QuantStudio™ 1 Real-Time PCR System
INSTALLATION, USE, AND MAINTENANCE
Firmware v1.0.x
Publication Number MAN0017853
Revision A.0
For Research Use Only. Not for use in diagnostic procedures.
Life Technologies Holdings Pte Ltd | Block 33 | Marsiling Industrial Estate Road 3 | #07-06, Singapore 739256
For descriptions of symbols on product labels or product documents, go to thermofisher.com/symbols-definition.
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. MAN0017853 (English)
Revision Date Description
A.0 10 October 2018 New document.
Important Licensing Information: These products may be covered by one or more Limited Use Label Licenses. By use of these products, you accept
the terms and conditions of all applicable Limited Use Label Licenses.
Trademarks: All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. TaqMan is a registered
trademark of Roche Molecular Systems, Inc., used under permission and license. Cy is a registered trademark of GE Healthcare. Microsoft and
Windows are trademarks of Microsoft Corporation. Pentium is a trademark of Intel Corporation. Google and Chrome are trademarks of Google, Inc.
©2018 Thermo Fisher Scientific Inc. All rights reserved.
Contents
About this guide ............................................................ 8
■
CHAPTER 1 Product information ....................................... 9
Instrument hardware description ................................................. 9
Instrument overview ........................................................ 9
Parts of the instrument ..................................................... 11
Parts of the home screen ................................................... 12
Software description ........................................................... 14
Instrument, desktop, and cloud software features ............................. 14
Folders, templates, experiments, and projects ................................ 15
Third-party software ....................................................... 16
Supported options for instrument and computer connections ........................ 16
Experiment types .............................................................. 18
■
CHAPTER 2 General procedures to operate the instrument ........ 20
Precautions for use ............................................................ 20
Power on the instrument ........................................................ 21
Power off the instrument ....................................................... 21
Sign in ........................................................................ 21
Sign out ....................................................................... 21
Load and unload a plate in the QuantStudio™ 1 Real-Time PCR Instrument ............ 22
Transfer, view, or manage files and results ........................................ 23
Transfer EDS files from the instrument home screen ........................... 23
View run history and delete or transfer files from the instrument ................ 23
Manage templates (EDT files) ............................................... 23
■
CHAPTER 3 Configure the instrument and manage
instrument profiles ....................................................... 25
Initial start‑up ................................................................. 25
Installation and instrument verification ........................................... 26
Use the instrument without signing in ............................................ 26
Create an administrator instrument profile during initial start-up .................... 27
Create a new instrument profile ................................................. 27
QuantStudio™ 1 Real-Time PCR System Installation, Use, and Maintenance Guide
3
Contents
Overview of Settings ............................................................ 28
Manage instrument settings ..................................................... 30
Manage the instrument name (Administrator only) ............................. 31
Enable Sleep Mode ........................................................ 31
Set the idling temperature for the heated cover ................................ 31
Configure the network drive ................................................. 31
OEM connection only (Administrator only) ..................................... 31
Select a Cloud region (Administrator only) .................................... 32
Set the date and time (Administrator only) .................................... 32
Configure the network ...................................................... 32
Restore factory defaults .................................................... 34
Select a language .......................................................... 34
Learn about the instrument ..................................................... 34
View instrument specifications .............................................. 34
View and export the License Agreement ...................................... 35
Manage home screen notifications ............................................... 35
Manage maintenance, service, and calibrations .................................... 35
Update instrument software (Administrator only) .............................. 35
Enable remote instrument monitoring (Administrator only) ..................... 36
View instrument statistics .................................................. 36
View instrument logs ....................................................... 36
Manage Users ................................................................. 36
Require instrument profile sign-in (Administrator only) ......................... 37
Manage the Sign Out Timer (Administrator only) ............................... 37
Manage instrument profiles ................................................. 37
Link an instrument profile with the Thermo Fisher Cloud ........................... 38
Link an existing instrument profile with the Thermo Fisher Cloud ................ 38
Create a new instrument profile and link with the Thermo Fisher Cloud .......... 38
■
CHAPTER 4 Create and run experiments on the instrument ....... 39
Workflow ..................................................................... 39
Run an experiment ............................................................. 40
Create and run an experiment from a template ................................ 40
Run an experiment from a saved file ......................................... 40
Repeat the last instrument run .............................................. 41
Edit an experiment before starting a run .......................................... 41
Enter or edit template properties ............................................ 41
Edit the run method ........................................................ 43
Define, assign, and view well details ......................................... 45
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QuantStudio™ 1 Real-Time PCR System Installation, Use, and Maintenance Guide
View, pause, or stop a run ....................................................... 46
View real-time data and plots on the instrument touchscreen ................... 46
Adjust the display of real-time plots on the instrument touchscreen .............. 47
Pause or stop an instrument run ............................................. 47
Lock the touchscreen during a run ........................................... 47
Transfer EDS files from the instrument home screen ............................... 48
■
CHAPTER 5 Calibrate and verify instrument performance ......... 49
Calibration and verification schedule ............................................. 49
Calibration descriptions ........................................................ 50
View the calibration status and set reminders ..................................... 51
View calibration status and set reminders in the instrument .................... 51
View calibration status and set reminders in the Cloud ......................... 51
Perform ROI/uniformity, background, and dye calibrations .......................... 52
Workflow: Calibration ...................................................... 52
Prepare a calibration plate .................................................. 52
Perform calibrations ....................................................... 53
View calibration images and transfer results to USB ........................... 54
Troubleshoot calibration failure ............................................. 55
Identify contamination ...................................................... 56
Create a background plate
Perform instrument verification using RNase P plates .............................. 57
Instrument verification description .......................................... 57
RNase P instrument verification plate ........................................ 58
Performance specifications pass criteria ..................................... 58
Prepare an RNase P plate ................................................... 58
Perform RNase P verification ............................................... 59
Troubleshoot verification failure ............................................. 61
Calibrate custom dyes .......................................................... 62
Custom dyes overview ...................................................... 62
Use a dilution series to determine an optimal custom dye concentration .......... 62
Calibrate the custom dye ................................................... 65
Calibrate for a custom melt curve experiment ..................................... 68
(optional)
......................................... 56
Contents
QuantStudio™ 1 Real-Time PCR System Installation, Use, and Maintenance Guide
5
Contents
■
CHAPTER 6 Maintain the instrument ................................. 70
Backup or restore the instrument ................................................ 70
Decontaminate the sample block ................................................. 71
Materials required ......................................................... 71
Clean the sample block ..................................................... 71
Detailed procedures for cleaning the sample block ............................. 73
Replace the instrument fuses .................................................... 73
Materials required ......................................................... 73
Replace the fuses .......................................................... 74
Prepare the instrument to store, move, or ship .................................... 74
Move the instrument ....................................................... 75
Return the instrument for service ............................................ 75
■
APPENDIX A Install and connect the instrument to a network ..... 77
Workflow: Install and connect to a network ........................................ 77
Before you begin ............................................................... 78
Instrument and computer connections ............................................ 78
Unpack and install the instrument ............................................... 79
Power on and follow the startup wizard ........................................... 80
Connect the instrument and the computer directly or to a LAN ....................... 80
Networking ................................................................... 81
Supported options for instrument and computer connections .................... 81
Control and monitor networked instruments .................................. 82
Ethernet port overview ..................................................... 83
Firewall ports that must be open ............................................ 83
Networking guidelines and best practices ..................................... 83
■
APPENDIX B Troubleshooting ......................................... 84
■
APPENDIX C Instrument specification and layout ................... 86
Configured system dimensions .................................................. 87
Instrument clearances ..................................................... 88
Electrical requirements ......................................................... 88
Environmental requirements .................................................... 89
Network requirements .......................................................... 90
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QuantStudio™ 1 Real-Time PCR System Installation, Use, and Maintenance Guide
■
APPENDIX D Parts and materials ..................................... 91
Kits, consumables, accessories, and reagents ..................................... 91
Consumables (96‑well, 0.2‑mL format) ............................................ 91
Accessories ................................................................... 92
General-use materials and consumables ......................................... 92
■
APPENDIX E Safety ..................................................... 93
Symbols on this instrument ..................................................... 94
Conformity symbols ........................................................ 95
Safety alerts on this instrument .................................................. 96
Location of safety labels on the instrument ................................... 97
Safety information for instruments not manufactured by Thermo Fisher Scientific ..... 97
Instrument safety .............................................................. 97
General .................................................................. 97
Physical injury ............................................................ 98
Electrical safety ........................................................... 98
Cleaning and decontamination ............................................... 98
Safety and electromagnetic compatibility (EMC) standards .......................... 98
Safety compliance ......................................................... 99
EMC ...................................................................... 99
Environmental design ..................................................... 100
Chemical safety ............................................................... 100
Biological hazard safety ........................................................ 101
Contents
■
Documentation and support ........................................... 102
Related documentation ........................................................ 102
Obtain information from the Help system ........................................ 102
Customer and technical support ................................................ 102
Limited product warranty ...................................................... 103
Index ..................................................................... 104
QuantStudio™ 1 Real-Time PCR System Installation, Use, and Maintenance Guide
7
About this guide
This guide provides information about installing, using, and maintaining the
QuantStudio™ 1 Real-Time PCR System. For information and instructions on
performing experiments on this system, refer to QuantStudio™ Design and Analysis
Desktop Software User Guide (Pub. No. MAN0010408).
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QuantStudio™ 1 Real-Time PCR System Installation, Use, and Maintenance Guide
1
■
Instrument hardware description ........................................ 9
■
Software description .................................................. 14
■
Supported options for instrument and computer connections .............. 16
■
Experiment types ..................................................... 18
Instrument hardware description
Product information
Instrument overview
The QuantStudio™ 1 Real-Time PCR System uses uorescence-based polymerase
chain reaction (PCR) reagents to perform the following types of experiments.
• Quantitative detection of target nucleic acid sequences (targets).
• Qualitative detection of targets.
• Qualitative analysis of the PCR product.
For more information, see “Experiment types“ on page 18.
The instrument is congured with a 96-well 0.2-mL xed block and a 3-color coupled
lter set.
The instrument can be run directly from the touchscreen to create and start
experiments. To design experiments or to analyze data, the instrument can be
integrated with the QuantStudio™ Design and Analysis Software.
An optional barcode scanner and optional wireless adapter can be ordered separately.
QuantStudio™ 1 Real-Time PCR System Installation, Use, and Maintenance Guide
9
Filters
Wavelength
(nm)
1
2
3
x1-m1 x2-m2 x4-m4
Emission
Spectra
Chapter 1
1
Instrument hardware description
Product information
Instrument filters and supported dyes
System dyes
The instrument use a coupled three-color lter set that supports the dyes shown in the
following table and gure. For more information about available spectral dye
calibration kits, contact Support.
Filter wavelength
Peak
filter
Color
(nm)
[1]
Factory-calibrated
dyes
Example
custom dyes
Excitation Emission
x1-m1 Blue 470 ± 15 520 ± 15
x2-m2 Green 520 ± 10 558 ± 12 VIC
x4-m4 Orange 580 ± 10 623 ± 14 ROX™, JUN
[1]
The central wavelengths are the optimized wavelengths.
[2]
The HEX™ and TET™ dyes from Thermo Fisher Scientific fall within the emission wavelength range of the
system, therefore they can be added and adapted for use on the instrument.
FAM™,
SYBR™ Green
™
SYT09
JOE™,
HEX™, TET™
™
Texas Red
[2]
™
10
1
x1-m1 — FAM™, SYBR™ Green
2
x2-m2 — VIC
™
3
x4-m4 — JUN™, ROX™, Texas Red
™
Custom dyes
The instrument can run assays designed with custom dyes. Custom dyes include the
following:
• Dyes that are not supplied by Thermo Fisher Scientic.
• Dyes or formulations of dyes that are not system dyes for the instrument.
To use a custom dye on the instrument, review the following requirements.
• Calibrate the instrument for the custom dye (see “Calibrate custom dyes“ on
page 62).
• Ensure that the custom dye excites and emits within the wavelength range of the
lters (see the lter-wavelength table in “System dyes“).
• Select a custom dye that does not overlap with other dyes used in the run (see the
lter-wavelength table in “System dyes“).
QuantStudio™ 1 Real-Time PCR System Installation, Use, and Maintenance Guide
1
2
3
Parts of the instrument
Chapter 1 Product information
Instrument hardware description
1
Touchscreen – Controls the instrument.
2
USB port – For connection to an external network drive or external data storage device.
3
Instrument drawer – Contains sample plate.
The instrument includes three additional USB ports on the back of the instrument.
Note: The instrument recognizes only one external storage device at a time for data
transfer.
1
QuantStudio™ 1 Real-Time PCR System Installation, Use, and Maintenance Guide
11
4
3
9
1
5
6
8
7
2
Chapter 1 Product information
1
Instrument hardware description
Parts of the home screen
1
Avatar and Instrument name
2
Help icon
3
Drawer status
4
Status dial
5
Current user name; instrument block type
Table 2 Parts of the home screen
Element of the
home screen
Avatar and
Function For more information, see...
Set by the administrator to uniquely identify instrument. “Manage the instrument name
Instrument name
Help icon Touch to launch the touchscreen Help system to access
step-by-step instructions.
Drawer status
• — The drawer is locked. The drawer locks during
experiment runs, calibration runs, and self
verification test runs. The drawer automatically
unlocks when a run is complete.
• — The drawer is unlocked.
• Drawer is open — The drawer is open. No message
displays when the drawer is closed.
6
Settings button
7
Buttons for accessing Experiment
Template files (EDT)
8
Connectivity icons
9
Sign In (or My Profile) button
(Administrator only)“ on page 31.
—
—
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QuantStudio™ 1 Real-Time PCR System Installation, Use, and Maintenance Guide
Chapter 1 Product information
Instrument hardware description
1
Element of the
home screen
Status dial
Current user
name and block
type
Settings button Touch Settings to configure, calibrate, or learn about
Buttons for
accessing
experiment and
template files
• When the instrument is in use — Displays the
sample block temperature, the elapsed run time,
and the run status.
You can swipe the dial to the left or touch to
access real-time views of the run.
• When the instrument is not in use — Displays Set up
run. You can start a run by touching the status dial.
Displays the user name of the current signed-in user and
the instrument block type.
Note: If no user is signed-in, the instrument defaults to
the Guest profile.
the instrument.
Load Experiment — Touch to open a user-created EDT
file from a Cloud account, USB, instrument folder, or
network drive.
Open Template — Touch to open a system EDT template
file.
Function For more information, see...
—
—
Chapter 3, “Configure the instrument
and manage instrument profiles“.
“Run an experiment from a saved
file“ on page 40 .
“Create and run an experiment from
a template“ on page 40“Run an
experiment from a saved file“ on
page 40 .
Connectivity icons
Sign In button
(My Profile button
when a user is
signed in)
Run Last — Touch to open the last EDT file run on the
instrument.
• If you are signed-in, the file opened will be the last
file you ran when signed-in.
• If you are not signed-in, the file opened will be the
last file the guest profile ran.
• — The instrument is connected to a wired
network.
• — The instrument is wirelessly connected.
• — A USB drive is plugged into the instrument.
• — The instrument is linked to a Cloud account.
• Touch Sign In to sign into an instrument profile
and link to a Cloud account.
• Touch My Profile to change instrument profile
settings, link to a Cloud account, or lock the
instrument during a run.
“Repeat the last instrument run“ on
page 41.
—
“Sign in“ on page 21.
QuantStudio™ 1 Real-Time PCR System Installation, Use, and Maintenance Guide
13
Chapter 1 Product information
1
Software description
Software description
Instrument, desktop, and cloud software features
The instrument and the software (desktop and cloud) include the features described
in the following table.
Feature Instrument Desktop Cloud
Use as guest (no sign in) 3 3 —
Create templates (unlocked or locked) — 3 3
Edit unlocked templates 3 3 3
Edit locked templates (password
assigned by template creator required)
Load system or user-created templates
(EDT file) to instrument
Change experiment settings in template
(EDT file) loaded on the instrument
Settings that can be changed in a locked
template (no password required):
• Properties: All settings
• Method: No changes allowed
• Plate: Sample names
Settings that can be changed in an
unlocked template:
• Properties: All settings
• Method: All settings
• Plate: Sample names
— 3 3
3 3 —
3
— —
14
Load plate in instrument 3 — —
Start run 3 3 —
View real-time data during a run 3 3 3
View instrument status (running,
calibration needed, and so on)
Analyze results — 3 3
Set calibration reminders 3 — 3
Review exported calibration or RNase P
verification results
QuantStudio™ 1 Real-Time PCR System Installation, Use, and Maintenance Guide
3 — 3
— 3 3
(
only RNase P
)
Chapter 1 Product information
Software description
1
Folders, templates, experiments, and projects
Term
Folders in Load
Experiment
Experiment
Template File (EDT)
Experiment Run
File (EDS)
Definition Supported in
Location in which you can store templates (EDT
files) on the instrument:
• My Instrument – Displayed if you are signed in
• Public – Location in which all experiments run
by guest users are stored
• USB – USB for manual transfer to and from a
computer
• Post Read – If you run an endpoint experiment,
the pre-read experiment is automatically saved
in this folder for post-read analysis
Default settings for an instrument run, can be
modified before instrument run.
Two types:
• Factory-provided, accessed from Open
Template (instrument) or Create Experiment
(desktop or cloud)
• User-created, accessed from Load Experiment
Settings and data for a completed instrument run. Instrument
Instrument
Instrument
Desktop
Cloud
Desktop
Template and
experiment
components
Properties
Method
Project Function in the Cloud Data Manager that is used for
secondary analysis applications. Does not apply to
the cloud software, which is a primary analysis
application.
Instrument Desktop Cloud
• Experiment file name
• Reagent information (Reagent
barcode, Lot#)
• Plate barcode
• Data destination (location for
auto-transfer of data)
• Comments (Tags are not used
at this time)
Thermal cycling conditions Thermal cycling conditions
• Experiment file name
• Plate barcode
• User name
• Instrument type
• Block type
• Experiment type
• Chemistry (reagent information)
• Run mode
• Comments
• (
Cloud software only
) Notifications
Cloud
Cloud
QuantStudio™ 1 Real-Time PCR System Installation, Use, and Maintenance Guide
15
Chapter 1 Product information
1
Supported options for instrument and computer connections
Template and
experiment
components
Instrument Desktop Cloud
Plate Sample names
You cannot edit targets/SNP assays
or tasks on the instrument.
Run Start and monitor a run in progress
View: Time remaining and
Temperature, Method, Plots
Pause, Resume, Stop a run
Results Not applicable Review plots
Export Not applicable Export results
Third-party software
Before installing third-party software on the computer running QuantStudio™ Design
and Analysis Desktop Software, conrm that the third-party software will not do the
following:
• Restrict Ethernet communication.
• Interfere with instrument or computer operation.
Define and assign samples, targets or SNP assays, and
tasks in the Quick Setup and Advanced Setup panes of the
Plate tab.
Start and monitor a run in
progress
View: Time remaining and
Temperature, Method, Plots
Monitor a run in progress
(link to Thermo Fisher Cloud
Instrument Details)
View: Time remaining and
Temperature, Method, Plots
Supported options for instrument and computer connections
We support the following direct, networked (LAN– local area network), or Cloud
congurations. Congurations other than those listed are not recommended. Select a
conguration that meets the needs of your laboratory's instrument, software, and
workow requirements.
IMPORTANT! Do not connect both an Ethernet cable and the Wi-Fi module
(Cat. No. A26774) to the instrument. Conguring the instrument for both wired and
wireless connection can interfere with instrument operation.
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QuantStudio™ 1 Real-Time PCR System Installation, Use, and Maintenance Guide
LAN
LAN
LAN
Supported options for instrument and computer connections
Chapter 1 Product information
Note: For detailed information about networking your instrument, see the
QuantStudio™ 1 Real-Time PCR System IT Checklist (Pub. No. MAN0018164).
Direct configuration option
• A computer provided by Thermo Fisher Scientific with the QuantStudio™ Design and Analysis Desktop Software
• Computer‑to‑instrument connection:
– Direct, wired connection between the computer and the instrument
using an Ethernet cable
1
IMPORTANT! A direct instrument‑to‑computer connection
with the LAN or the Cloud configurations.
Networked configuration option
• A computer provided by Thermo Fisher Scientific with the QuantStudio™ Design and Analysis Desktop Software
• The computer and instrument must be on the same subnet mask.
• Computer‑to‑LAN connection
– Wired connection to the network using an Ethernet cable –
– Wireless connection to the network
• Instrument‑to‑LAN connection
– Wired connection to the network using an Ethernet cable –
– Wireless connection to the network using the instrument Wi‑Fi module
Thermo Fisher Cloud configuration option
• Internet access and a computer with the Chrome™ web browser to access the Cloud
• Computer‑to‑Cloud connection
– Wired connection to the internet using an Ethernet cable –
– Wireless connection to the internet
(select an option)
(select an option)
(select an option)
:
cannot
:
:
be combined
or
–
or
–
or
–
• Instrument‑to‑Cloud connection
– Wired connection to the network using an Ethernet cable –
– Wireless connection to the network using the instrument Wi‑Fi module
QuantStudio™ 1 Real-Time PCR System Installation, Use, and Maintenance Guide
(select an option)
:
or
–
17
Chapter 1 Product information
1
Experiment types
Experiment types
Purpose
Standard curve experiment
Determines absolute
target quantity in
samples.
Relative standard curve experiment
Determines relative
target quantity in
samples.
Description
1. The software measures amplification of the target in a standard dilution series and in
test samples.
2. The software generates a standard curve using data from the standard dilution series.
3. The software uses the standard curve to interpolate the absolute quantity of target in
the test samples.
1. The software measures amplification of the target of interest and of an endogenous
control target in a standard dilution series, in a reference (calibrator) sample, and in
test samples.
The endogenous control is a target that is expressed equally in all samples; examples of
endogenous controls are β‐actin, GAPDH, and 18S ribosomal RNA. The software can
algorithmically incorporate multiple endogenous control targets in relative
quantification calculations.
The reference sample is used as the basis for relative quantification results (or
1× sample). For example, in a study of drug effects on gene expression, an untreated
control is an appropriate reference sample.
2. The software generates standard curves for the target of interest and the endogenous
control using data from the corresponding standard dilution series.
3. The software uses the standard curves to interpolate the quantities of the target of
interest and the endogenous control in each sample. The target quantity in each sample
is then normalized to the sample's endogenous control quantity.
4. To determine the relative quantity of the target in test samples, the software divides the
normalized target quantity in the sample by the normalized target quantity in the
reference sample.
Comparative C
Determines relative
target quantity in
samples.
(DDCt) experiment
t
18
1. The software measures amplification of the target of interest and of an endogenous
control target in a reference (calibrator) sample and in test samples.
The endogenous control is a target that is expressed equally in all samples; examples of
endogenous controls are β‐actin, GAPDH, and 18S ribosomal RNA. The software can
algorithmically incorporate multiple endogenous control targets in relative
quantification calculations.
The reference sample is used as the basis for relative quantification results (or
1× sample). For example, in a study of drug effects on gene expression, an untreated
control is an appropriate reference sample.
2. The measurements for the target of interest are normalized to the endogenous control.
3. To determine the relative quantity of the target in test samples, the software compares
the normalized ΔCq (ΔCt or ΔCrt) for the sample to the normalized ΔCq (ΔCt or ΔCrt) for
the reference sample.
QuantStudio™ 1 Real-Time PCR System Installation, Use, and Maintenance Guide
Chapter 1 Product information
Experiment types
1
Purpose
Genotyping experiment
Detects single
nucleotide
polymorphism (SNP)
variants of a target
nucleic acid
sequence.
Presence/absence experiment
Determines the
presence or absence
of a target nucleic
acid sequence in a
sample.
Description
Genotyping experiments use preformulated TaqMan® SNP Genotyping Assays that include
the following components:
• Two sequence-specific primers for amplification of sequences containing the SNP of
interest
• Two allele-specific TaqMan® probes for Allele 1 and Allele 2
1. The software normalizes the fluorescence of the reporter dyes to the fluorescence of
2. The software plots the normalized reporter dye signal of each sample well on an Allelic
3. The software algorithmically clusters the sample data, and assigns a genotype call to
The software calls the target present or absent based on an algorithmically determined call
threshold. (The call threshold is different from the Ct threshold; the Ct threshold is not used
to make calls.)
the passive reference dye in each well.
Discrimination Plot, which contrasts the reporter dye intensities of the allele-specific
probes.
the samples of each cluster according to its position on the plot.
Melt curve experiment
Determines the
melting temperature
(Tm) of the
amplification
products of a PCR
that used
intercalating dyes.
In the software, melt curve analysis is included in the default run method for any experiment
type that uses intercalating dyes.
1. The software plots a melt curve based on the fluorescence of the dye with respect to
change in temperature.
2. Using the melt curve, the software calculates the melting temperature (Tm).
QuantStudio™ 1 Real-Time PCR System Installation, Use, and Maintenance Guide
19
2
■
Precautions for use ................................................... 20
■
Power on the instrument .............................................. 21
■
Power o the instrument .............................................. 21
■
Sign in .............................................................. 21
■
Sign out ............................................................. 21
■
Load and unload a plate in the QuantStudio™ 1 Real-Time PCR Instrument .. 22
■
Transfer, view, or manage les and results ............................... 23
Precautions for use
General procedures
to operate the instrument
CAUTION! PHYSICAL INJURY HAZARD. Do not remove the instrument
cover. There are no components inside the instrument that you can safely
service yourself. If you suspect a problem, contact technical support.
CAUTION! FIRE HAZARD. For continued protection against the risk of re,
replace fuses only with listed and certied fuses of the same type and rating as
those currently in the instrument.
CAUTION! PHYSICAL INJURY HAZARD. During instrument operation, the
sample block temperature can reach 100°C. Allow it to cool to room
temperature before handling.
CAUTION! Before using a cleaning or decontamination method other than
those recommended by Thermo Fisher Scientic, conrm with Thermo Fisher
Scientic that the proposed method will not damage the instrument.
CAUTION! Use at caps for tubes. Rounded caps can damage the heated cover.
20
QuantStudio™ 1 Real-Time PCR System Installation, Use, and Maintenance Guide
Power on the instrument
Touch anywhere on the touchscreen to determine if the instrument is in sleep
1.
mode. If the home screen is displayed, the instrument is already powered on.
If the home screen does not display,
2.
power on the instrument by pressing the
switch on the rear panel.
If left unaended (for about two hours), the
instrument automatically enters sleep mode
(enabled by default) to conserve power.
Note: To customize the sleep mode seing,
touch
Seings4Sleep Mode.
Seings4Instrument
Power off the instrument
Chapter 2
General procedures to operate the instrument
Power on the instrument
2
Sign in
The instrument operates in low-power mode when not in use. However, the
instrument can be powered o completely so that the components use no power.
Note: To power o the instrument for >1 week, see “Prepare the instrument to store,
move, or ship“ on page 74.
Power o the instrument using the power switch on the back of the instrument.
1.
Power o the computer.
2.
Create an instrument prole before signing into the instrument. See “Create a new
instrument prole“ on page 27.
Note: An instrument prole is a user account specically for the instrument. It is not
related to any other user account for the system or software.
In the home screen, touch Sign In.
1.
Touch Sign In, then select your username.
2.
Enter your PIN, then touch Enter.
3.
Sign out
In the home screen, touch
1.
Touch Sign Out.
2.
QuantStudio™ 1 Real-Time PCR System Installation, Use, and Maintenance Guide
My Prole.
21
Chapter 2 General procedures to operate the instrument
2
Load and unload a plate in the QuantStudio™ 1 Real-Time PCR Instrument
Load and unload a plate in the QuantStudio™ 1 Real-Time PCR
Instrument
CAUTION! Use at caps for 0.2-mL tubes. Rounded caps can damage the
heated cover.
Load the plate.
1.
Open the instrument drawer.
a.
Load the plate onto the plate adapter so that the following criteria are met.
b.
• Well A1 of the plate is in the top-left corner of the plate adapter.
• The barcode faces the front of the instrument.
Note: Do not remove the black plate adapter before loading a plate or tube
strips. If used, tube strips can t loosely in the adapter, but the heated cover
will apply the appropriate pressure to seat the tube strips securely in the
adapter.
Close the instrument drawer.
c.
When the run ends, unload the plate.
2.
Open the instrument drawer.
a.
Remove the plate.
b.
Close the instrument drawer.
c.
CAUTION! PHYSICAL INJURY HAZARD. During instrument operation,
the plate temperature can reach 100°C. Allow it to cool to room
temperature before handling.
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QuantStudio™ 1 Real-Time PCR System Installation, Use, and Maintenance Guide
Chapter 2 General procedures to operate the instrument
Transfer, view, or manage files and results
In the home screen, when a run ends, touch Transfer File.
Transfer EDS
files
from the
instrument home
screen
1.
Select the data destination for the EDS le.
2.
Navigate to and select a folder.
3.
Touch OK.
4.
Touch Transfer.
5.
Transfer, view, or manage files and results
2
View run history
and delete or
transfer files from
the instrument
Manage templates
(EDT files)
Note: Touch
In the home screen, touch Seings4Run History.
• Touch an individual run record to view its details, then complete one of the
following actions:
– Touch Delete to delete the run record.
– Touch Transfer to export the run data.
• Touch Manage to select multiple run records for simultaneous viewing, deletion,
or transfer.
Note:
Guests (users not signed-in) can only view guest run records.
·
Users signed into their instrument proles can also view their own run records.
·
Administrators can view all run records.
·
Note: If the connection between the instrument and the desktop software is
interrupted during the run, the instrument still completes the run. However, the run
data (EDS le) must be transferred from the instrument to the desktop software using
a USB drive or a network drive.
This feature applies to templates (EDT les) on a
manage run results les (EDS les), see “Transfer EDS les from the instrument home
screen“ on page 23.
Seings4Run History to transfer EDS les at any time.
USB or in My Instrument. To
In the home screen, touch Load Experiment.
1.
Touch USB or My Instrument.
2.
Touch Manage Files.
3.
(Optional) Navigate through the My Instrument, Public, USB, and Post Read
4.
folders to access an EDT le. Folder availability depends on your sign-in status.
Touch one or more les to select for managing.
5.
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23
Chapter 2 General procedures to operate the instrument
2
Transfer, view, or manage files and results
Delete or copy the les.
6.
• Touch Delete Files, then conrm deletion.
• Touch Copy Files, select a le destination, then touch Paste Files.
Touch Done.
7.
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QuantStudio™ 1 Real-Time PCR System Installation, Use, and Maintenance Guide
3
Configure the instrument and
manage instrument profiles
■
Initial start-up ....................................................... 25
■
Installation and instrument verication ................................. 26
■
Use the instrument without signing in .................................. 26
■
Create an administrator instrument prole during initial start-up ........... 27
■
Create a new instrument prole ........................................ 27
■
Overview of Seings .................................................. 28
■
Manage instrument seings ........................................... 30
■
Learn about the instrument ............................................ 34
■
Manage home screen notications ...................................... 35
■
Manage maintenance, service, and calibrations ........................... 35
Initial start‑up
■
Manage Users ....................................................... 36
■
Link an instrument prole with the Thermo Fisher Cloud ................. 38
Perform these tasks during initial instrument start-up or after you restore factory
defaults (see “Restore factory defaults“ on page 34).
(Optional) Select one of the following options.
1.
• Congure the instrument for either wired connection or wireless network
connection (see “Congure the network“ on page 32).
• Touch Neither/Decide Later.
(Optional) Enter an instrument name (see “Manage the instrument name
2.
(Administrator only)“ on page 31).
Set the date and time (see “Set the date and time (Administrator only)“ on
3.
page 32).
Select one of the following options.
4.
• Select a Cloud region (see “Select a Cloud region (Administrator only)“ on
page 32).
• Touch Next to continue.
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Chapter 3 Configure the instrument and manage instrument profiles
3
Installation and instrument verification
Create an administrator prole (see “Create an administrator instrument prole
5.
during initial start-up“ on page 27).
Select one of the following options.
6.
• Link the instrument prole to the Thermo Fisher Cloud (see “Link an existing
instrument prole with the Thermo Fisher Cloud“ on page 38).
• Touch Skip.
Installation and instrument verification
Before the rst use of the instrument, complete the following tasks:
• Install the instrument (see “Unpack and install the instrument“ on page 79).
• Verify instrument performance (see “Perform instrument verication using
RNase P plates“ on page 57).
Note:
Instruments are factory calibrated, so no calibration is necessary at installation.
·
However, we recommend that you verify instrument performance before using
the instrument.
Regular calibration and verication should be performed according to the
·
calibration and verication schedule (see “Calibration and verication
schedule“ on page 49).
Use the instrument without signing in
If the instrument is congured by an Administrator to allow guest access
( Seings4Manage Users4Sign In Required set to o), you can use the
instrument without signing in.
The following limits are in place if you do not sign in to the instrument:
• All actions are recorded to Guest user prole.
• You have access only to the Public folder for selecting and storing experiments.
• You cannot transfer data to the Cloud (only to USB or network drive).
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QuantStudio™ 1 Real-Time PCR System Installation, Use, and Maintenance Guide
Chapter 3 Configure the instrument and manage instrument profiles
Create an administrator instrument profile during initial start-up
Create an administrator instrument profile during initial start-up
During initial start-up, the user is automatically prompted to create an administrator
instrument prole. See “Initial start-up“ on page 25.
• The rst instrument prole that is created during installation is given
administrator privileges.
• Administrators can grant administrative privileges to other users. See “Manage
all instrument proles (Administrator only)“ on page 37.
Touch Name, enter a username, then touch Done.
1.
Touch PIN, enter a four-digit numerical password, then touch Enter.
2.
Note: Touch the Show PIN checkbox to switch PIN display on or o.
Touch Conrm PIN, then repeat step 2.
3.
Touch Create prole.
4.
3
Create a new instrument profile
In the home screen, touch
1.
Touch Name, enter a username, then touch Done.
2.
Touch PIN Code, enter a four-digit numerical password, then touch Enter.
3.
Note: Touch the Show PIN checkbox to switch PIN display on or o.
Touch Conrm PIN, then repeat step 2.
4.
Touch Create prole.
5.
Sign in to the prole you just created. See Sign in.
6.
Note: To enable access to the Thermo Fisher Cloud, see “Link an instrument prole
with the Thermo Fisher Cloud“ on page 38.
Sign In, then touch Get Started.
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Chapter 3 Configure the instrument and manage instrument profiles
3
Overview of Settings
Overview of Settings
Touch Seings in the home screen to congure seings as needed.
Access to many seings are restricted to administrator instrument proles.
Touch for step-by-step instructions on conguring seings.
Options
Instrument Settings
Instrument Name
(Administrator only)
Sleep Mode Enable the instrument to enter a standby mode after a set length of inactivity.
Heated Cover Temperature Set the idling temperature for the heated cover (before it enters sleep mode).
Network Drive
Insert Plate Reminder Enable a reminder to insert a plate before starting a run from the instrument.
OEM Connection Only
(Administrator only)
Cloud Region
(Administrator only)
[1]
Description
Enter a unique instrument name, and
Specify a default network drive for transferring files from the instrument.
Required for API access to the instrument. When enabled, the software (desktop and
cloud) cannot connect to the instrument.
API access to the instrument is exclusive to authorized OEM partners.
Specify the regional server location to access the Thermo Fisher Connect Dashboard.
Note: Once you set a Cloud region, restore factory defaults to change the region.
(optional)
set an instrument avatar.
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QuantStudio™ 1 Real-Time PCR System Installation, Use, and Maintenance Guide
Chapter 3 Configure the instrument and manage instrument profiles
Options Description
Date/Time Set time zone and date and time formats.
Network Connection Set wired or wireless network connection for the instrument.
Restore Factory Defaults Restore the instrument to the factory settings.
IMPORTANT! Back up the instrument before restoring factory defaults (see “Backup
or restore the instrument“ on page 70).
Note: Restoring an instrument to the factory defaults results in the following setting
changes:
Instrument profiles and files stored on the instrument are deleted, including all EDS
·
files and any custom dye calibrations.
The most recent valid ROI/Uniformity, Background, and system dye calibrations are
·
not deleted.
Language Specify the language to display on the touchscreen.
About Instrument
Overview of Settings
3
About Instrument Displays the instrument Model Name, Block Serial Number, and Firmware Version.
License Agreement Displays the End User Software License Agreement and the Limited Product Warranty.
You can export the License Agreement to a USB drive.
Notifications
— Enable home screen notifications of instrument errors and software updates. This
function is not related to the Notifications function in the cloud software.
The number of new, unviewed notifications displays over Settings in the home screen.
Maintenance and Service
Software Update
(Administrator only)
Monitoring
(Administrator only)
Instrument Statistics Displays instrument usage information including Block Cycle Count and LED Life.
Calibrations
Update the instrument software.
Enable the Remote Monitoring Service to automatically notify Thermo Fisher Scientific
support teams in real-time of potential instrument problems.
The service monitors and sends general
monitor or send
• Perform calibrations
– ROI and Uniformity
– Dye
– Custom (including Background calibration)
• View calibration history and set calibration reminders in History and Reminders
customer
data.
instrument
data, but the service does not
RNase P Verification Perform instrument performance verification using an RNase P plate.
Self Verification Test Check the instrument hardware functions.
Log View and export Instrument Run Log.
QuantStudio™ 1 Real-Time PCR System Installation, Use, and Maintenance Guide
29
Chapter 3
3
Manage instrument settings
Options Description
Backup / Restore
Ship Prep Mode Place the instrument in a safe state for moving or long term storage.
Run History
— Displays the instrument runs and whether the EDS file for the run was transferred.
Manage Users
Configure the instrument and manage instrument profiles
• Backup the instrument
• Restore an instrument backup
Touch a run to view the details or to transfer or delete (Administrator only) the EDS file.
[1]
Sign In Required
(Administrator only)
Sign Out Timer
(Administrator only)
Manage Profiles
(Administrator only)
[1]
Also available to standard and guest instrument profiles.
Enable only signed-in users to access the instrument for any task, including accessing
Settings. Enabling this feature disables the guest profile access to the instrument.
Note: Instrument runs must be started from the desktop software, and actions during
an instrument run are automatically logged to the guest instrument profile (even if a
user was signed into the instrument).
Set the time length of inactivity before a user is automatically signed out.
Access the profile information for the instrument.
Manage instrument settings
In the home screen, touch Seings4Instrument Seings to access the following
functions.
“Manage the instrument name (Administrator only)“ on page 31
“Enable Sleep Mode“ on page 31
“Set the idling temperature for the heated cover“ on page 31
30
“Congure the network drive“ on page 31
“OEM connection only (Administrator only)“ on page 31
“Select a Cloud region (Administrator only)“ on page 32
“Set the date and time (Administrator only)“ on page 32
“Congure the network“ on page 32
“Restore factory defaults“ on page 34
“Select a language“ on page 34
QuantStudio™ 1 Real-Time PCR System Installation, Use, and Maintenance Guide
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