ThermoFisher Scientific QuantStudio 1 Plus Installation and operating instructions

For Research Use Only. Not for use in diagnostic procedures.
QuantStudio™1 Plus Real-Time PCR System
INSTALLATION, USE, AND MAINTENANCE
Publication Number MAN0024786
Revision A.0

Thermo Fisher Scientific (Shanghai) Instruments Co., Ltd. | T71-6, No. 211, Qin Qiao road, China (Shanghai) Free Trade Zone, China
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. MAN0024786
Revision Date Description
A.0 8 April 2021 New document for the QuantStudio™1 Plus Real-Time PCR System.
Important Licensing Information: This product may be covered by one or more Limited Use Label Licenses. By use of this product,
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
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©2021 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
Features of the instrument, desktop, and Thermo Fisher™Connect software ...... 14
Folders, templates, experiments, and projects ................................. 15
Third-party software ....................................................... 17
Supported options for instrument and computer connections ........................ 17
Experiment types .............................................................. 19
■CHAPTER 2 General procedures to operate the instrument ................... 21
Precautions for use ............................................................. 21
Power on the instrument ........................................................ 22
Power o the instrument ........................................................ 22
Sign in ........................................................................ 22
Sign out ...................................................................... 23
Load and unload a plate in the QuantStudio™1 Plus Real-Time PCR Instrument ....... 23
Transfer, view, or manage files and results ......................................... 24
Transfer EDS files from the instrument home screen ............................ 24
View run history and delete or transfer files from the instrument ................. 24
Manage templates (EDT files) ................................................ 25
■CHAPTER 3 Configure the instrument and manage instrument profiles ..... 26
Initial start‑up .................................................................. 26
Installation and instrument verification ............................................ 27
Use the instrument without signing in ............................................. 27
Create an administrator instrument profile during initial start-up ...................... 27
Create a new instrument profile .................................................. 28
Overview of Settings ........................................................... 29
QuantStudio™1 Plus Real-Time PCR System Installation, Use, and Maintenance Guide 3

Manage instrument settings ..................................................... 31
Manage the instrument name (Administrator only) .............................. 32
Enable Sleep Mode ........................................................ 32
Set the idling temperature for the heated cover ................................ 32
Configure the network drive ................................................. 32
OEM connection only (Administrator only) ..................................... 33
Select a region for Thermo Fisher™Connect (Administrator only) ................. 33
Set the date and time (Administrator only) ..................................... 33
Configure the network ...................................................... 33
Restore factory defaults .................................................... 35
Select a language .......................................................... 35
Learn about the instrument ...................................................... 35
View instrument specifications .............................................. 35
View and export the License Agreement ...................................... 36
Manage home screen notifications ............................................... 36
Manage maintenance, service, and calibrations .................................... 36
Update instrument software (Administrator only) ............................... 36
Enable remote instrument monitoring (Administrator only) ....................... 37
View instrument statistics ................................................... 37
View instrument logs ....................................................... 37
Manage Users ................................................................. 38
Require instrument profile sign-in (Administrator only) .......................... 38
Manage the Sign Out Timer (Administrator only) ............................... 38
Manage instrument profiles ................................................. 38
Link an instrument profile to Thermo Fisher™Connect .............................. 39
Link an existing instrument profile to Thermo Fisher™Connect .................. 40
Create a new instrument profile and link to Thermo Fisher™Connect ............. 40
■CHAPTER 4 Create and run experiments on the instrument .................. 41
Workflow ..................................................................... 41
Run an experiment ............................................................. 42
Create and run an experiment from a template ................................ 42
Run an experiment from a saved file ......................................... 42
Repeat the last instrument run ............................................... 43
Edit an experiment before starting a run .......................................... 44
Enter or edit template properties ............................................. 44
Edit the run method ........................................................ 45
Define, assign, and view well details ......................................... 48
View, pause, or stop a run ....................................................... 49
View real-time data and plots on the instrument touchscreen .................... 49
Adjust the display of real-time plots on the instrument touchscreen .............. 49
Pause or stop an instrument run ............................................. 50
Lock the touchscreen during a run ........................................... 50
Transfer EDS files from the instrument home screen ................................ 50
Contents
4QuantStudio™1 Plus Real-Time PCR System Installation, Use, and Maintenance Guide

■CHAPTER 5 Calibrate and verify instrument performance ..................... 52
Calibration and verification schedule ............................................. 52
Calibration descriptions ......................................................... 53
View the calibration status and set reminders ...................................... 54
View calibration status and set reminders in the instrument ..................... 54
View calibration status and set reminders in Thermo Fisher™Connect ............ 54
Perform ROI/uniformity, background, and dye calibrations .......................... 55
Workflow: Calibration ...................................................... 55
Prepare a calibration plate .................................................. 56
Perform calibrations ........................................................ 57
View calibration images and transfer results to USB ............................ 58
Troubleshoot calibration failure .............................................. 59
Identify contamination ...................................................... 59
Create a background plate (optional) ......................................... 60
Perform instrument verification using RNase P plates ............................... 60
Instrument verification description ........................................... 61
RNase P instrument verification plate ........................................ 61
Performance specifications pass criteria ...................................... 62
Prepare an RNase P plate ................................................... 62
Perform RNase P verification ................................................ 63
Troubleshoot verification failure .............................................. 64
Calibrate custom dyes .......................................................... 65
Custom dyes overview ..................................................... 65
Use a dilution series to determine an optimal custom dye concentration .......... 65
Calibrate the custom dye ................................................... 67
Calibrate for a custom melt curve experiment ...................................... 70
■CHAPTER 6 Maintain the instrument ............................................ 73
Backup or restore the instrument ................................................ 73
Decontaminate the sample block ................................................ 74
Materials required .......................................................... 74
Clean the sample block ..................................................... 74
Detailed procedures for cleaning the sample block ............................. 76
Replace the instrument fuses .................................................... 77
Materials required .......................................................... 77
Replace the fuses .......................................................... 77
Prepare the instrument to store, move, or ship ..................................... 78
Move the instrument ....................................................... 78
Return the instrument for service ............................................ 79
Contents
QuantStudio™1 Plus Real-Time PCR System Installation, Use, and Maintenance Guide 5

■APPENDIX A Install and connect the instrument to a network ................ 80
Workflow: Install and connect to a network ........................................ 80
Before you begin ............................................................... 81
Instrument and computer connections ............................................ 81
Unpack and install the instrument ................................................ 82
Power on and follow the startup wizard ........................................... 83
Connect the instrument and the computer directly or to a LAN ....................... 84
Networking .................................................................... 85
Supported options for instrument and computer connections ................... 85
Control and monitor networked instruments ................................... 86
Ethernet port overview ..................................................... 87
Firewall ports that must be open ............................................. 87
Networking guidelines and best practices ..................................... 87
■APPENDIX B Troubleshooting .................................................... 88
■APPENDIX C Instrument specification and layout .............................. 90
Configured system dimensions .................................................. 91
Instrument clearances ...................................................... 92
Electrical requirements ......................................................... 92
Environmental requirements ..................................................... 93
Network requirements .......................................................... 93
■APPENDIX D Parts and materials ................................................ 95
Kits, consumables, accessories, and reagents ..................................... 95
Consumables (96‑well, 0.2‑mL format) ............................................ 95
Accessories .................................................................. 96
General-use materials and consumables .......................................... 96
■APPENDIX E Safety ............................................................... 98
Symbols on this instrument ..................................................... 98
Conformity symbols ........................................................ 99
Safety alerts on this instrument ................................................. 100
Location of safety labels on the instrument .................................. 100
Safety information for instruments not manufactured by Thermo Fisher Scientific ..... 101
Instrument safety ............................................................. 101
General ................................................................. 101
Physical injury ............................................................ 101
Electrical safety .......................................................... 101
Cleaning and decontamination ............................................. 102
Contents
6QuantStudio™1 Plus Real-Time PCR System Installation, Use, and Maintenance Guide

Safety and electromagnetic compatibility (EMC) standards ......................... 102
Safety compliance ........................................................ 102
EMC .................................................................... 103
Environmental design ..................................................... 103
Chemical safety .............................................................. 104
Biological hazard safety ....................................................... 105
■APPENDIX F Documentation and support ..................................... 106
Related documentation ........................................................ 106
Customer and technical support ................................................ 106
Limited product warranty ...................................................... 106
Index ..................................................................................... 107
Contents
QuantStudio™1 Plus 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 Plus Real-
Time PCR System. For information and instructions on performing experiments on this system, see the
QuantStudio™Design and Analysis SC Software v1.0 User Guide (Pub. No. MAN0024784).
8QuantStudio™1 Plus Real-Time PCR System Installation, Use, and Maintenance Guide

Product information
■Instrument hardware description ........................................................ 9
■Software description .................................................................. 14
■Supported options for instrument and computer connections .............................. 17
■Experiment types ..................................................................... 19
Instrument hardware description
Instrument overview
The QuantStudio™1 Plus Real-Time PCR System uses fluorescence-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 19.
The instrument is configured with a 96-well 0.2-mL fixed block and a 4-color coupled filter 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 SC Software v1.0.
The instrument can be used with the Thermo Fisher™Connect Platform.
1
QuantStudio™1 Plus Real-Time PCR System Installation, Use, and Maintenance Guide 9

An optional barcode scanner and optional wireless adapter can be ordered separately.
Instrument filters and supported dyes
System dyes
The instrument uses a coupled four-color filter set that supports the dyes shown in the following table
and figure. For more information about available spectral dye calibration kits, contact Support.
Table 1 Filters and supported dyes
Peak filter Color
Filter wavelength[1] Factory-calibrated
dyes Example custom dyes
Excitation Emission
x1-m1 Blue 470 ± 15 nm 520 ± 15 nm FAM™dye,
SYBR™Green SYT09
x2-m2 Green 520 ± 10 nm 558 ± 12 nm VIC™dye JOE™dye, HEX™dye,
TET™dye[2]
x4-m4 Orange 580 ± 10 nm 623 ± 14 nm ROX™dye, JUN™dye Texas Red™dye
x5-m5 Red 640 ± 10 nm 682 ± 14 nm MUSTANG PURPLE™
dye, Cy®5LIZ™dye
[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.
Filters
Wavelength
(nm)
1 2 34
x1-m1 x2-m2 x4-m4 x5-m5
Emission
Spectra
1x1-m1—FAM™dye, SYBR GREEN™dye
2x2-m2—VIC™dye
3x4-m4—JUN™dye, ROX™dye, Texas Red™dye
4x5-m5—Cy®5, MUSTANG PURPLE™dye
Custom dyes
The instrument can run assays that are designed with custom dyes. Custom dyes include the following
dyes:
•Dyes that are not supplied by Thermo Fisher Scientific.
•Dyes or formulations of dyes that are not system dyes for the instrument.
Chapter 1 Product information
Instrument hardware description
1
10 QuantStudio™1 Plus Real-Time PCR System Installation, Use, and Maintenance Guide

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 65).
•Ensure that the custom dye excites and emits within the wavelength range of the filters (see Table 1
on page 10).
•Select a custom dye that does not overlap with other dyes that are used in the run (see Table 1 on
page 10).
Parts of the instrument
1
2
3
1Touchscreen—Controls the instrument.
2USB port—For connection to an external network drive or external data storage device.
3Instrument drawer—Holds the 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.
Chapter 1 Product information
Instrument hardware description 1
QuantStudio™1 Plus Real-Time PCR System Installation, Use, and Maintenance Guide 11

Parts of the home screen
4
3
9
5
6
8 7
2
1
1Instrument name
2Help icon
3Drawer status
4Status dial
5Current user name and instrument block type
6Settings button
7Buttons for accessing experiment template files (EDT)
8Connectivity icons
9Sign In (or My Profile) button
Table 2 Parts of the home screen
Part of the home
screen Function More information
Instrument name Set by the administrator to uniquely identify instrument. “Manage the instrument name
(Administrator only)” on page 32
Help icon Touch to launch the touchscreen Help system to access
step-by-step instructions.
—
Chapter 1 Product information
Instrument hardware description
1
12 QuantStudio™1 Plus Real-Time PCR System Installation, Use, and Maintenance Guide

Table 2 Parts of the home screen (continued)
Part of the home
screen Function More information
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.
—
Status dial •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.
—
Current user
name and block
type
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.
—
Settings button Touch Settings to configure, calibrate, or learn about
the instrument.
Chapter 3, “Configure the instrument
and manage instrument profiles”
Buttons for
accessing
experiment and
template files
Load Experiment — Touch to open a user-created EDT
file from a Thermo Fisher™Connect account, USB,
instrument folder, or network drive.
“Run an experiment from a saved
file” on page 42 .
Open Template — Touch to open a system EDT
template file.
“Create and run an experiment from
a template” on page 42
“Run an experiment from a saved
file” on page 42
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.
“Repeat the last instrument run” on
page 43
Chapter 1 Product information
Instrument hardware description 1
QuantStudio™1 Plus Real-Time PCR System Installation, Use, and Maintenance Guide 13

Table 2 Parts of the home screen (continued)
Part of the home
screen Function More information
Connectivity
icons
•— 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 Thermo Fisher™
Connect account.
—
Sign In button
(My Profile button
when a user is
signed in)
•Touch Sign In to sign into an instrument profile
and link to a Thermo Fisher™Connect account.
•Touch My Profile to change instrument profile
settings, link to a Thermo Fisher™Connect account,
or lock the instrument during a run.
“Sign in” on page 22
Software description
Features of the instrument, desktop, and Thermo Fisher™Connect software
The instrument and the software (desktop and Thermo Fisher™Connect) include the features described
in the following table.
Software feature Instrument Desktop Thermo Fisher™
Connect
Use as guest (no sign in) ✓✓—
Create templates (unlocked or locked) — ✓ ✓
Edit unlocked templates ✓✓✓
Edit locked templates (password assigned by
template creator required)
—✓ ✓
Load system or user-created templates (EDT file)
to instrument
✓✓—
Chapter 1 Product information
Software description
1
14 QuantStudio™1 Plus Real-Time PCR System Installation, Use, and Maintenance Guide

(continued)
Software feature Instrument Desktop Thermo Fisher™
Connect
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
✓— —
Load plate in instrument ✓— —
Start run ✓✓—
View real-time data during a run ✓✓✓
View instrument status (running, calibration
needed, and so on)
✓—✓
Analyze results — ✓ ✓
Set calibration reminders ✓—✓
Review exported calibration or RNase P
verification results
—✓ ✓
(only RNase P)
Folders, templates, experiments, and projects
Term Definition Supported in
Folders in Load
Experiment
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
Instrument
Chapter 1 Product information
Software description 1
QuantStudio™1 Plus Real-Time PCR System Installation, Use, and Maintenance Guide 15

(continued)
Term Definition Supported in
Experiment Template
File (EDT)
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 Thermo
Fisher™Connect)
•User-created, accessed from Load Experiment
Instrument
Desktop
Thermo Fisher™
Connect
Experiment Run File
(EDS)
Settings and data for a completed instrument run. Instrument
Desktop
Thermo Fisher™
Connect
Project Function in the Cloud Data Manager that is used for secondary
analysis applications. Does not apply to Thermo Fisher™
Connect software, which is a primary analysis application.
Thermo Fisher™
Connect
Template and
experiment
components
Instrument Desktop Thermo Fisher™Connect
Properties •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)
•Experiment file name
•Plate barcode
•User name
•Instrument type
•Block type
•Experiment type
•Chemistry (reagent information)
•Run mode
•Comments
•(Thermo Fisher™Connect only) Notifications
Method Thermal cycling conditions Thermal cycling conditions
Plate Sample names
You cannot edit targets/SNP
assays or tasks on the instrument.
Define and assign samples, targets or SNP assays, and
tasks in the Quick Setup and Advanced Setup panes of the
Plate tab.
Run Start and monitor a run in progress
View: time remaining and
temperature, method, plots
Pause, resume, stop a run
Start and monitor a run in
progress
View: time remaining and
temperature, method, plots
Monitor a run in progress
(link to Thermo Fisher™
Connect Instrument Details)
View: time remaining and
temperature, method, plots
Chapter 1 Product information
Software description
1
16 QuantStudio™1 Plus Real-Time PCR System Installation, Use, and Maintenance Guide

(continued)
Template and
experiment
components
Instrument Desktop Thermo Fisher™Connect
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 SC
Software v1.0, confirm that the third-party software will not do the following:
•Restrict Ethernet communication.
•Interfere with instrument or computer operation.
Supported options for instrument and computer
connections
We support the following direct, networked (LAN–local area network), or Thermo Fisher™Connect
configurations. Configurations other than those listed are not recommended. Select a configuration that
meets the needs of your laboratory's instrument, software, and workflow requirements.
IMPORTANT! Do not connect both an Ethernet cable and the Wi‑Fi module (Cat. No. A26774) to
the instrument. Configuring the instrument for both wired and wireless connection can interfere with
instrument operation.
Chapter 1 Product information
Supported options for instrument and computer connections 1
QuantStudio™1 Plus Real-Time PCR System Installation, Use, and Maintenance Guide 17

Note: For detailed information about networking your instrument, see the QuantStudio™1 Plus Real-
Time PCR System IT Checklist (Pub. No. MAN0017226).
Direct configuration option
•A computer provided by Thermo Fisher Scientific with the QuantStudio™Design and Analysis SC Software
v1.0
•Computer‑to‑instrument connection:
–Direct, wired connection between the computer and the instrument
using an Ethernet cable
IMPORTANT! A direct instrument‑to‑computer connection cannot be
combined with the LAN or the Thermo Fisher™Connect configurations.
Networked configuration option
•A computer provided by Thermo Fisher Scientific with the QuantStudio™Design and Analysis SC Software
v1.0
•The computer and instrument must have the same subnet mask within the same network.
•Computer‑to‑LAN connection (select an option):
–Wired connection to the network using an Ethernet cable –or –
–Wireless connection to the network
LAN
LAN
•Instrument‑to‑LAN connection (select an option):
–Wired connection to the network using an Ethernet cable –or –
–Wireless connection to the network using the instrument Wi‑Fi module
Thermo Fisher™Connect configuration option
•Internet access and a computer with the Chrome™web browser to access Thermo Fisher™Connect
•Computer‑to‑Thermo Fisher™Connect connection (select an option):
–Wired connection to the internet using an Ethernet cable –or –
–Wireless connection to the internet
LAN
•Instrument‑to‑Thermo Fisher™Connect connection (select an option):
–Wired connection to the network using an Ethernet cable –or –
–Wireless connection to the network using the instrument Wi‑Fi module
Chapter 1 Product information
Supported options for instrument and computer connections
1
18 QuantStudio™1 Plus Real-Time PCR System Installation, Use, and Maintenance Guide

Experiment types
Purpose Description
Standard curve experiment
Determines absolute
target quantity in
samples.
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.
Relative standard curve experiment
Determines relative
target quantity in
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 eects 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 Ct(DDCt) experiment
Determines relative
target quantity in
samples.
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 eects 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(ΔCtor ΔCrt) for the sample to the normalized ΔCq(ΔCtor ΔCrt) for
the reference sample.
Chapter 1 Product information
Experiment types 1
QuantStudio™1 Plus Real-Time PCR System Installation, Use, and Maintenance Guide 19

Purpose Description
Genotyping experiment
Detects single
nucleotide
polymorphism (SNP)
variants of a
target nucleic acid
sequence.
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
the passive reference dye in each well.
2. The software plots the normalized reporter dye signal of each sample well on an Allelic
Discrimination Plot, which contrasts the reporter dye intensities of the allele-specific
probes.
3. The software algorithmically clusters the sample data, and assigns a genotype call to
the samples of each cluster according to its position on the plot.
Presence/absence experiment
Determines the
presence or absence
of a target nucleic
acid sequence in a
sample.
The software calls the target present or absent based on an algorithmically determined call
threshold. (The call threshold is dierent from the Ctthreshold; the Ctthreshold is not used
to make calls.)
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).
Chapter 1 Product information
Experiment types
1
20 QuantStudio™1 Plus Real-Time PCR System Installation, Use, and Maintenance Guide