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
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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
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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
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Genetic Analyzer Instrument and Software Getting Started Guide

• Samples are stable for 16–24 hours on the instrument.
• Load a maximum of 48 samples per plate if you use a long run module (Long
Seq, Long Seq BDX, and Long Frag Analysis). The long fragment analysis run
modules can take >24 hours to run an entire 96-well plate.
• Add samples to plates in columns. The default injection order is: A1–D1, E1–H1,
A2–D2, E2–H2....A12–D12, E12–H12.
1 3
2 4
1Injection group 1, wells A1–D1
2Injection group 2, wells E1–H1
3Injection group 3, wells A2–D2
4Injection group 4, wells E2–H2
Prepare the instrument
IMPORTANT! Do not power on the instrument until it has been installed and set up
by a Thermo Fisher Scientic representative.
Press the On/O switch on the rear panel.
1. Touch Seings4Consumable status.
2. Ensure that:
•Sucient consumables are installed for the run.
• Installed consumables have not exceeded their expiry date.
Display Cartridge Cathode buffer
NA Not installed on the instrument. Not installed on the instrument.
White OK for use. OK for use.
Plate layout and
loading guidelines
Power on the
instrument
Check the
consumables
status
Chapter 2 Prepare the samples and the instrument
Prepare the instrument
2
SeqStudio
™
Genetic Analyzer Instrument and Software Getting Started Guide
11

Display Cartridge Cathode buffer
Yellow OK for use, but:
• 1–25 injections remain for the capillary
array, or
• It will exceed the manufacturer's expiry
date within 2 weeks, or
• It will exceed the maximum number of
days allowed on the instrument within
2 weeks[1]
OK for use, but:
• 1–25 injections remain for the cathode
buffer, or
• It will exceed the manufacturer's expiry
date within 2 days or
• It will exceed the maximum number of
days allowed on the instrument (14 days)
within 2 days
Red 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 allowed on the instrument is 120 days for the SeqStudio™Genetic Analyzer Cartridge (Cat. No. A33671) and
180 days for the SeqStudio™Genetic Analyzer Cartridge v2 (Cat. No. A41331). For more information, see SeqStudio
™
Genetic Analyzer
Instrument and Software User Guide .
See SeqStudio™ Genetic Analyzer Instrument and Software User Guide if a new
Cathode Buer Container is required.
See SeqStudio™ Genetic Analyzer Instrument and Software User Guide if a new
cartridge is required.
3. Touch Close, then touch .
The Eject plate command is disabled for a few minutes after you insert a cartridge. If
you are loading the CBC, sample plate, and cartridge at the same time, you can save
time by loading the CBC and sample plate before you insert the cartridge.
For information on loading the individual components, see:
• “Prepare and load the plate or tubes“ on page 14
•SeqStudio™ Genetic Analyzer Instrument and Software User Guide
In the home screen:
Load the CBC, the
sample plate, and
the cartridge
Chapter 2 Prepare the samples and the instrument
Prepare the instrument
2
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SeqStudio
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Genetic Analyzer Instrument and Software Getting Started Guide

1. Touch , touch Eject plate, then open the instrument door when prompted.
2. Press the release buon on the autosampler to open the lid, then remove the
CBC.
2
1
1Release button
2Location of CBC
3. Check the buer ll level:
a. Remove the CBC.
b. Ensure that the level of buer is
above the ll line.
If the buer is at or below the ll
line, see SeqStudio™ Genetic
Analyzer Instrument and Software
User Guide.
If the buer is above the ll line,
reinsert the CBC.
4. Place the plate or tube assembly rmly
in the autosampler.
5. 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.
6. Touch Retract plate, then close the instrument door when 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 SeqStudio™ Genetic Analyzer Instrument and Software
User Guide).
10. Close the instrument door.
1
1Replace if buffer is at or below the fill
line
1
1New CBC buffer level
Chapter 2 Prepare the samples and the instrument
Prepare the instrument
2
SeqStudio
™
Genetic Analyzer Instrument and Software Getting Started Guide
13

Prepare and load the plate or tubes
On a clean and level surface:
1. Prepare the sample according to your application protocol, 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 briey
to collect the contents at the boom
of each well.
Centrifuge the plate assembly again
if the contents are not at the boom
of the wells.
4. Heat-denature as required.
5. Place the plate on ice for 3 minutes.
Load the plate onto the instrument immediately or keep the plate on ice and protected
from light until it is loaded onto the instrument.
On a clean and level surface:
1. Place the tubes in the MicroAmp™ 96-well tray, then place the tray retainer over
the tubes.
2. Prepare the sample according to your application protocol, then pipet the sample
into the tubes.
3. Place a septum on the tubes.
a. Align the holes of the septa with
the tubes.
b. Press gently until the septum
are inserted into position in
each tube.
Prepare the plate
1 2
1Plate
2Septum
Prepare the tubes
1
2
3
4
1Septum
296-well retainer
38-tube strip
4MicroAmp™96-well tray
Chapter 2 Prepare the samples and the instrument
Prepare and load the plate or tubes
2
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SeqStudio
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Genetic Analyzer Instrument and Software Getting Started Guide

4. Centrifuge the tube assembly briey to collect the contents at the boom of each
tube.
Centrifuge the tube assembly again if the contents are not at the boom 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.
In the home screen:
1. Touch , touch Eject plate, then open the instrument door when prompted.
2. Press the release buon on the autosampler to open the lid.
3. Check the buer ll level:
a. Remove the CBC.
b. Ensure that the level of buer is
above the ll line.
If the buer is at or below the ll
line, see SeqStudio™ Genetic
Analyzer Instrument and Software
User Guide.
If the buer is above the ll line,
reinsert the CBC.
4. Place the plate or tube assembly rmly
in the autosampler.
5. 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.
6. Touch Retract plate, then close the instrument door when prompted.
When the run is complete:
1. Touch , touch Eject plate, then open the instrument door when prompted.
2. Press the release buon on the autosampler to open the lid.
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.
Load the plate or
the tube assembly
1
1Replace if buffer is at or below the fill
line
1
1New CBC buffer level
Unload the plate
or the tube
assembly
Chapter 2 Prepare the samples and the instrument
Prepare and load the plate or tubes
2
SeqStudio
™
Genetic Analyzer Instrument and Software Getting Started Guide
15

Set up a plate using default settings
(Plate Manager)
■Access the Plate Manager .............................................. 16
■Create or open a plate setup PSM le ................................... 17
■Enter plate properties ................................................. 17
■Assign wells: Sample and run information ............................... 18
■Save a plate setup in the Plate Manager ................................. 20
Access the Plate Manager
• To access the Plate Manager from your Connect cloud-based platform account:
a. Sign in to thermosher.com/
connect.
b. In the My apps list, select
SeqStudio™ Plate Manager.
If SeqStudio™ Plate Manager is not
listed under My apps, scroll down
in the All apps list.
• To access the Plate Manager from the
desktop:
a. Select Start4All Programs4Applied Biosystems4Plate Manager4Plate
Manager.
3
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SeqStudio
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Genetic Analyzer Instrument and Software Getting Started Guide

Create or open a plate setup PSM file
1. Click to display the home screen.
2. In the Plate setup screen, create or open a plate setup:
If you are running the Plate Manager on the Connect cloud-based platform:
Click... To...
New Create a new plate setup or to create a plate setup from a
template.
Open from cloud Open a plate 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 Plate Manager (PSM file) or in
another application (CSV file).
Enter plate properties
In the Properties tab:
1. (Optional) Edit the Plate name, Barcode, or Owner.
Chapter 3 Set up a plate using default settings (Plate Manager)
Create or open a plate setup PSM file
3
SeqStudio
™
Genetic Analyzer Instrument and Software Getting Started Guide
17

2. Select an option in the Plate setup security eld.
•Hidden—Prevents other users from using or accessing the plate on the
instrument. Your analysis seings are saved with the plate setup, and are
used the next time that you open or create a hidden plate. However, the
analysis seings will not be available to other system users.
•Shared—Allows other users to access and edit the plate on the instrument.
Your analysis seings are saved with the plate setup, and are used the next
time that you open or create a shared plate. Your analysis seings will be
available to other 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
seings on the same plate.
4. Select the analysis seings. If needed, edit the seings (see SeqStudio™ Genetic
Analyzer Instrument and Software User Guide).
5. (Optional for Sequencing or Mixed
plate) Select the I am analyzing my
data with Sanger variant analysis
software checkbox.
The amplicon and specimen elds
are added to the Plate view, and the
aributes are automatically added to the default le name conventions (see the
software help for more information).
This feature is useful in secondary analysis software applications that organize
les based on amplicon and specimen information (Connect cloud-based
platform applications: Variant Analysis (VA) module, Next-generation
Conrmation (NGC) module; desktop applications: SeqScape™ Software,
Variant Reporter™ Software, Minor Variant Finder Software).
6. Click Next.
Assign wells: Sample and run information
This procedure describes using the Plate view. Alternatively, you can click and use
keyboard short-cuts to enter information. See “Keyboard shortcuts for the sample
table“ on page 59.
1. In the Plate screen, select one or more injection groups: Click a well to select one
injection 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.
Chapter 3 Set up a plate using default settings (Plate Manager)
Assign wells: Sample and run information
3
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Genetic Analyzer Instrument and Software Getting Started Guide

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 groups are selected when you edit the Sample name
or Sample type, both wells with the same capillary number are edited. For
example, if injection groups A1–D1 and E1–H1 are selected, and you change the
Sample name to "Test" for well E1, the Sample name for well A1 is also changed
to "Test".
4. (Fragment/HID analysis only) Select the Sample type for each well: Allelic ladder,
Negative control, Positive control, or Sample.
5. (Fragment/HID analysis only) Select a size standard for the selected injection
groups.
6. (HID analysis only) Select a kit for the selected injection groups (enables marker-
to-marker pull-up reduction).
7. Select a Dye set for the selected injection groups.
Chapter 3 Set up a plate using default settings (Plate Manager)
Assign wells: Sample and run information
3
SeqStudio
™
Genetic Analyzer Instrument and Software Getting Started Guide
19

8. Select a Run module for the selected injection groups.
Note: Run module 1 is used for the rst injection you specify. If you specify
replicate injections, additional run module elds are added. For information, see
SeqStudio™ Genetic Analyzer Instrument and Software User Guide.
9. Click Next and proceed to “Save a plate setup in the Plate Manager“ on page 20.
Save a plate setup in the Plate Manager
After you assign wells to a plate setup:
1. In the Save the plate setup dialog box, modify any seings as needed.
Chapter 3 Set up a plate using default settings (Plate Manager)
Save a plate setup in the Plate Manager
3
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SeqStudio
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Genetic Analyzer Instrument and Software Getting Started Guide