Thermo Scientific Applied Biosystems SeqStudio Genetic... User manual

For Research Use Only. Not for use in diagnostic procedures.
SeqStudio™Genetic Analyzer
GETTING STARTED GUIDE
Create and run plate setups, monitor runs, and view results
for use with:
SeqStudio™Data Collection Software v1.2
SeqStudio™Genetic Analyzer Cartridge (Cat. No. A33671)
SeqStudio™Genetic Analyzer Cartridge v2 (Cat. No. A41331)
SeqStudio™Plate Manager
SeqStudio™Remote Monitoring App
Publication Number MAN0018654
Revision A.0

Manufacturer:
Life Technologies Holdings Pte Ltd |
Block 33 |
Marsiling Industrial Estate Road 3 |
#07-06, Singapore 739256
Products:
SeqStudio™Genetic Analyzer
SeqStudio™Data Collection Software
SeqStudio™Plate Manager (desktop)
SeqStudio™Genetic Analyzer Cartridge
SeqStudio™Genetic Analyzer Cartridge v2
Security, Auditing, and E‑signature (SAE) v2.0 module
Manufacturer: Life Technologies
Corporation | 200 Oyster Point Blvd |
South San Francisco, CA 94080 |
USA
Products:
SeqStudio™Remote Monitoring App
Manufacturer: Life Technologies
Corporation | 35 Wiggins Avenue |
Bedford, MA 01730
Products:
SeqStudio™Genetic Analyzer Cathode Buffer Container
The information in this guide is subject to change without 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. MAN0018654
Revision Date Description
A.0 1 November 2019 New getting started guide for SeqStudio™Data Collection Software v1.2.
The v1.2 software includes options for HID kits. This getting started guide
replaces Pub. No. MAN0017464.
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.
©2019 Thermo Fisher Scientific Inc. All rights reserved.

Contents
■CHAPTER 1 Product information ....................................... 6
Product description ............................................................. 6
Workflow ...................................................................... 7
■CHAPTER 2 Prepare the samples and the instrument ................ 9
Prepare the samples ............................................................ 9
Sample preparation guidelines ............................................... 9
Plate layout and loading guidelines .......................................... 11
Prepare the instrument ......................................................... 11
Power on the instrument ................................................... 11
Check the consumables status .............................................. 11
Load the CBC, the sample plate, and the cartridge ............................. 12
Prepare and load the plate or tubes .............................................. 14
Prepare the plate .......................................................... 14
Prepare the tubes .......................................................... 14
Load the plate or the tube assembly .......................................... 15
Unload the plate or the tube assembly ........................................ 15
■CHAPTER 3 Set up a plate using default settings (Plate
Manager) .................................................................. 16
Access the Plate Manager ....................................................... 16
Create or open a plate setup PSM file ............................................. 17
Enter plate properties .......................................................... 17
Assign wells: Sample and run information ........................................ 18
Save a plate setup in the Plate Manager ........................................... 20
■CHAPTER 4 Set up a plate using default settings (instrument) .... 22
Sign in ........................................................................ 22
(Optional) Set up for auto export of sample data files (AB1 and FSA) .................. 23
Create or import a plate setup ................................................... 24
Export or delete a plate setup (PSM file) ...................................... 24
Enter plate properties .......................................................... 25
Assign wells: run module, size standard, dye set, and kit ............................ 26
SeqStudio
™
Genetic Analyzer Instrument and Software Getting Started Guide
3

Assign wells: sample name, sample type, and custom fields ......................... 26
Save and/or run a plate setup .................................................... 27
■CHAPTER 5 Start and monitor a run .................................. 28
Load the plate or the tube assembly .............................................. 28
Select a plate setup and start a run ............................................... 29
Start a run on the instrument .................................................... 30
Monitor a run from the Connect cloud-based platform .............................. 31
Open the Remote Monitoring App from Instrument Connect App ................ 31
View notifications from the instrument on your Connect cloud-based
platform account .......................................................... 32
Pause or cancel an injection in the Remote Monitoring App ..................... 32
View results in the Remote Monitoring App on the Connect cloud-based platform .. 33
Monitor a run from a mobile device ............................................... 36
Monitor a run from the instrument ............................................... 39
View the run status ........................................................ 39
View real-time results ...................................................... 39
Pause a plate or cancel or stop injections ..................................... 40
View results when the run is completed ...................................... 41
(Optional) View the injection list, change injection settings or order, or
specify replicates and re-injections .......................................... 42
■CHAPTER 6 View and analyze results ................................. 43
View results in the Remote Monitoring App on the Connect cloud-based platform ...... 43
View results on the instrument .................................................. 44
View results when the run is completed ...................................... 44
View results for a previously run plate (run history) ............................ 48
Edit injection parameters and re-inject samples ............................... 50
Export a report (QC report) .................................................. 50
Export results from the instrument (sample data files and QC reports) ................ 50
Analyze data ................................................................... 51
Secondary analysis software ................................................ 51
■APPENDIX A Link the instrument to your Connect cloud-
based platform account—detailed instructions ....................... 53
Workflow: Set up the instrument for access to the Connect cloud-based platform ...... 53
Register and obtain a Connect cloud-based platform account ........................ 54
Link the instrument from a mobile device ......................................... 54
Create a Connect cloud-based platform PIN and generate the QR code on
the instrument ............................................................ 54
Register the instrument with the Instrument Connect App ...................... 55
Link the instrument using a link code ............................................. 56
Contents
4
SeqStudio
™
Genetic Analyzer Instrument and Software Getting Started Guide

■APPENDIX B Keyboard shortcuts for Plate Manager ................ 59
Keyboard shortcuts for the sample table .......................................... 59
■Documentation and support ............................................. 61
Related documentation ......................................................... 61
Customer and technical support ................................................. 61
Limited product warranty ....................................................... 62
Contents
SeqStudio
™
Genetic Analyzer Instrument and Software Getting Started Guide
5

Product information
■Product description .................................................... 6
■Workow ............................................................ 7
Product description
The Applied Biosystems™ SeqStudio™ Genetic Analyzer with SeqStudio™ Data
Collection Software is a uorescent 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.
You can use the data collection software on the instrument to create and run plate
setups, monitor runs, and view results. You can also use the optional SeqStudio™ Plate
Manager and Remote Monitoring App to perform some of these functions.
For complete information on using the instrument and software, see SeqStudio™
Genetic Analyzer Instrument and Software User Guide (Pub. No. MAN0018646).
1
6
SeqStudio
™
Genetic Analyzer Instrument and Software Getting Started Guide

Workflow
Prepare the samples and the instrument
Prepare the samples
(page 9)
▼
Prepare the instrument
(page 11)
▼
Prepare and load the plate or tubes
(page 14)
Create a plate setup
SeqStudio™Plate Manager SeqStudio™Genetic Analyzer
Access the Plate Manager
(page 16)
Sign in
(page 22)
▼ ▼
Create or open a plate setup PSM file
(page 17)
Create or import a plate setup
(page 24)
▼ ▼
Enter plate properties
(page 17)
Enter plate properties
(page 25)
▼ ▼
Assign wells: Sample and run information
(page 18)
Assign wells: run module, size standard, dye set, and kit
(page 26)
▼ ▼
Save a plate setup in the Plate Manager
(page 20)
Assign wells: sample name, sample type, and custom
fields
(page 26)
▼
Save and/or run a plate setup
(page 27)
▼
(Optional) Set up for auto export of sample data files
(AB1 and FSA)
(page 23)
Chapter 1 Product information
Workflow
1
SeqStudio
™
Genetic Analyzer Instrument and Software Getting Started Guide
7

Start a run
Load the plate or the tube assembly
(page 15)
▼
Select a plate setup and start a run
(page 29)
▼
Start a run on the instrument
(page 30)
Monitor a run
Connect cloud-based platform[1] Mobile device SeqStudio™Genetic Analyzer
• View results in the Remote
Monitoring App on the Connect
cloud-based platform
(page 33)
• View notifications from the
instrument on your Connect
cloud-based platform account
(page 32)
• Pause or cancel an injection in
the Remote Monitoring App
(page 32)
Monitor a run from a mobile device
(page 36)
• View the run status
(page 39)
• View real-time results
(page 39)
• Pause a plate or cancel or stop
injections
(page 40)
[1] The Connect cloud-based platform is not supported for HID analysis.
View and analyze results
View results in the Remote Monitoring App on the Connect cloud-based platform
(page 33)
▼
View results on the instrument
(page 44)
▼
Export results from the instrument (sample data files and QC reports)
(page 50)
▼
Analyze data
(page 51)
Chapter 1 Product information
Workflow
1
8
SeqStudio
™
Genetic Analyzer Instrument and Software Getting Started Guide

Prepare the samples and the
instrument
■Prepare the samples ................................................... 9
■Prepare the instrument ................................................ 11
■Prepare and load the plate or tubes ..................................... 14
Prepare the samples
Sample preparation guidelines
Item Guidelines
Plates and tubes • Use MicroAmp™Optical 96-Well Reaction Plate or MicroAmp™Reaction Tubes with
a tray and retainer set.
IMPORTANT! Fast plates are not compatible with the SeqStudio™Genetic
Analyzer. Fast plates will damage the cartridge.
• Use the appropriate septa for plates and tubes.
• See SeqStudio
™
Genetic Analyzer Instrument and Software User Guide for more
information.
Fragment and HID analysis
sample preparation
Intensity (RFU)
Size (bp)
• Prepare the samples as recommended by the kit for fragment analysis.
• Use a 10–20 µL sample volume.
• Ensure that Hi‑Di™Formamide is fresh.
– Hi‑Di™Formamide should not undergo more than two freeze-thaw cycles (one
to aliquot and one for use).
– Use the same day after thawing.
• For more information, see DNA Fragment Analysis by Capillary Electrophoresis
User Guide (Pub. No. 4474504).
2
SeqStudio
™
Genetic Analyzer Instrument and Software Getting Started Guide
9

Item Guidelines
Sequence analysis sample
preparation
• Prepare sequencing reactions according to kit instructions, and purify the
extension products with ethanol precipitation, 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 BigDye XTerminator
™
Purification Kit
Protocol (Pub. No. 4374408).
IMPORTANT! Use the appropriate run modules for samples prepared with
BigDye XTerminator™Purification Kit.
• Use a 10–20 µL sample volume for samples that are prepared with Hi‑Di™
Formamide.
• Ensure that Hi‑Di™Formamide is fresh.
– Hi‑Di™Formamide should not undergo more than two freeze-thaw cycles (one
to aliquot and one for use).
– Use the same day after thawing.
• Do not resuspend samples in water, which can decrease sample stability.
• For more information, see DNA Sequencing by Capillary Electrophoresis
Chemistry Guide Second Edition (Pub. No. 4305080).
Chapter 2 Prepare the samples and the instrument
Prepare the samples
2
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SeqStudio
™
Genetic Analyzer Instrument and Software Getting Started Guide