following ways Link the instrument from a mobile device page 185 Link the instrument using a link code page 186 Network requirements The instrument is factory configured for IPv4 TCP IP communication and includes a fast Ethernet adapter 10 100 Mbps with a RJ45 type connector for integrating the device into a local area network LAN By default the i...

Page 185: ...Do you have a local instrument profile Description Yes 1 Touch Sign in then enter your PIN 2 In the home screen touch Setup run 3 In the Setup run screen touch Cloud No Touch Get started4Connect 5 Touch Mobile devices The QR code is displayed Create a Connect cloud based platform PIN and generate the QR code on the instrument Appendix B Link the instrument to your Connect cloud based platform acco...

Page 186: ...sing a link code 1 From the instrument Sign In screen navigate to the Connect to the Thermo Fisher Cloud screen Do you have a local instrument profile Description Yes 1 Touch Sign in then enter your PIN 2 In the home screen touch Setup run 3 In the Setup run screen touch Cloud No Touch Get started4Connect Register the instrument with the Instrument Connect App Appendix B Link the instrument to you...

Page 187: ...sed platform account on a separate computer Go to thermofisher com connect Appendix B Link the instrument to your Connect cloud based platform account detailed instructions Link the instrument using a link code B SeqStudio Genetic Analyzer Instrument and Software User Guide 187 ...

Page 188: ...5 Select SeqStudio then click Next Appendix B Link the instrument to your Connect cloud based platform account detailed instructions Link the instrument using a link code B 188 SeqStudio Genetic Analyzer Instrument and Software User Guide ...

Page 189: ...and connected to your Connect cloud based platform account The first time the instrument is linked the software automatically Creates a Connect cloud based platform instrument profile with the First Name and Last Name from your Connect cloud based platform account Registers the instrument in the InstrumentConnect software Appendix B Link the instrument to your Connect cloud based platform account ...

Page 190: ...tform instrument profile and PIN 2 In the home screen of the instrument touch Settings4Instrument settings4Email notifications Note If you are signed in with a local instrument profile instead of a Connect platform instrument profile the Email notifications button is not displayed on the Instrument Settings screen Appendix B Link the instrument to your Connect cloud based platform account detailed...

Page 191: ...hich you want to receive email notifications then touch Done Appendix B Link the instrument to your Connect cloud based platform account detailed instructions Set up email notifications from the instrument B SeqStudio Genetic Analyzer Instrument and Software User Guide 191 ...

Page 192: ...stem dye sets are available from Thermo Fisher Scientific System dye sets Fragment HID analysis dye sets Sequence analysis dye sets D DS 30 DS 31 E5 DS 02 F DS 32 G5 DS 33 J6 DS 36 J6 T DS 37 E_BigDye Terminator v1 1 Z_BigDye Terminator v3 1 Z_BigDye Direct Custom dye sets are any dyes that are not available from Thermo Fisher Scientific Custom dye sets require manual calibration C Overview of sys...

Page 193: ...calibration for system and custom dyes Sequence analysis dye sets Do not typically require manual calibration Fragment analysis dye sets Manual calibration is recommended one time before use Note With high quality sample data it is possible for auto calibration to pass using the factory calibration HID analysis dye sets Manual calibration is required for each dye set one time before use To determi...

Page 194: ...alibration or manual calibration has been performed 2 Manual calibration is not required A manual calibration has been performed 3 Manual calibration is not required The factory calibration has been optimized for the instrument by auto calibration 4 Manual calibration is recommended Auto calibration has been performed but only 2 capillaries passed 5 Manual calibration is not required A manual cali...

Page 195: ...et for the dye set In the home screen 1 Touch Settings4Maintenance and Service4Calibration4Dye Calibration 2 Touch the injection group for the dye set in the plate then touch Dye set Perform a system dye calibration Appendix C Dye calibration and install standard checks Calibrate dyes C SeqStudio Genetic Analyzer Instrument and Software User Guide 195 ...

Page 196: ...luorescence signal It is a measure of the consistency between the final matrix and the data from which it was computed A Quality Value of 1 0 indicates high consistency providing an ideal matrix with no detected pull up pull down peaks In rare cases a high Quality Value can be computed for a poor matrix This can happen if the matrix standard contains artifacts leading to the creation of one or mor...

Page 197: ...e if a capillary passes or fails are Dye Set Quality Value Minimum Condition Number Maximum AnyDye 0 8 default 20 0 default D 0 8 8 5 E 0 95 5 5 E5 0 95 6 0 F 0 95 8 5 G5 0 95 13 5 J6 0 95 8 0 J6 T 0 95 8 0 Z 0 95 5 5 Add a custom dye set to the software based on a system dye 1 In the home screen touch Settings4Maintenance and Service4 Calibration4Dye calibration 2 Touch Custom Dye 3 Touch Add Per...

Page 198: ...ftware using the Any Dye template 1 In the home screen touch Settings4Maintenance and Service4 Calibration4Dye calibration 2 Touch Custom Dye 3 Touch Add 4 Select Any Dye to use as a starting point for the custom dye settings All dyes are selected by default Appendix C Dye calibration and install standard checks Calibrate dyes C 198 SeqStudio Genetic Analyzer Instrument and Software User Guide ...

Page 199: ...rd Disable deselect the Reduce selection checkbox to indicate that the system dye should not be analyzed reported or used for auto calibration 1 1 Order of dyes in the custom dye set 6 Touch Next enter dye set parameters then touch Next 7 Enter a Dye set name then touch Save Perform a custom dye calibration Before you begin Prepare the dye set calibration standards and plate as described in the pr...

Page 200: ... failed calibration Close the calibration screen then start a new calibration Add a custom dye to the Plate Manager or another instrument To add a custom dye set to the Plate Manager a Open a plate setup that specifies the custom dye set of interest b Export a plate setup that specifies the custom dye see Export or delete a plate setup PSM file on page 138 c Open the exported plate setup in the Pl...

Page 201: ... baseline calibration to optimally reduce pull up false secondary peaks under a true peak 5 A manual dye calibration and an auto dye calibration have been performed 2 Touch a dye set A thumbnail of each capillary calibration spectrum is displayed with the q and c values see Spectral Quality Value on page 196 and Condition number on page 197 3 Touch and to view a full screen calibration spectrum fo...

Page 202: ...ouch Settings4Maintenance and Service4 Calibration4Dye calibration4Custom dye4Manage 1 Touch the custom dye set 2 Touch Import or Export Import or export a custom dye set Appendix C Dye calibration and install standard checks Calibrate dyes C 202 SeqStudio Genetic Analyzer Instrument and Software User Guide ...

Page 203: ...required before the install check GlobalFiler Allelic Ladder from one of the following installation kits SeqStudio HID and Sequencing Installation Kit Cat No A46180 SeqStudio HID Installation Kit Cat No A46182 You can include multiple injection groups multiple applications and or multiple chemistries on an install run plate For example you can prepare an install run plate that contains replictate ...

Page 204: ...up on the plate to select a location for the install standards A plate can be set up with different injection groups for one install run 3 Touch Chemistry then select the type of install run Select None to cancel the selection 4 Repeat the steps above for additional injection groups and or multiple chemistries 5 Touch Start Run Perform an install run Appendix C Dye calibration and install standard...

Page 205: ... touch Results To view results for a previous install run touch Settings4Maintenance and Service4Install run4Install run history View install run results Appendix C Dye calibration and install standard checks Perform an install run C SeqStudio Genetic Analyzer Instrument and Software User Guide 205 ...

Page 206: ... least 1 warning quality alert was triggered At least 1 failing quality alert was triggered For information on quality alerts see Data quality alerts on page 119 Sizecalling and basecalling quality alerts on page 119 Appendix C Dye calibration and install standard checks Perform an install run C 206 SeqStudio Genetic Analyzer Instrument and Software User Guide ...

Page 207: ...is install run pass fail criteria Result Acceptance criteria Allele peaks 15 for all four capillaries Size standard peaks 34 for all four capillaries Standard deviation of the observed allele fragment sizes for all 4 capillaries 0 15 base pairs bp Appendix C Dye calibration and install standard checks Perform an install run C SeqStudio Genetic Analyzer Instrument and Software User Guide 207 ...

Page 208: ...eria for install checks is an uninterrupted segment of bases with an average Quality Value QV of 30 BigDye Terminator v3 1 Capillaries with QV30 CRL 500 bp pass BigDye Terminator v1 1 Capillaries with a QV30 CRL 500 bp pass The remaining results on the screen are for information only 1 Touch Settings4Maintenance and Service4Install run4Install run history 2 Touch the install run of interest 3 Touc...

Page 209: ...Example fragment analysis run report Appendix C Dye calibration and install standard checks Perform an install run C SeqStudio Genetic Analyzer Instrument and Software User Guide 209 ...

Page 210: ... screen 1 Touch Settings4Maintenance and Service4Install run history View the install run history Appendix C Dye calibration and install standard checks Perform an install run C 210 SeqStudio Genetic Analyzer Instrument and Software User Guide ...

Page 211: ...uch Done Note If the screen is blank when you click Done no install runs are present for the chemistry you selected Appendix C Dye calibration and install standard checks Perform an install run C SeqStudio Genetic Analyzer Instrument and Software User Guide 211 ...

Page 212: ...e pull up reduction function For more information see Calibrate dyes on page 192 Allelic ladder We recommend that you inject one allelic ladder for each set of 24 samples in HID runs 1 allelic ladder per 6 injections Allelic ladders that are injected under the same conditions are recommended to accurately genotype samples in the secondary analysis software IMPORTANT Variation in laboratory tempera...

Page 213: ... an HID plate To enable select the appropriate kit from the Kits list To disable select None from the Kits list Note Kit is displayed when None is selected To display this screen where you select a kit Select or create a plate set up touch the Plate tab then select Edit In the Edit Plate screen swipe up to find the Kit field then select a kit from the dropdown list Note You can also select a kit f...

Page 214: ...agment analysis applications Traditionally use POP 4 Polymer Because of its polymer concentration and molecule size POP 4 Polymer has single basepair resolving power within the size range for forensic STR amplification kits and runs faster About POP 1 Polymer We are introducing POP 1 Polymer for the SeqStudio Genetic Analyzer which can be used for all applications on the instrument For smaller fra...

Page 215: ...ment page 105 View and analyze results View results on the instrument on page 111 Export results from the instrument sample data files and QC reports page 121 Analyze data in a secondary analysis software application HID install run Item Description Components of the install check reaction GeneScan 600 LIZ Size Standard v2 0 Cat No 4408399 Hi Di Formamide Cat No 4311320 or 4440753 GlobalFiler Alle...

Page 216: ...ution Range The range of bases over which the resolution peak spacing interval divided by the peak width at half max in a GS600 size standard sample sized with a third order fit is 1 2 The GeneScan 500 LIZ Size Standard was not included in the HID validation of the instrument Category Items Dye sets G5 DS 33 J6 DS 36 J6 T DS 37 Size standards GS500 250 LIZ GS600_LIZ_ 60 460 GS600_LIZ_ 80 400 Kits ...

Page 217: ... to a USB or a network drive 2 Access the Manage kits screen From Actions Plate properties tab Touch More options4Manage kits Home screen Touch Settings4Run settings 4Kits 3 Touch Import select the location of the kit file Select the kit then touch Import The kit file is loaded in the software Appendix D Create and run an HID plate Manage kits HID applications only D SeqStudio Genetic Analyzer Ins...

Page 218: ...e 16 Fragment analysis run modules Run module Resolution range Approximate run time Sizing precision Compatible size standards SNaPshot 40 120 bp 25 minutes 40 120 0 5 GeneScan 120 LIZ Size Standard FragAnalysis 60 460 bp 1 45 minutes 60 460 0 15 All except GeneScan 1200 LIZ Size Standard LongFragAnalysis 2 60 600 bp 1 2 hours 60 460 0 15 461 600 0 3 601 800 0 45 GeneScan 600 LIZ Size Standard v2 ...

Page 219: ...width at half max in a GS600 size standard sample sized with a third order fit is 1 2 The GeneScan 500 LIZ Size Standard was not included in the HID validation of the instrument Note The following size standards have not been validated for use with the instrument A default size standard definition is not provided in the software GeneScan 350 ROX Size Standard GeneScan 400HD ROX dye Size Standard A...

Page 220: ...dio Genetic Analyzer SeqStudio Genetic Analyzer Cartridge A33671 SeqStudio Genetic Analyzer Cartridge v2 A41331 SeqStudio Genetic Analyzer Cathode Buffer Container A33401 Reservoir Septa for Cathode Buffer Container A35640 SeqStudio Integrated Capillary Protector A31923 Tubes plates and other consumables MicroAmp Optical 96 Well Reaction Plate 4316813 MicroAmp Optical 96 Well Reaction Plate with B...

Page 221: ... DS 33 GeneScan Installation Standards with GeneScan 600 LIZ Size Standard v2 0 4376911 HID analysis size standards and installation standard GeneScan 500 LIZ Size Standard 2 4322682 GeneScan 600 LIZ Size Standard v2 0 4408399 SeqStudio HID and Sequencing Installation Kit A46180 SeqStudio HID Installation Kit A46182 1 For fragment analysis This size standard has not been validated for use with the...

Page 222: ...t to lift or move the instrument without professional assistance The crated instrument is heavy Any incorrect lifting or moving of the crated instrument can cause serious injury Instrument clearances During instrument setup and maintenance it is necessary to access the back and sides of the instrument If the back of the instrument faces a wall it will be necessary to have enough space to rotate th...

Page 223: ...ort and storage 20 C to 60 C 4 F to 140 F Transient category Installation categories II Overvoltage category Installation categories II Vibration Ensure that 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 the instrument in an environment designated pollution degree...

Page 224: ...nal voltage Rated voltage Circuit required Rated frequency Rated power 100 240 10 VAC 1 10 A 50 60 Hz 400 W 1 If the supplied power fluctuates beyond the rated voltage a power line regulator may be required High or low voltages can adversely affect the electronic components of the instrument Electrical protective devices We recommend several protective devices to protect the system in environments...

Page 225: ...rminate the function of and thereby damage the components of the computer and the instrument Note A dedicated line and ground between the instrument computer and the building s main electrical service can also prevent problems caused by power fluctuations Network requirements The instrument is factory configured for IPv4 TCP IP communication and includes a fast Ethernet adapter 10 100 Mbps with a ...

Page 226: ...priate fire extinguisher for use on or near the equipment The types and sizes of fire extinguishers shall be suitable for use on electrical and chemical fires as specified in current codes regulations and or standards and with approval of the Fire Marshall or other authority having jurisdiction The installation of appropriate fire extinguishers shall be in addition to other fire protection systems...

Page 227: ...nt 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 also be used to alert against unsafe practices WARNING Indicates a pote...

Page 228: ...ordinances for proper disposal provision and contact customer service for information about responsible disposal options Ne pas éliminer ce produit avec les déchets usuels non soumis au tri sélectif MISE EN GARDE Pour minimiser les conséquences négatives sur l environnement à la suite de l élimination de déchets électroniques ne pas éliminer ce déchet électronique avec les déchets usuels non soumi...

Page 229: ...ux Lire les fiches signalétiques FS avant de manipuler les produits CAUTION Hazardous waste Refer to SDS s and local regulations for handling and disposal MISE EN GARDE Déchets dangereux Lire les fiches signalétiques FS et la réglementation locale associées à la manipulation et à l élimination des déchets DANGER Class 3B III visible and or invisible laser radiation present when open and interlocks...

Page 230: ...rating the instrument Disconnect power before servicing WARNING 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...

Page 231: ...nicipal waste Follow local municipal waste ordinances for proper disposal provision and contact customer service for information about responsible disposal options WARNING LASER HAZARD Under normal operating conditions the SeqStudio Genetic Analyzer is categorized as a Class 1 laser product However removing the protective covers and defeating the interlock s may result in exposure to the internal ...

Page 232: ...nt for measurement control and laboratory use Part 2 010 Particular requirements for automatic and semi automatic laboratory equipment for analysis and other purposes EN 60825 1 Safety of lasers products Part 1 Equipment classification and requirements EMC Reference Description EU Directive 2014 30 EU European Union EMC Directive EN 61326 1 Electrical equipment for measurement control and laborato...

Page 233: ...t appareil est conforme aux CNR d Industrie Canada applicables aux appareils radio exempts de licence L exploitation est autorisée aux deux conditions suivantes 1 l appareil ne doit pas produire de brouillage et 2 l utilisateur de l appareil doit accepter tout brouillage adioélectrique subi même si le brouillage est susceptible d en compromettre le fonctionnement Environmental design Reference Des...

Page 234: ...mical 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 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 m...

Page 235: ...nts before working with potentially biohazardous materials Follow all applicable local state provincial and or national regulations The following references provide general guidelines when handling biological samples in laboratory environment U S Department of Health and Human Services Biosafety in Microbiological and Biomedical Laboratories BMBL 5th Edition HHS Publication No CDC 21 1112 Revised ...

Page 236: ...User Guide 4474504 DNA Sequencing by Capillary Electrophoresis Chemistry Guide Second Edition 4305080 Troubleshooting Sanger sequencing data MAN0014435 Customer and technical support Visit thermofisher com support for the latest service and support information Worldwide contact telephone numbers Product support information Product FAQs Software patches and updates Training for many applications an...

Page 237: ... 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 SeqStudio Genetic Analyzer Instrument and Software User Guide 237 ...

Page 238: ...um days allowed on instrument 39 CBC See cathode buffer Cloud See Connect cloud based platform condition number 196 Connect cloud based platform analysis software 29 auto export default location 133 browser requirements 25 disconnect instrument 49 open plate setup default location 132 operating system requirements 25 connect instrument to the Connect cloud based plat form See link consumables stat...

Page 239: ...r 49 view results 111 instrument conditions during run 117 instrument name 148 instrument profile delete 152 PIN change 52 153 Instrument cartridge history view or export 160 IP address 130 147 K kit HID analysis only marker to marker pull up re duction 67 79 kit HID import 217 L limited product warranty 237 load cartridge 161 CBC sample plate and cartridge order 41 plate 92 tubes 92 lock instrume...

Page 240: ...ity of error 117 spectral calibration 196 See also QV QV probability of error 117 QV ranges 116 QV30 CRL 208 R raw data 171 raw trace remote monitor 100 re inject remote monitor 100 re injection 91 105 120 related documentation 169 236 remote monitor analyzed trace 102 EPT plot 101 pause or cancel run 99 raw trace 100 re inject 100 view results 99 110 remove plate associated with inactive user 155...

Page 241: ...pectral calibration condition number 196 quality value 196 SQ 113 support customer and technical 236 symbols safety 227 system dye 192 T template plate setup 122 123 terms and conditions 237 Thermo Fisher Cloud See Connect cloud based plat form troubleshooting log file export 170 tube type supported 37 U update software 150 W warranty 237 wired or wireless instrument connection 149 Index SeqStudio...

Page 242: ...thermofisher com support thermofisher com askaquestion thermofisher com 4 November 2019 ...

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