SeqStudio Genetic Analyzer Instrument and Software User Guide sw ver 1.1 Rev A.0 Oct 2017

Manufacturer: Multiple Life Technologies Corporation manufacturing sites are responsible for manufacturing the products associated with the workflow covered in this guide. Corporate entity: Life Technologies Corporation | Carlsbad, CA 92008 USA | Toll Free in USA 1 800 955 6288 The information in this guide is subject to change without notice. DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, LIFE TECHNOLOGIES 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. MAN0016138 Revision

Date

Description

A.0

19 October 2017

New document for v1.1 software. Quick references only (MAN0016144 and MAN0017087) were provided for v1.0 software.

Important Licensing Information: These products may be covered by one or more Limited Use Label Licenses. By use of these products, you accept the terms and conditions of all applicable Limited Use Label Licenses. TRADEMARKS: All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. ©2017 Thermo Fisher Scientific Inc. All rights reserved.

Contents

■ CHAPTER 1 Product information... 11 Instrument overview... 12 Parts of the instrument... 13 Instrument status indicator... 14 ™

SeqStudio Genetic Analyzer consumables... 14 ™ SeqStudio Genetic Analyzer Cartridge... 15 ™ SeqStudio Genetic Analyzer Cathode Buffer Container... 18 Radio frequency identification... 19 Important notice regarding use of consumables that exceed supported limits... 19 Software features... 20 ™

SeqStudio Plate Manager overview... 23 Computer and operating system options... 23 Recommended browsers... 24 ™

SeqStudio Remote Monitoring App overview... 25 Network connection options... 26 Experiment types... 26 Data output... 27 Secondary analysis software... 28 Workflow: Cloud or desktop... 30 Workflow: instrument... 31

■ CHAPTER 2 Prepare the samples and the instrument... 32 Precautions for use... 32 Power on the instrument... 33 Sign in... 33 Sign in with the Guest instrument profile... 33 Sign out... 34 Parts of the home screen... 34

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Contents

Prepare the samples... 35 Sample preparation guidelines... 35 Plate layout and loading guidelines... 37 Prepare the plate... 37 Prepare the tubes... 38 Prepare the instrument... 39 Check the consumables status... 39 Load the CBC, the sample plate, and the cartridge... 40

■ CHAPTER 3 Use the instrument with the Thermo Fisher Cloud... 42 Understanding instrument and Cloud interaction... 42 "Connect" versus "link"... 42 First user who links is assigned administrator role... 42 Local versus Cloud instrument profiles... 43 If you link when you are signed in to the instrument... 43 If you link when you are not signed in to the instrument... 44 Cloud instrument profile roles and functions... 46 For more information on using the Thermo Fisher Cloud... 46 Cloud administrators for an instrument... 47 Cloud administrator functions... 47 Assign instrument administrator role to other users... 47 Manage the users and administrators of your instrument... 48 Disconnect individual users from an instrument... 49 Register and obtain a Cloud account... 49 Link the instrument to your Thermo Fisher Cloud account... 50 Change your own Cloud instrument profile PIN... 51 Set up email notifications from the instrument... 52

■ CHAPTER 4 Create or modify a plate setup from the

Plate Manager... 53 Overview of plate setup settings... 53 Set up a plate using default settings (Plate Manager)... 55 Access the Plate Manager on the Cloud... 55 Access the Plate Manager on the desktop... 55 Create or open a plate setup PSM file... 55 Enter plate properties... 56

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Assign wells: Sample and run information... 57 Save a plate setup in the Plate Manager... 58 Additional plate settings (Plate Manager)... 59 Specify replicate injections... 59 Edit analysis settings... 59 Modify the default file name convention... 60 Hide or share a plate (Plate setup security)... 60 Define custom fields... 61

■ CHAPTER 5 Create or modify a plate setup from the instrument . . 62 PSM and CSV plate setup files for import into the instrument... 63 Shared (public), hidden (my plates), and guest plate setup files... 64 Overview of plate setup settings... 65

(Optional) Set up for auto export of sample data files (AB1 and FSA)... 66 Set up a plate using default settings (instrument)... 66 Create or import a plate setup... 66 Enter plate properties... 67 Assign wells: run module, size standard, and dye set... 69 Assign wells: sample name, sample type, and custom fields... 70 Set optional plate settings (instrument)... 71 Specify replicate injections... 71 Modify analysis settings... 72 Modify the default file name convention... 72 Hide or share a plate (Plate setup security)... 73 Define custom fields... 73 (Optional) View the injection list, change injection settings or order, or specify replicates and re-injections... 75

■ CHAPTER 6 Start and monitor a run... 76 Load the plate or the tube assembly... 76 Select a plate setup and start a run... 77 Automatic file cleanup... 78 Lock the touchscreen... 79 Monitor a run from the Thermo Fisher Cloud... 79 Open the Remote Monitoring App from Instrument Connect App... 79 Open the Remote Monitoring App from the Plate Manager... 81 View notifications from the instrument on the Cloud... 83 View results in the Remote Monitoring App on the Cloud... 83 Monitor a run from a mobile device... 87

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Monitor a run from the instrument... 89 (Optional) View the injection list, change injection settings or order, or specify replicates and re-injections... 89 View the run status... 89 View real-time results... 90 Pause a plate or cancel or stop injections... 90 View results for the current plate... 91 Unload the plate or the tube assembly... 95

■ CHAPTER 7 View and analyze results... 97 View results in the Remote Monitoring App on the Cloud... 97 View results on the instrument... 98 View results for the current plate... 98 View results for a previously run plate (run history)... 104 Edit injection parameters and re-inject samples... 104 Export a report (QC report)... 105 Export results from the instrument (sample data files and QC reports)... 105 Analyze data... 106

■ CHAPTER 8 Manage the software (Plate Manager)... 107 Add a custom dye calibration to the Plate Manager... 107 Download a plate setup template as a CSV file... 107 Save a plate setup as a PDF... 108 Save a plate setup as a CSV file... 108 Create a plate setup template... 108 Delete plate setups... 109 Manage email notifications in the Thermo Fisher Cloud... 110 Manage run modules... 110 Run module settings... 111 Run modules, read lengths, size ranges, and run times... 111 Manage size standards... 112 Manage analysis settings... 113 Fragment analysis settings (size calling)... 113 Sequencing settings (base calling)... 115

■ CHAPTER 9 Manage the software (instrument)... 117 Connect the instrument to a network drive... 117 Determine IP address for a computer on a network... 117 Create folders and enable network folder sharing... 118 Connect to a network drive... 119 Set up a default Cloud location for opening plate setups... 119 Set up a default Cloud location for saving results (auto export)... 120

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SeqStudio™ Genetic Analyzer Instrument and Software User Guide

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Set up a default network location for opening plate setups... 120 Set up a default network location for saving results (auto export)... 121 Link the instrument to your Thermo Fisher Cloud account... 123 Lock the touchscreen... 124 Manage plate setups... 125 Export or delete a plate setup (PSM file)... 125 Import a plate setup from a CSV or PSM file... 126 Manage run settings (instrument)... 126 Manage run modules... 126 Manage size standard definitions... 128 Manage analysis settings... 129 Modify the default file name convention... 134 Manage instrument settings... 135 Display instrument hardware and software information... 135 Change the instrument name... 135 Enable Demo mode... 135 Manage date and time settings... 135 Manage the network configuration... 136 Check for software updates (administrator only)... 137 Manage instrument profiles on the instrument... 138 Local instrument profile roles and functions... 138 Create a local instrument profile for another user (administrator only)... 138 Change the role of a local instrument profile (administrator only)... 139 Delete an instrument profile from an instrument (administrator only)... 139 Delete the PIN for a local instrument profile (administrator only)... 139 Create your own local instrument profile... 140 Change your own local instrument profile PIN... 140 Manage storage space... 140 Automatic file cleanup... 140 Export or delete a plate setup (PSM file)... 141 Export results from the instrument (sample data files and QC reports)... 141 Delete a run history... 142 Back up user data (plates and results) (administrator only)... 142

■ CHAPTER 10 Maintain the instrument... 143 Regular maintenance tasks... 143 Check the cathode buffer fill level... 143 Clean the instrument exterior and touchscreen... 144 Clean the autosampler... 144 Manage the cartridge... 145 ™ SeqStudio Genetic Analyzer Cartridge storage... 145 Set cartridge storage mode (administrator only)... 145 Check or export the Instrument-cartridge history... 146 Check or export the cartridge history... 146 SeqStudio™ Genetic Analyzer Instrument and Software User Guide

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Contents

Fill the capillary array and refresh the polymer delivery system... 147 ™ Remove the SeqStudio Genetic Analyzer Cartridge... 147 Insert the cartridge... 147 Store the cartridge... 149 ™ SeqStudio Integrated Capillary Protector... 150 Long-term on-instrument cartridge storage... 151 Install cathode buffer... 151 ™ SeqStudio Genetic Analyzer Cathode Buffer Container storage... 151 ™ Remove the SeqStudio Genetic Analyzer Cathode Buffer Container... 151 ™ Assemble the SeqStudio Genetic Analyzer Cathode Buffer Container (CBC)... 152 Insert the Cathode Buffer Container... 153

■ APPENDIX A Troubleshooting... 154 Troubleshooting resources... 154 Troubleshooting workflow... 155 Export log files for plates, install runs, injections, and instrument... 155 View the raw data and the EPT plot... 156 Data quality alerts... 156 Sizecalling and basecalling quality alerts... 156 Check size standard quality... 157 Instrument troubleshooting... 158 Cartridge troubleshooting... 159 Sample and data troubleshooting... 160 EPT data... 164 Software troubleshooting... 165 Service tools... 167

■ APPENDIX B Link the instrument to your Cloud account-

detailed instructions... 168 Workflow: Set up the instrument for Thermo Fisher Cloud access... 168 Network requirements... 169 Link the instrument from a mobile device... 169 Create a Cloud PIN and generate the QR code on the instrument... 169 Register the instrument with the Instrument Connect App... 170 Link the instrument using a link code... 170 Link the instrument using your Cloud account... 174 Set up email notifications from the instrument... 176

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SeqStudio™ Genetic Analyzer Instrument and Software User Guide

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■ APPENDIX C Dye calibration and install standard checks... 177 Calibrate dyes... 177 Overview of system dye set and custom dye set calibration... 177 System versus custom dyes... 177 Factory, auto, and manual calibration... 178 Determine if manual calibration is required... 178 Perform a system dye calibration... 180 Perform a custom dye calibration... 182 View the dye calibration history... 186 Import or export a custom dye set... 187 Perform an install run... 188 Overview of install checks... 188 Perform an install run... 189 View install run results... 190 Export the install run report... 193 View the install run history... 195

■ APPENDIX D Run modules... 197 Run modules, read lengths, size ranges, and run times... 197

■ APPENDIX E Parts and materials... 198 Required materials not supplied... 198

■ APPENDIX F Instrument specifications and layout... 200 Instrument dimensions... 200 Instrument clearances... 200 Environmental requirements... 201 Electrical requirements... 202 Electrical protective devices... 202 Network requirements... 203 Safety requirements... 203 Safety practices... 203 Required safety equipment... 204

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Contents

■ APPENDIX G Safety... 205 Symbols on this instrument... 205 Conformity symbols... 206 Safety alerts on this instrument... 207 Safety information for instruments not manufactured by Thermo Fisher Scientific... 208 Instrument safety... 208 General... 208 Physical injury... 208 Electrical... 208 Cleaning and decontamination... 209 Instrument component and accessory disposal... 209 Laser... 209 Safety and electromagnetic compatibility (EMC) standards... 209 Safety compliance... 210 EMC... 210 Environmental design... 211 Radio compliance... 211 Chemical safety... 212 Biological hazard safety... 213

■ Documentation and support... 214 Related documentation... 214 Customer and technical support... 214 Limited product warranty... 215

Index... 216

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Product information

■ ■ ■ ■ ■ ■ ■ ■ ■ ■ ■ ■

Instrument overview... 12 Parts of the instrument... 13 SeqStudio™ Genetic Analyzer consumables... 14 Software features... 20 SeqStudio™ Plate Manager overview... 23 SeqStudio™ Remote Monitoring App overview... 25 Network connection options... 26 Experiment types... 26 Data output... 27 Secondary analysis software... 28 Workflow: Cloud or desktop... 30 Workflow: instrument... 31

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Chapter 1 Product information

Instrument overview

Instrument overview The Applied Biosystems™ SeqStudio™ Genetic Analyzer with SeqStudio™ Data Collection Software is a fluorescent dye-labeled genetic analysis system using capillary electrophoresis technology. It enables both sequencing and fragment analysis applications without the need to switch polymer type or capillary array length. The instrument uses the SeqStudio™ Genetic Analyzer Cartridge. It is a self-contained, replaceable cartridge with: • A 4-capillary array • A universal polymer capable of performing sequencing and fragment analysis • A polymer delivery system (PDS) • Anode buffer

The SeqStudio™ Genetic Analyzer automatically: • Performs an optical alignment each time 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. Plate setup can be done directly on the touchscreen, on a computer with SeqStudio™ Plate Manager, or on the Thermo Fisher Cloud. A run can be monitored directly on the instrument touchscreen or remotely on the Thermo Fisher Cloud.

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SeqStudio™ Genetic Analyzer Instrument and Software User Guide

Chapter 1 Product information

Parts of the instrument

1

Parts of the instrument 1 2

3

4

Figure 1 Front of the instrument Front panel indicator-Shows the status of the instrument Touchscreen-User interface 3 Door-Provides access to the cartridge, the cathode buffer, and sample plate or tubes 4 USB port 1 2

1 2 3 4

5

Figure 2 Interior of the instrument Cartridge rails 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 1 2

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SeqStudio™ Genetic Analyzer consumables

4

1

2

3

Figure 3 Rear of the instrument RJ45 ethernet port USB port 3 Power receptacle 4 On/Off switch 1 2

Instrument status indicator Indicator

Instrument status

All lights off

Powered off or in Cartridge storage mode.

Blue light (blinking)

Starting up.

Blue light

Ready to start a run or run is in progress.

Amber light (blinking)

Run is paused, door is open, or error state.

SeqStudio™ Genetic Analyzer consumables Description

Cat. No.

Amount

Storage

SeqStudio™ Genetic Analyzer Cartridge

A33671

SeqStudio™ Genetic Analyzer Cathode Buffer Container

A33401

1 package of 4

See page 151

SeqStudio™ Integrated Capillary Protector

A31923

1 (single-use) for future storage

See page 150

14

1 cartridge with a SeqStudio™ Integrated Capillary Protector attached for shipment and storage.

See page 17

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Chapter 1 Product information

SeqStudio™ Genetic Analyzer consumables

SeqStudio™ Genetic Analyzer Cartridge

1

The SeqStudio™ Genetic Analyzer Cartridge is a 4-capillary, self-contained, replaceable cartridge for use with the SeqStudio™ Genetic Analyzer. The cartridge contains a capillary array, a polymer delivery system, polymer, and anode buffer for 125 injections (500 samples). The cartridge can be used for up to four months after the first use, if it is stored correctly and has not passed the labeled expiry date. The SeqStudio™ Cartridge has a radio frequency identification (RFID) tag, which is used by the instrument to track remaining usage and expiration. The cartridge is shipped with an optics cover and an Integrated Capillary Protector.

1

Remove Before Insertion

2

4

3

Figure 4 Cartridge with optics cover and Integrated Capillary Protector Optics cover Optics cover hand hold (for removing the optics cover) 3 Integrated Capillary Protector 4 Cartridge hand hold 1 2

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SeqStudio™ Genetic Analyzer consumables

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.

1

2

4

3

5

6

Figure 5 Parts of the cartridge 1 2 3 4 5 6

Universal polymer-Supplies polymer to the polymer delivery pump. Polymer delivery system-Pumps polymer into the capillary array. Anode buffer reservoir-Genetic Analysis running buffer to support electrophoresis. Optical detection window Cartridge track-To insert the cartridge into the instrument. Capillary array (cathode end)-Tips of the four capillaries that enable electrophoretic separation of fluorescent-labeled DNA fragments.

6

1

2

3

4

5

Figure 6 Parts of the polymer delivery system 1 2 3 4 5 6

16

Universal polymer Polymer valve Syringe Capillary fitting (anode end) Buffer valve Anode buffer reservoir

SeqStudio™ Genetic Analyzer Instrument and Software User Guide

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SeqStudio™ Genetic Analyzer consumables

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SeqStudio™ Genetic Analyzer Cartridge storage Condition Shipping

Description Is shipped at 2–8°C. Store upright at 2–8°C upon receipt. Save the white storage box and optics cover for off-instrument cartridge storage.

On-instrument storage

For routine use, can be used and stored on the instrument for up to 4 months. If you store the cartridge on-instrument: • The instrument must be powered on. • A Cathode Buffer Container must also be installed. The instrument keeps the components under the following conditions when it is powered on and in Cartridge storage mode: • Optical detection window-Covered • Capillary array electrodes-Submerged in cathode buffer (buffer must be above the fill line in the Cathode Buffer Container) • Polymer-Chilled • Anode buffer-Ambient temperature

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 intermittant use, can be stored off-instrument (upright, with an integrated capillary protector (ICP) and optics cover installed) until the expiry date on the label or up to 4 months after first use (see “Store the cartridge“ on page 149). 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 different instrument, if it was stored properly at 2–8°C and has not expired or exceeded 125 injections. Information about the cartridge installation and usage is retained in the cartridge history (Settings4Cartridge4Instrument–cartridge history).

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SeqStudio™ Genetic Analyzer consumables

SeqStudio™ Genetic Analyzer Cathode Buffer Container

The SeqStudio™ Genetic Analyzer Cathode Buffer Container (CBC) contains running buffer for capillary electrophoresis. The container has two compartments. The rear compartment provides the cathode buffer for electrophoresis. The front compartment is for capillary wash and waste. The CBC requires a Reservoir Septa. See “Assemble the SeqStudio™ Genetic Analyzer Cathode Buffer Container (CBC)“ on page 152. 1 2 3 5

4

Figure 7 SeqStudio™ Genetic Analyzer Cathode Buffer Container with Reservoir Septa Reservoir Septa Notch (inserted towards the rear right in the 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 2

4

1

2

3

Figure 8 Autosampler Location of plate or tubes Release button 3 Location of Cathode Buffer Container 4 Location to position the Cathode Buffer Container notch 1 2

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Radio frequency identification

1

The cartridge and cathode buffer have radio–frequency identification (RFID) tags. The instrument reads and tracks: • Expiry date (shelf life) • Remaining injections (usage) • Serial number (cartridge only) • Lot number (cathode buffer only)

Table 1 RFID tag read/write events and consumables status updates Component Cartridge

RFID read When a cartridge inserted. The first time a new cartridge is loaded into an instrument, the manufacturer expiry date is listed for Expiry time in the Consumable status screen.

Cathode buffer

• When the autosampler initializes. • When a plate is retracted.

[1]

RFID write

Consumables status update

• The Expiry time is reset from the manufacturer expiry date to 4 months from the current date of installation.

Every 8 hours and/or before each run[1]:

• After the cartridge has been loaded and before it is ejected, its cartridge history record is updated to include its usage on this instrument.

• When a cartridge is within 2 weeks of expiry date. • When the number of injections is approaching the 125‑injection limit.

• During each injection, injection count and remaining polymer volume are updated. • The first time a new CBC is Every 8 hours and/or before loaded on an instrument, the each run[1]: installation date is recorded on • When the CBC is within the CBC. 2 days of expiry date. • After each injection, the • When the number of injection count is updated. injections is approaching the 125‑injection limit.

If either limit is met, an email notification is also sent to any Cloud users who are linked to this instrument

Important notice regarding use of consumables that exceed supported limits

BEFORE DISMISSING THE WARNING THAT THE CONSUMABLES HAVE REACHED SUPPORTED LIMITS AND CONTINUING WITH OPERATION OF THE INSTRUMENT, PLEASE READ AND UNDERSTAND THE FOLLOWING IMPORTANT NOTICE AND INFORMATION: Life Technologies does not recommend the use of consumables that exceed supported limits. The recommended limits are designed to promote the production of high quality data and minimize instrument downtime. Reagent and consumable lifetime minimum performance are based on testing and studies that use reagents and consumables that have not exceeded supported limits. The use of consumables beyond the supported limits may impact data quality or cause damage to the instrument or capillary array. The cost of repairing such damage is NOT covered by any Life Technologies product warranty or service plan. Customer use of expired consumables is at customer's own risk and without recourse to Life Technologies. For example, product warranties do not apply to defects resulting from or repairs required due to misuse, neglect, or accident including, without limitation, operation outside of the environmental or use specifications or not in conformance

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Chapter 1 Product information Software features

with Life Technologies instructions for the instrument system, software, or accessories. Please see your specific service contract or limited product warranty for exact language regarding coverage and ask your Life Technologies representative if you have further questions.

Software features The instrument can be operated directly from the touchscreen using the SeqStudio™ Data 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 Thermo Fisher Cloud. These plate setups can be saved to and accessed from the instrument from: • A network drive • A USB drive • The Thermo Fisher Cloud You can monitor runs directly from the instrument or from the SeqStudio™ Remote Monitoring App. Table 2 Features of the software SeqStudio™ Data Collection Software

SeqStudio™ Plate Manager (desktop)

SeqStudio™ Plate Manager (Cloud)

Remote Monitoring App

Create a new plate setup

✓

✓

✓

-

Enter plate properties

✓

✓

✓

-

Set up plate wells

✓

✓

✓

-

Feature Plate setup

Advanced options for plate setup Edit sample properties

✓

✓

✓

-

Edit plate setup

✓

✓

✓

-

Manage size standards

✓

✓

✓

-

Manage run modules (including edit a run module)

✓

✓

✓

-

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SeqStudio™ Genetic Analyzer Instrument and Software User Guide