HB-2006-001 1099000 UM IAS RGQ QRexBasic 1015 WW

October 2015
Q-Rex Software User

Manual
For use with the Rotor-Gene® Q instruments
Sample to Insight
Contents
1 Introduction
..............................................................................................................1-2
1.1 Provided user manuals
......................................................................................................1-2
1.2 About this user manual
......................................................................................................1-3
1.3 General information
......................................................................................................1-3
1.3.1 Technical
.......................................................................................1-3
assistance
1.3.2 Policy.......................................................................................1-4
statement
1.3.3 Version
.......................................................................................1-4
management
1.3.4 Intended
.......................................................................................1-4
use
1.4 Getting help
......................................................................................................1-5
2 Safety
..............................................................................................................2-2
information
2.1 Proper Use
......................................................................................................2-3
2.2 Electrical safety
......................................................................................................2-5
2.3 Environment
......................................................................................................2-6
2.4 Biological safety
......................................................................................................2-6
2.4.1 Samples
.......................................................................................2-7
2.5 Chemicals
......................................................................................................2-8
2.5.1 Toxic.......................................................................................2-8
fumes
2.6 Waste disposal

......................................................................................................2-8
2.7 Mechanical hazards
......................................................................................................2-9
3 Getting
..............................................................................................................3-2
started
3.1 Minimum specifications
......................................................................................................3-2
3.2 Install or upgrade the Q-Rex Software
......................................................................................................3-2
3.3 Install plug-ins
......................................................................................................3-12
3.4 Uninstall the Q-Rex Software
......................................................................................................3-12
3.5 Start the software
......................................................................................................3-13
3.6 First login
......................................................................................................3-13
Q-Rex Software User Manual 10/2015 2

3.7 First configuration
......................................................................................................3-15
4 Basic..............................................................................................................4-2
concepts and general software use
4.1 Concepts
......................................................................................................4-2
4.1.1 User .......................................................................................4-2
roles
4.1.2 Experiments
.......................................................................................4-4
and templates
4.1.3 Plug-in
.......................................................................................4-4
concept
4.2 General software use
......................................................................................................4-5
4.2.1 Use of
.......................................................................................4-5
color
4.2.2 Displaying
.......................................................................................4-7
errors and warnings
4.2.3 Entering
.......................................................................................4-8
data
4.2.4 Working
.......................................................................................4-9
with tables
4.2.5 Selecting
.......................................................................................4-11
samples
4.3 Q-Rex workspace
......................................................................................................4-12
4.4 General elements
......................................................................................................4-12
4.4.1 Menu
.......................................................................................4-13
4.4.2 Main
.......................................................................................4-14
toolbar
4.4.3 Button
.......................................................................................4-17
bar
4.4.4 Status
.......................................................................................4-18
bar
4.5 Environments
......................................................................................................4-18
4.5.1 My Q-Rex
.......................................................................................4-19
4.5.2 Experiments
.......................................................................................4-20
4.5.3 Service
.......................................................................................4-22
4.5.4 Configuration
.......................................................................................4-23
5 Manage
..............................................................................................................5-2
experiments and templates
5.1 Manage favorite templates
......................................................................................................5-2
5.2 View recent experiments
......................................................................................................5-4
6 Set up
..............................................................................................................6-2
an experiment
6.1 Set......................................................................................................6-2
up a new experiment
6.1.1 Create
.......................................................................................6-2
an experiment

Create a blank
.............................................................................6-2
experiment
Create an experiment
.............................................................................6-5
using a template
Create an experiment based on an existing
experiment .............................................................................6-6
6.1.2 Define
.......................................................................................6-6
general information
Add kit information
.............................................................................6-9
6.1.3 Define
.......................................................................................6-10
the run profile
Define basic
.............................................................................6-11
profile settings
Define the .............................................................................6-12

thermal profile
Add an acquisition
.............................................................................6-27
6.1.4 Define
.......................................................................................6-34
a sample layout
Define sample
.............................................................................6-35
details
Define targets
.............................................................................6-37
Define sample
.............................................................................6-38
groups
Configure concentration
.............................................................................6-39
number format
Assign well.............................................................................6-39
names to tubes
Manually define
.............................................................................6-39
auto-gain tubes
Import sample
.............................................................................6-40
information
6.2 Set up an experiment via wizard
......................................................................................................6-42
6.2.1 Set up
.......................................................................................6-42
an experiment from a QIAgility result file
6.2.2 Set up
.......................................................................................6-45
an experiment from a QIAGEN kit
7 Run ..............................................................................................................7-2
an experiment
7.1 Start a run
......................................................................................................7-2
7.2 View a running experiment
......................................................................................................7-3
7.3 View fluorescence curves during a run
......................................................................................................7-4
7.4 View profile progress
......................................................................................................7-5
7.4.1 Adjust.......................................................................................7-5
run duration
7.4.2 View .......................................................................................7-6
auto-gain optimization progress
7.5 Stop a run
......................................................................................................7-7
8 Analyze
..............................................................................................................8-2
an experiment

8.1 Add......................................................................................................8-2
an analysis
8.2 Analysis overview

......................................................................................................8-3
8.3 View Fluorescence plots
......................................................................................................8-4
8.3.1 Modify
.......................................................................................8-6
plot view
8.3.2 Copy.......................................................................................8-8
plot to clipboard
8.4 Select tubes for analysis
......................................................................................................8-8
8.5 Remove an analysis
......................................................................................................8-10
8.6 Define analysis parameters
......................................................................................................8-11
8.6.1 Filter
.......................................................................................8-12
data
8.6.2 Normalize
.......................................................................................8-13
curves
8.6.3 Define
.......................................................................................8-14
Cq threshold
8.6.4 Analyze
.......................................................................................8-15
melt curves
8.7 View results
......................................................................................................8-17
8.7.1 Tubes
.......................................................................................8-18
View
8.7.2 Replicates
.......................................................................................8-19
View
8.7.3 Groups
.......................................................................................8-21
View
9 Reports
..............................................................................................................9-2
and exports
9.1 Reports
......................................................................................................9-2
9.2 Exports
......................................................................................................9-5
9.3 Experiment audit trail
......................................................................................................9-8
9.4 Copy and paste
......................................................................................................9-9
10 Administrative
..............................................................................................................10-2
tasks
10.1 View the system audit trail
......................................................................................................10-2
10.2 Manage users
......................................................................................................10-3
10.3 Manage cyclers
......................................................................................................10-5
10.4 Customize settings
......................................................................................................10-7
11 Troubleshooting
..............................................................................................................11-2
11.1 Error messages and error codes
......................................................................................................11-4
11.2 System setup
......................................................................................................11-7

11.3 Operation
......................................................................................................11-8
12 Glossary
..............................................................................................................12-2
13 Appendices
..............................................................................................................13-2
13.1 Appendix A – Supported file types
......................................................................................................13-2
13.2 Appendix B – License terms
......................................................................................................13-3
13.3 Appendix C – Liability clause
......................................................................................................13-7
13.4 Appendix D – Important notes
......................................................................................................13-8
13.5 Copyright information
......................................................................................................13-10

Introduction
1 Introduction
Thank you for choosing the Q-Rex Software. We are confident it will become an integral part of your
laboratory.
The Q-Rex Software is designed for use in combination with the Rotor-Gene Q instrument for
instrument operation, experimental design and data analysis. The Q-Rex Software provides a user-
friendly interface with options for pre-designed or customizable Rotor-Disc layout and thermal
profiles, as well as advanced data analysis functionality for streamlined processing of your qPCR
assays.
The Q-Rex Software enables:
Multi-experiment analysis by simply opening multiple experiments at once in the software
Seamless integration with QIAGEN instruments and reagent kits through pre-installed wizards
Easy setup of thermal profiles with "drag and drop" functionality
Customizable sample editing for optimal flexibility in data collection
Expandable analysis capabilities through optional plug-ins
The Q-Rex Software consists of different components that work together. The core application is
complemented by a range of plug-ins that power specific analyses and enable different formats to
visualize results. The core application and at least 1 plug-in are required to work with the Q-Rex
Software. Additional plug-ins can be installed according to workflow and analysis needs. Not all plug-
ins are available in all countries. Please visit www.qiagen.com to learn more about our
continuously expanding portfolio of plug-ins.
1.1 Provided user manuals

The core application, as well as every available plug-in, has its own user manual with specific
information about the functionality of the different Q-Rex Software components. These user manuals
provide context-sensitive help that can be accessed by simply pressing the F1 key. When installing
additional plug-ins, the corresponding user manuals are automatically added to the existing help
system. Alternatively, the different user manuals can be accessed, read or printed as *.pdf files.
Q -Re x S oftw are Use r Provides a description of the software and describes functions that are
M anual common to the core application and all plug-ins. Information for
troubleshooting is also provided.
Q-Rex Software plug-in Provide details on the use of specific plug-ins and their functionalities.
user manuals
Q-Rex Software User Manual 10/2015 1-2

1.2 About this user manual
This user manual provides information about the functions and features of the Q-Rex Software.
Please refer to the Rotor-Ge ne Q Use r M anual for complete information about the proper care,
maintenance and use of the Rotor-Gene Q instrument.
This user manual describes the features of the software and associated tools to enable you to
manage and modify files and analyses.
Information about the Q-Rex Software is provided in the following sections:
Introduction
Getting started
Basic concepts and general software use
Manage experiments and templates
Set up an experiment
Run an experiment
Analyze an experiment
Reports and exports
Administrative tasks
Troubleshooting
Glossary
Appendices
1.3 General information
1.3.1 Technical assistance
At QIAGEN, we pride ourselves on the quality and availability of our technical support. Our
Technical Service Departments are staffed by experienced scientists with extensive practical and
theoretical expertise in sample and assay technologies and the use of QIAGEN products. If you have
any questions or experience any difficulties regarding the Rotor-Gene Q, Q-Rex Software or
QIAGEN products in general, please do not hesitate to contact us.
QIAGEN customers are a major source of information regarding advanced or specialized uses of
our products. This information is helpful to other scientists as well as to the researchers at QIAGEN.
We therefore encourage you to contact us if you have any suggestions about product performance
or new applications and techniques.
For technical assistance and more information, please see our Technical Support Center at
www.qiagen.com/Support.

1.3.2 Policy statement
It is the policy of QIAGEN to improve products as new techniques and components become
available. QIAGEN reserves the right to change specifications at any time.
In an effort to produce useful and appropriate documentation, we appreciate your comments on this
user manual. Please contact QIAGEN Technical Services.
1.3.3 Version management
This document is the Q -Re x S oftw are Use r M anual, version 1.0, which provides information about
the Q-Rex Software, version 1.0.
1.3.4 Intended use
The Q-Rex Software is a program for the operation of the Rotor-Gene Q instrument and the analysis
of resulting data. The Q-Rex Software is a real-time application suitable for use with quantitative
polymerase chain reaction (qPCR) and melt curve analysis in molecular biology applications, as well
as for other applications performed on the Rotor-Gene Q instrument, such as concentration
measurement, protein analysis and enzyme kinetics.
When using the Q-Rex Software to operate the Rotor-Gene Q instrument in combination with
QIAGEN kits indicated for use with Rotor-Gene Q instruments, the user must verify that the Q-Rex
Software is appropriate for the applications described in the respective QIAGEN kit handbooks. The
Q-Rex Software should not be used for applications and kits indicated for use with other Rotor-Gene
Q software.
The Q-Rex Software is intended for Life Science purposes only.
If the Q-Rex Software is used to operate the Rotor-Gene Q instrument in combination with kits other
than QIAGEN kits, it is the user’s responsibility to validate the performance of such a product
combination for any particular application.
The Q-Rex Software and the Rotor-Gene Q instrument are intended for use by professional users,
such as technicians and physicians trained in molecular biological techniques and the operation of
the Rotor-Gene Q instrument.

1.4 Getting help
The Q-Rex Software comes with a detailed help system. The help is provided as *.pdf and as *.chm
files (compiled help file). The following image shows the help page corresponding to the login screen
as an example.
The Q-Rex Software has a context-sensitive help system. Press F1 at any time to display a context-
sensitive help page.
Using the Q-Rex Software Help

The help file contains two functional areas: a tool bar and tabs.

The tool bar includes the functions to navigate through help pages:
Name Icon Description
Hide or Show Hides the left-hand side navigation panel. To display the
navigation panel again, click Show, which replaces Hide.
Back Returns to the previous screen.
Forward Returns to the screen displayed before clicking Back.
Print Allows you to print:

the selected topic
the selected heading and all subtopics
Select one option and click OK to confirm or Cancel to go
back.
Options Opens the Options menu with the following entries:
The navigation panel contains the following tabs:
Name Description
Contents Browse the help content by topic.
Search Search for specific help topics.
Favorites Save and manage shortcuts to specific help topics.

Safety information
2 Safety information
The Q-Rex Software was specifically developed for use with the Rotor-Gene Q. Before using the Q-
Rex Software, read this user manual carefully and pay particular attention to the safety information.
The instructions and safety information in the user manual must be followed to ensure safe operation
of the instrument and to maintain the instrument in a safe condition.
The Q -Re x S oftw are Use r M anual does not provide detailed information about the Rotor-Gene Q
hardware and maintenance. The Q -Re x S oftw are Use r M anual only describes the functionality of the
Q-Rex Software in combination with the Rotor-Gene Q.
Note: The terms "Rotor-Gene Q" and "Rotor-Gene Q instrument" used in this manual apply to all
Rotor-Gene Q instruments.
Note: Translations of the Safety Information in French and German are available in the Rotor-Ge ne
Q Use r M anual.
Safety information for the Rotor-Gene Q

The following types of safety information appear throughout the Rotor-Ge ne Q Use r M anual.
WARNING The term WARNING is used to inform you about situations that could result
in personal injury to you or other persons.
Details about these circumstances are given in a box like this one.
CAUTION The term CAUTION is used to inform you about situations that could result in
damage to the instrument or other equipment.
Details about these circumstances are given in a box like this one.
The advice given in the Rotor-Ge ne Q Use r M anual is intended to supplement, not supersede, the
normal safety requirements prevailing in the user’s country.

2.1 Proper Use
WARNING/ Risk of personal injury and material damage [W1]

CAUTION
Improper use of the Rotor-Gene Q may cause personal injuries or damage
to the instrument.
The Rotor-Gene Q must only be operated by qualified personnel who have
been appropriately trained.
Servicing of the Rotor-Gene Q must only be performed by QIAGEN Field
Service Specialists.
QIAGEN charges for repairs that are required due to incorrect maintenance.

CAUTION
The Rotor-Gene Q is too heavy to be lifted by one person. To avoid personal
injury or damage to the instrument, take care when lifting.

CAUTION
Do not attempt to move the Rotor-Gene Q during operation.
CAUTION Damage to the instrument [C1]

Avoid spilling water or chemicals onto the Rotor-Gene Q. Damage caused by
water or chemical spillage will void your warranty.
Note: in case of emergency, switch off the Rotor-Gene Q at the power switch at the back of the
instrument and unplug the power cord from the power supply port.

CAUTION
Do not try to open the lid during an experiment or while the Rotor-Gene Q is
spinning. Otherwise, if you overcome the lid lock and reach inside, you risk
contact with parts that are hot, electrically live or moving at high speed, and
you may injure yourself and damage the instrument.

CAUTION
If you need to stop an experiment quickly, turn off the power to the
instrument, then open the lid. Let the chamber cool before reaching inside.
Otherwise you risk injury by touching parts that are hot.

CAUTION
If the equipment is used in a manner not specified by the manufacturer, the
protection provided by the instrument may be impaired.

CAUTION
Loose paper underneath the Rotor-Gene Q interferes with instrument
cooling. It is recommended that the area beneath the instrument is kept free
of clutter.

Always use a locking ring on the rotor. This stops caps from coming off tubes
during an experiment. If caps come off during an experiment, they may
damage the chamber.
If you touch the Rotor-Gene Q during an experiment, while you are charged with static electricity, in
severe cases the Rotor-Gene Q may reset. However, the software will restart the Rotor-Gene Q and
continue the experiment.

2.2 Electrical safety
Disconnect the line power cord from the power outlet before servicing.
WARNING Electrical hazard [W8]

Any interruption of the protective conductor (earth/ground lead) inside or
outside the instrument or disconnection of the protective conductor terminal is
likely to make the instrument dangerous.
Intentional interruption is prohibited.
Lethal voltages inside the instrument
When the instrument is connected to line power, terminals may be live, and
opening covers or removing parts is likely to expose live parts.
To ensure satisfactory and safe operation of the Rotor-Gene Q:

Connect the line power cord to a line power outlet that has a protective conductor (earth/ground).
Do not adjust or replace internal parts of the instrument.
Do not operate the instrument with any covers or parts removed.
If liquid has spilled inside the instrument, switch off the instrument, disconnect it from the power
outlet and contact QIAGEN Technical Service.
If the instrument becomes electrically unsafe, prevent other personnel from operating it, and contact
QIAGEN Technical Service. The instrument may be electrically unsafe when:
The line power cord appears to be damaged.
It has been stored for a prolonged period of time in conditions which are outside of the “Storage
Conditions” outlined in the Rotor-Ge ne Q Use r M anual.
It has been subjected to severe transport stresses.
WARNING Electrical hazard [W9]

The instrument has an electrical compliance label which indicates the voltage
and frequency of the power supply as well as fuse ratings. The equipment
should only be operated under these conditions.

2.3 Environment
Operating conditions
WARNING Explosive atmosphere [W10]

The Rotor-Gene Q is not designed for use in an explosive atmosphere.
WARNING Risk of explosion [W11]

The Rotor-Gene Q is intended for use with reagents and substances supplied
with QIAGEN kits. Use of other reagents and substances may lead to fire or
explosion.

Direct sunlight may bleach parts of the instrument and cause damage to
plastic parts.
The Rotor-Gene Q must be located out of direct sunlight.
2.4 Biological safety

Specimens and reagents containing materials from humans should be treated as potentially
infectious. Use safe laboratory procedures as outlined in publications such as Biosafety in
Microbiological and Biomedical Laboratories, HHS (www.cdc.gov/od/ohs/biosfty/biosfty.htm).

2.4.1 Samples
Samples may contain infectious agents. You should be aware of the health hazard presented by such
agents, and should use, store and dispose of such samples according to the required safety
regulations.
WARNING Samples containing infectious agents [W12]

Some samples used with this instrument may contain infectious agents.
Handle such samples with the greatest of care and in accordance with the
required safety regulations.
Always wear safety glasses, 2 pairs of gloves and a lab coat.
The responsible body (e.g., laboratory manager) must take the necessary
precautions to ensure that the surrounding workplace is safe and that the
instrument operators suitably trained and not exposed to hazardous levels of
infectious agents as defined in the applicable Safety Data Sheets (SDSs) or
OSHA,* ACGIH† or COSHH‡ documents.
Venting for fumes and disposal of wastes must be in accordance with all
national, state and local health and safety regulations and laws.
* OSHA: Occupational Safety and Health Administration (United States of America).

†
ACGIH: American Conference of Government Industrial Hygienists (United States of America).
‡
COSHH: Control of Substances Hazardous to Health (United Kingdom).

2.5 Chemicals
WARNING Hazardous chemicals [W13]

Some chemicals used with this instrument may be hazardous or may become
hazardous after completion of the protocol run.
Always wear safety glasses, gloves and a lab coat.
The responsible body (e.g., laboratory manager) must take the necessary
precautions to ensure that the surrounding workplace is safe and that the
instrument operators are not exposed to hazardous levels of toxic substances
(chemical or biological) as defined in the applicable Safety Data Sheets
(SDSs) or OSHA,* ACGIH† or COSHH‡ documents.
Venting for fumes and disposal of wastes must be in accordance with all
national, state and local health and safety regulations and laws.
* OSHA: Occupational Safety and Health Administration (United States of America).

†
ACGIH: American Conference of Government Industrial Hygienists (United States of America).
‡
COSHH: Control of Substances Hazardous to Health (United Kingdom).
WARNING Risk of fire [W14]

When cleaning the Rotor-Gene Q with alcohol-based disinfectant, leave the
Rotor-Gene Q door open to allow flammable vapors to disperse.
Only clean the Rotor-Gene Q when worktable components have cooled
down.
2.5.1 Toxic fumes
If working with volatile solvents or toxic substances, you must provide an efficient laboratory
ventilation system to remove vapors that may be produced.
2.6 Waste disposal

Used consumables, plasticware and containers may contain certain hazardous chemicals or
contagious/biohazardous materials. Such wastes must be collected and disposed of properly
according to local safety regulations.

2.7 Mechanical hazards
The lid of the Rotor-Gene Q must remain closed during operation of the instrument.
WARNING Moving parts [W15]

To avoid contact with moving parts during operation of the Rotor-Gene Q,
the instrument must be operated with the lid closed.

CAUTION
Open and close the lid of the Rotor-Gene Q carefully to avoid trapping
fingers or clothing.

Make sure that the rotor and locking ring are installed correctly.
If the rotor or locking ring show signs of mechanical damage or corrosion, do
not use the Rotor-Gene Q; contact QIAGEN Technical Service.

The Rotor-Gene Q must not be used if the lid is broken or if the lid lock is
damaged.
Make sure that the rotor and locking ring are installed correctly.
Only use rotors, locking rings and consumables designed for use with the
Rotor-Gene Q. Damage caused by the use of other consumables will void
your warranty.

When the Rotor-Gene Q is started immediately after delivery in cold
climates, mechanical parts can block.

Allow the instrument to acclimatize to room temperature for at least one hour
before turning the instrument on.
WARNING Moving parts [W17]

In case of breakdown caused by power failure, remove the power cord and
wait 10 minutes before attempting to manually open the lid.
CAUTION Risk of overheating [W18]

To ensure proper ventilation, maintain a minimum clearance of 10 cm at the
sides and rear of the Rotor-Gene Q.
Slits and openings that ensure the ventilation of the Rotor-Gene Q must not
be covered.
WARNING Hot surface [W19]

The Rotor-Gene Q chamber can reach temperatures above 120°C (248°F).
Avoid touching it when it is hot.
WARNING Hot surface [W20]

When a run is paused, the Rotor-Gene Q will not be cooled completely to
room temperature. Exercise caution before handling the rotor or any tubes in
the instrument.

Getting started
3 Getting started
This section of the user manual describes the system requirements for the Q-Rex Software and its
installation and configuration before use.
Minimum specifications
Install or upgrade Q-Rex Software
Install plug-ins
Uninstall Q-Rex Software
Start the software
First login
First configuration
3.1 Minimum specifications

The computer used for setup and execution of runs and data analysis should have the following
minimum specifications:
Microsoft® Windows® 7 or 8.1 (32-bit or 64-bit) Operating System
Intel® Core™ 2 Duo, 1.66 GHz or higher

2 GB of RAM
10 GB free hard drive capacity
Display resolution of 1280 x 800 pixels
USB port
Pointer device (mouse or similar)
To view reports generated in PDF format, a PDF reader must be installed on the computer. Adobe®
Reader ® can be downloaded at www.adobe.com.
3.2 Install or upgrade the Q-Rex Software

To install or upgrade the Q-Rex Software:
1. Ensure that the computer meets the minimum requirements (see Minimum specifications).
2. Use a Windows account with administrator privileges.
3. Close any programs running on the computer.
4. Download the latest version of the Q-Rex Software from www.qiagen.com or insert an
installation CD.

Installation from a CD
The setup wizard automatically opens the Q-Rex Software setup window. Click Install to start
the installation.
If the setup does not start automatically, double-click the setup.exe file in the CD-drive folder.
Installation from setup file
Use Windows Explorer to locate the downloaded setup file and double-click it.

5. The Setup Wizard will open to guide you through the installation routine.
Note: Depending on your system configuration, the installation routine may ask you to restart
the computer:
In this case, select Restart Later and complete the installation, then restart manually.
6. Read the license agreement and check the "agree" box to enable the next steps. If you do not
agree, please contact QIAGEN Technical Services. Otherwise, click Install to continue.

The installation progress will be displayed:
7. Select your region and click Next to continue.

8. The Setup Wizard will check whether the required version of Microsoft .NET framework is
installed on your computer. If so, the Wizard will proceed to step 9. Otherwise, the .NET
framework will be installed automatically. Read the displayed license terms and check "accept
license terms" to enable the next steps. Please contact QIAGEN Technical Services if you do not
agree. Otherwise, click Install to continue.

The progress of the installation is displayed:

Once the .NET installation is complete, click Finish to continue.

9. The installation routine will ask you to agree to a license agreement for a different component.
Check "accept license terms" to enable the next steps. Please contact QIAGEN Technical
Services if you do not agree. Otherwise, click Install to continue.

The Setup Wizard will confirm that the installation was completed.

Note: Depending on the configuration of your computer, the Setup Wizard may ask you to
install a device driver during the installation process. Agree to the installation, otherwise the
Rotor-Gene Q will not be supported.
10. The Q-Rex Software can now be started.
Note: If the computer is connected to a network, network policy settings may prevent you from
completing the installation. For more information, contact your system administrator.

3.3 Install plug-ins
The following analysis plug-ins are automatically included in the installation of the Q-Rex Software:
Q-Rex Basic Plug-in
Q-Rex Absolute Quantification Plug-in
Q-Rex Gene Expression Plug-in
Additionally, the following wizards are installed:
QIAgility® Wizard
QIAGEN Kit Wizard
More plug-ins or wizards will become available over time. Please check www.qiagen.com for
additional information and installation instructions.
For more details about Q-Rex Software plug-ins, please see Plug-in concept.
3.4 Uninstall the Q-Rex Software

To uninstall the Q-Rex Software together with its default plug-ins and wizards:
Windows 7
1. In the Windows Start menu, select: All Programs > QIAGEN > QRex > Uninstall Q-Rex
(or the custom path defined during installation)
2. Confirm that you wish to uninstall the software.
Windows 8.1
1. Press the Windows key to switch to the Start screen.

2. Type "Q-Rex".
3. Select Uninstall Q-Rex from the list of displayed icons.

4. Confirm that you wish to uninstall the software.
Note: Do not attempt to uninstall the QIAGEN Rotor-Gene Q Device Driver manually if any other
software for the Rotor-Gene Q is installed.
3.5 Start the software
To start the Q-Rex Software, double-click on the desktop. Alternatively, you can start the
software from the Windows Start menu or screen.
Windows 7
1. In the Windows Start menu, select: All Programs > QIAGEN > Q-Rex > Q-Rex (or the
custom path defined during installation)
Windows 8.1
1. Press the Windows key to switch to the Start screen.

2. Type "Q-Rex".
3. Select Q-Rex from the list of displayed icons.
The Q -Re x S oftw are Use r M anual (this publication) can be accessed at any time in the software by
pressing the F1 key or by clicking Help in the toolbar.
3.6 First login

After successfully installing the Q-Rex Software, you will be prompted to log in as administrator.
1. In the User ID field, enter "admin".

2. Leave the Password field empty.

3. Confirm with OK.
The software will prompt for the entry of a new password upon the first run. In this dialog, leave the
Old password field empty (no password has been set) and, if you wish, enter a new password. The
content of the two fields for the new password must be identical. If the New password field is left
empty, the Confirm new password field must also be empty.
We highly recommend setting a password at this point to limit access to the default administrator
account. Passwords can be set and modified at any time, including the administrator password. See
Manage users for more details.

3.7 First configuration
After installing the Q-Rex Software, we recommend checking the configuration of the software and
adapting it to personal preferences, if needed. The configuration can be displayed and modified by
selecting the Configuration environment from the top navigation bar and clicking the Settings tab.
Note: Options available under other tabs are explained in Manage users and Manage cyclers.
The following is a description of the settings that can be configured in the Settings tab.
Language
Choose your preferred language for the application. Please note that some of the text items are not
translated, either because they are controlled by the operating system rather than the application, or
because they refer to specific names that have no translation (like product names). For details, see
Language under Customize settings.
Be careful when changing the language. Selecting a language that you do not understand may make
it difficult to switch back.

Reporting
Select the images that will be displayed in the header and footer of reports. Supported file formats
are: .bmp, .jpg, .png. For details, see Reporting under Customize settings.
Concentration number format

Set the default notation (decimal/scientific) and decimal places for calculated concentration values of
samples. This only sets the default number format for new experiments. The number format can be
defined separately for each experiment when editing the relevant tube information (see Define
sample details).
User Management
In the left field, set the number of days after which the Q-Rex Software requires users to change
their password. If this field is left empty, passwords do not expire. In the right field, select the desired
password policy (simple, medium or strong). A stronger policy requires more complicated passwords
and affords a higher level of security. For details, see User Management under Customize settings.

Email Notification
Configure the e-mail settings for support packages, which are used to send information to QIAGEN
Technical Service when needed. For details, see Email Notification under Customize settings.
Click Save to save any changes made.

Click Show saved settings to dismiss unsaved changes and restore the saved settings.
Note: All settings can be changed at a later time. Detailed information on global settings can be
found under Customize settings.

Basic concepts and general software use
4 Basic concepts and general software use
Basic concepts and general use of the Q-Rex Software are explained in this section.
Concepts
General software use
Q-Rex workspace
General elements
Environments
4.1 Concepts
Q-Rex Software builds on underlying concepts about:
User roles
Experiments and templates
Plug-ins
4.1.1 User roles
Access to certain Q-Rex Software functions is restricted to users with specific roles:
Role Permissions
Operator The Operator may:

Set up, run and analyze experiments
Create reports for experiments
Change his or her own password
The Operator cannot create a support package.
Administrator In addition to the permissions of the Operator, the Administrator may:

Configure the system settings
Manage users
Manage cyclers
View the audit trail
Send support packages to QIAGEN
Service The Service user has the same permissions as an Administrator.

The functions listed above can be found in the following environments:
Administrator
Environment Tab Description Operator Service
My Q-Rex – The user can access the My Q- + +

Rex environment
Experiments – The user can access the + +

Experiments environment
Service System Audit The user can access the System – +

Trail Audit Trail tab in the Service
environment
Support The user can access the Support – +

Package Package tab in the Service
environment
Configuration Settings The user can access the Settings – +

tab in the Configuration
environment
User The user can access the User – +

management Management tab in the
Configuration environment
Cycler The user can access the Cycler – +

management Management tab in the
Configuration environment

4.1.2 Experiments and templates
Q-Rex Software distinguishes between experiments and templates.

An experiment summarizes all information related to a cycler run, including setup
information, raw and normalized data, analysis settings, results and audit trail
information. This information is stored in a single file with extension *.qrex.
If you perform a similar experiment multiple times, it is useful to create a template,

which you can use to set up experiments faster. A template can save all setup
information including run profile, target definitions, sample groups and layout, as well
as analysis, report and export settings. Due to logical dependencies, there are some
constraints to the information that can be stored in a template file (*.qret):
The run profile information is only saved if a rotor type has been defined
Targets or a sample layout are only saved if an acquisition has been defined
Analysis settings are only saved if sample information and targets have been
defined
For more details, see Manage experiments and templates.
4.1.3 Plug-in concept
The functionality of the Q-Rex Software can be extended with plug-ins. A plug-in can be installed as
an addition to the core application, which has several advantages:
As a user, you can add new functionality to the Q-Rex Software without having to re-validate
established workflows that rely on a specific software version.
QIAGEN can deliver new analysis algorithms in shorter time intervals because it is not necessary
to release an entire software.
The Q-Rex Software uses plug-ins for analyses. In the analysis selection menu, you will see only
those analyses for which a plug-in has been installed. A description of each analysis plug-in can be
found in its corresponding user manual.
Furthermore, plug-ins are used for advanced wizards that guide experiment setup. These wizards
are described in set up an experiment via wizard.

4.2 General software use
General software use concepts of the Q-Rex Software include standard ways of:
Using color
Displaying errors and warnings
Entering data
Working with tables
Selecting samples
4.2.1 Use of color
To make it easier to find and enter information into the Q-Rex Software, data are presented in fields
that follow a consistent color scheme throughout the software.
Color of field Description

Light blue The field is interactive and clickable.
Dark blue The field is interactive and selected.
Gray The field is read-only (informative field).
Yellow The field is interactive and requires input (mandatory field).

Example
The following screenshot shows a dialog in the Q-Rex Software, highlighting the different field types.

4.2.2 Displaying errors and warnings
Errors and warnings are essential information. These messages point to problems or errors that must
be corrected or accounted for when interpreting results. Q-Rex Software differentiates between 3
different problem levels:
Description of the
Priority Name Icon functionality Action required by user
1 System error A combination of incidents User interaction required
requiring action
3 Warning Situation could be User interaction possible, but

optimized by further input. not mandatory
Software has automatically
adjusted input values due to
invalid entries.
Value is within technically
allowed range but outside
the recommended range.
4 Information A message containing User interaction not possible

additional information about
the current situation
Example of an embedded warning message

The following screenshot shows the warning that appears when an entered value is outside the
recommended range. The warning icon appears next to the relevant entry field and a tooltip with the
warning message is displayed when you position the mouse pointer over the icon.

Example of a pop-up error message
The following is a screenshot of a pop-up error message. Each error or warning message includes a
unique ID number. When contacting QIAGEN Technical Service for assistance, make sure to have
the Message ID ready.
4.2.3 Entering data
Shortcuts
The following hot keys are available in the Q-Rex Software:
Click F1 to open the help file
Use Ctrl+C and Ctrl+V to copy and paste
Use Tab and the cursor arrow keys to navigate from one field to another
Esc cancels data in a selected table cell
Return commits input entered into a table cell

Validation of data entry
An entry field is highlighted in yellow when data entered is invalid. By rolling the mouse pointer over
the field, you display a tooltip with details about the validation error. The following screenshot shows
an invalid entry in the field Reaction Volume. The value entered is outside the specified range.
4.2.4 Working with tables
Sorting data in tables

Some tables in the Q-Rex Software allow you to sort data by column. Upon clicking the header of a
column in a sortable table, a sort indicator icon ( ) appears in the header and the data in the table
are sorted according to this column. The direction of the icon indicates the sort order:
The data are sorted by the indicated column in ascending order.
The data are sorted by the indicated column in descending order.
To toggle the sorting order from ascending to descending or vice versa, click the column header with
the sort indicator icon. To sort the data in the table according to another column, click the respective
column header.
The results table below is sorted by the Sample name column in ascending order.

Selecting cells
A selected cell in a table is highlighted in dark blue. To select two or more non-adjacent cells, hold
down the Ctrl key and click the desired cells. A group of adjacent cells can be selected by clicking
the first cell, holding down the Shift key, and clicking the last cell. You can also click the first cell
and, while holding down the mouse button, drag the mouse pointer to the last cell.
Copying data from a table

To copy data from a table, select the cells to be copied and then press Ctrl+C. Use Ctrl+V to paste
the content into another area within the Q-Rex Software or into another software for further
processing.
Context menu
Tables in the Q-Rex Software have context menus with several commands. Any context menu is
opened by right-clicking a selected cell. In the Sample Layout table, values for the columns Color,
Style, Sample Groups, Type, Target and Unit are defined by selecting options from their
corresponding context menu. Entries for the Name and Concentration columns are typed in
manually.

4.2.5 Selecting samples
You can select samples in a table or graphic using the following key strokes:
Shift + left-click To select two or more adjacent samples, left-click the first sample of the
group, hold down the Shift key and left-click the last sample to be
contained in the selection.
Ctrl + left-click To select two or more non-adjacent samples, hold Ctrl and left-click the
desired samples.
To deselect samples, hold Ctrl and left-click the selected sample.
Left-click + hold To select an area of adjacent samples, left-click the first sample you want
to select and, holding down the mouse button, drag the mouse pointer to
the last sample. You can deselect a group of adjacent samples in the same
way.

4.3 Q-Rex workspace
The Q-Rex Software workspace is divided into the following elements:
Menu
Main toolbar
Environment-specific working area (Environments)
Button bar
Status bar
4.4 General elements

The Q-Rex Software uses a modern, task-focused GUI design to make interacting with the software
intuitive. General elements of the user interface are:
Menu
Main toolbar
Button bar
Status bar

4.4.1 Menu
The Main menu has two sub-menus: File and Help.
File menu
Menu item Description
Open experiment Opens an experiment from an existing
file.
Create experiment Creates a new experiment without
data.
Create experiment Creates a new experiment based on a
from template saved template with file extension
*.qret. The new experiment is
populated with experiment data from
the template file (except from sample
information).
Save Saves the current experiment. If you
have not specified a file name, you
will be prompted to do so.
Save as Saves the current experiment with a
new file name.
Save as template Saves the current experiment as a
template.
Import Rex/Ret Imports a *.rex or *.ret file that has
File been created with the Rotor-Gene Q
Software.
A new experiment includes the content
of the .rex file that can be mapped to
a Q-Rex experiment. Save the new
experiment with Save as to keep the
new Q-Rex format.
Note: Some components of the old
files are not supported in the Q-Rex

Software and cannot be imported,
e.g., the pages function.
Log in Allows you to log in as a user.
This option is available only after
starting the application or after logging
out.
Log out Logs you out as a user. The login
screen appears.
Change password Changes your current password. A
dialog appears where you can enter
your current and new passwords.
Service login This login is for QIAGEN service
technicians only.
Exit Closes the application.
Help menu
Menu item Description
Help Opens the help function.
About Opens a dialog with the copyright

notice and the version number of the
software.
4.4.2 Main toolbar
The Main toolbar consists of two areas: Environment icons and Instrument icons

Environment icons
Switch between environments by clicking the corresponding icon in the Main toolbar. The icon of
the active environment is highlighted.
Environment Description
Access My Q-Rex to create or open experiments and templates.
Enter the Experiments environment to set up and analyze experiments.
Find the System Audit Trail and Support Package functions in the Service
environment.
Manage settings, cyclers and user accounts in the Configuration

environment.
Instrument icons
The instrument icon on the right of the Main toolbar is used to inspect the connection to a cycler,
the status of a cycler run and any maintenance issues.
Symbol Description Action

Instrument is connected The software automatically detects when a
cycler is connected and reports the instrument
serial number or name, if the connected cycler
is registered.
A run can be started.
Instrument not connected Make sure the cycler is switched on prior to

starting a run.
Note: The software may take some time to

establish a connection.
Note: The icon is not active.

Instrument is connected and When you click the icon during a run, the Run
running step of the experiment is displayed.
To return to setting up another experiment,

click the corresponding tab visible under the
Main toolbar.
Run finished Clicking the icon displays the finished run of the
experiment.
To return to setting up another experiment,

click the corresponding tab visible under the
Main toolbar.
An error occurred during the Click the icon to display the run step of the
run experiment and the error message.

4.4.3 Button bar
The Button bar is located at the bottom of the screen and displays buttons specific to the active screen
in a given environment. Generally, you will find the Save experiment button here.

4.4.4 Status bar
The Status bar is always visible and displays information about the active user session.
Date Shows the current date.

User name Shows first and last name of the logged in user.
Log out button Logs out the current user. A warning appears if data in an experiment
have not been saved.
4.5 Environments
Switch between the four environments of the Q-Rex Software by clicking the corresponding icon in
the main toolbar. The icon of the active environment is highlighted.
Environment Description
Access My Q-Rex to create or open experiments and templates.
Enter the Experiments environment to set up and analyze experiments.
Find the System Audit Trail and Support Package functions in the Service
environment.
Manage settings, cyclers and user accounts in the Configuration

environment.

4.5.1 My Q-Rex
The My Q-Rex environment bundles all tasks for creating and opening both experiments and
templates.
The My Q-Rex environment is divided into 3 fields:
Create Experiment
Use Create Experiment on the left side of the My Q-Rex environment to create a new experiment,
with or without support of a wizard. Wizards to set up an experiment in the Q-Rex Software are
available through plug-ins that are loaded upon starting up the application. By default, the Q-Rex
Software comes with two wizards, the QIAGEN Kit Wizard and the QIAgility Wizard.
Additional wizards may be added in the future. Icons for these would appear next to the two wizards
already included in the Q-Rex Software.
Favorite templates
In Favorite Templates, the middle section of the My Q-Rex environment, you can create
experiments based on previously saved templates. All data fields in the new experiment are
populated with existing data from the template. For details, see Create an experiment using a
template.

All favorite templates are listed below the headline. For information on how to add templates to the
list, see Manage favorite templates.
Recent Experiments
You can access recently used experiments under Recent Experiments on the right side of the My
Q-Rex environment. Open and edit a recent experiment or use it to transfer its data to a new
experiment. For details, refer to View recent experiments or Create an experiment from an existing
experiment, respectively.
All recently saved experiments are listed below the headline.
4.5.2 Experiments
The Experiment environment is where experiments are set up, executed (run) and analyzed, where
reports are created and more. To work on an experiment, create or open it in the My Q-Rex
environment.
Changes made to an experiment are made permanent upon saving the experiment. To start a run,
the corresponding experiment must be saved.
A maximum of 8 experiments can be open at any given time in the Q-Rex Software. Attempting to
open more than 8 experiments triggers a warning message.
The screen of the experiment environment has 4 main sections: the Experiment tab list, the Step
Marker, the Main panel and the Button bar.
Experiment tab list
Tabs for each open experiment are displayed at the top of the Experiments environment. If an
experiment name is too long to be displayed on the tab, the displayed name is truncated followed by
ellipses. Place the mouse pointer over the tab for a few seconds to display the full experiment name
in a tooltip.
Modifying any step in an experiment causes an asterisk (*) to appear next to the experiment name in
the tab to indicate that changes have not yet been saved. The asterisk disappears when you save the
experiment.
Clicking in the tab closes the experiment. If the experiment contains unsaved changes, you will
be asked if the experiment should be closed (the unsaved changes will be lost in this case).
The icon on the right is a shortcut to open an experiment. Clicking it displays a dialog where
you can select the desired file.
is a shortcut to open a new experiment. Clicking it creates an empty new experiment.

Step Marker
The Step Marker guides you through an experiment and allows you to navigate between different
aspects of an experiment. Each experiment step is associated with content in the main panel. To
switch to another step, click the corresponding step in the Step Marker.
Note: We recommend working through experiment steps in sequence, however, you can navigate
between any two steps at any time (assumed the destination step is active).
Note: A step appears yellow when it contains required input fields with wrong or missing data. If any
step in an experiment is yellow, you cannot start the cycler run.
Main panel
All experiment-specific information is displayed in the Main panel, and all changes to the
experiment are done in this panel. The content depends on the step selected in the Step Marker.
Button bar
The Button bar at the bottom of the Experiments environment displays buttons for experiment
functions that are not related to a specific step, such as Save experiment and Start run.
The Start run button is enabled only if all preconditions for a new run are met (e.g., all required
values have been defined during setup) and if the experiment has not already been run. For details
on how to start a run, see Start a run.

Selecting Save experiment saves the active experiment. If the experiment has not been named, you
are prompted to enter a name for the experiment. If the experiment already has a name (for
instance if an existing experiment was opened), the existing file will be replaced.
Clicking the small arrow to the right of Save experiment displays a menu with additional choices.
Save experiment as... or Save template as... opens a dialog to enter a new name for the
experiment or template and then saves the file under the entered name.
4.5.3 Service
The Service environment bundles tasks for troubleshooting and facilitates communicating with
QIAGEN Technical Service when you need assistance.
This environment is organized into 2 functions, accessed by clicking the respective tab under the
Main toolbar:
Tab Description
System Audit Trail Allows you to view the system audit trail. This tab is only available to the user
role Administrator.
Support Package Creates a support package to assist communicating with QIAGEN Technical
Services in case you have a problem. Review the Troubleshooting for further
assistance.

4.5.4 Configuration
The Configuration environment bundles all tasks to customize the Q-Rex Software to meet your
needs. You can define application settings, as well as manage users and cyclers.
This environment is organized into 3 configuration functions, accessed by clicking the respective tab
under the Main toolbar:
Tab Description
Settings Define general settings like language and concentration number
format, customize reports, select a password policy, set up mail
notifications, etc.
See customize settings for more information.
User management Manage user accounts, such as creating or modifying users and their
roles, as well as activating and deactivating user accounts.
See manage users for more information.
Cycler management Manage cyclers connected to the Q-Rex Software, such as adding or
removing cyclers, and recording their last verification date.
Refer to manage cyclers for more information.

5 Manage experiments and templates
Two fields of the My Q-Rex environment allow you to:
Manage favorite templates
View recent experiments
5.1 Manage favorite templates

Each user can maintain a customized list of templates in the Favorite templates field.
The field is initially empty. Templates can be added or removed from the list, and new experiments
can be created based on these templates (see Create an experiment from a template). Additionally,
you can create experiments based on templates that are not contained in the list of favorite
templates.

You can place up to 11 files in the list of favorite templates. Once you have reached this number,
remove a template from the list to add another.
Template names that are too long to display within the available space are truncated and followed by
ellipses. Place the mouse pointer over the template name for a few seconds to display the full name
in a tooltip.
Adding a template to the list of favorite templates
Click to add a template to the list. This opens a dialog where you can select a template file to
be added.
Removing a template from the list of favorite templates
1. Position the mouse pointer over a favorite template in the list to reveal an icon.
2. Click the icon to open a drop-down menu with two entries.

3. Select Remove template from favorites to remove the template from the list.
Removing a template from the list does not delete or modify the template file.
Note: To open *.rex or *.ret files, go to the File menu and choose Import Rex/Ret File.

5.2 View recent experiments
An experiment that is recently run or saved is added to the Recent Experiments list.
A maximum of 11 experiments appear in this list. Once this number is reached, the oldest entry of
the list is automatically removed when a new entry is added.
Experiment names that are too long to display within the available space are truncated and followed
by ellipses. Place the mouse pointer over the experiment name for a few seconds to display the full
name in a tooltip.
Removing an experiment from the list of recent experiments
1. Position the mouse pointer over an experiment in the list to reveal a drop-down menu icon.
2. Clicking the icon displays a menu with 3 items:
3. Select Remove experiment from recent to remove the experiment from the list. Removing an
experiment from the list does not delete or modify the file.
Opening an experiment from the list of recent experiments

Either click the experiment name or open the sub-menu as described above and select Open.
Note: To open *.rex or *.ret files, go to the File menu and choose Import Rex/Ret File.
Creating an experiment from a file in the recent experiments list
1. Position the mouse pointer over the desired experiment to reveal the drop-down menu icon and
click.
2. Select Create experiment from recent to set up a new experiment, based on the selected
one.
The new experiment contains the information stored in the selected experiment.
3. The new experiment can be executed directly by clicking Start Run.

Set up an experiment
6 Set up an experiment
You can set up an experiment by defining a run profile and sample layout, as described in Set up a
new experiment. You can also set up an experiment based on a QIAgility results file or for a specific
QIAGEN kit. For details, see Set up an experiment via wizard.
6.1 Set up a new experiment

The standard procedure to set up a new experiment involves the following steps:
Create an experiment
Define general information
Define the run profile
Define the sample layout
6.1.1 Create an experiment
A new experiment can be created in 3 different ways:

From a blank experiment
From an existing experiment
From a template
6.1.1.1 Create a blank experiment
1. Enter the My Q-Rex environment by clicking the My Q-Rex symbol in the Main toolbar.
2. Click New experiment in the Create Experiment field.

3. A blank experiment opens as a new tab in the Experiments environment. In the Step Marker,
General is preselected:
Note: You can also create a new experiment directly in the Experiments environment. Click
the icon located in the upper right corner of the screen.
4. Define basic information about the experiment under each of the steps in the Step Marker.
Note: The Run button remains inactive until all required information is entered in the Run
Profile step.
Note: Some of the described methods and functionalities may not apply to future plug-ins.

Step in Step Marker Available definitions
General (1) Enter basic information about the experiment, including:
(optional)
Comment
Experiment operator
Creation date
Assay setup file or worklist
Template
Kit information
For details, see Define general information.
Run profile (2) Define basic settings for a run with the options:
Import Run Profile
Rotor type
Reaction volume
Lay out the thermal profile by:
Entering cycling conditions
Adding acquisitions
Editing channels for acquisitions
For details, see Define the run profile.
Sample layout (3) Define samples:
Set line styles and colors for amplification curves
Name samples
Assign sample types
Set concentration values and unit, if applicable
Enter information about samples:
Define targets
Define sample groups
Configure views
Set concentration number format
Assign well names to tubes
Manually define auto-gain tubes
For details, see Define the sample layout.

6.1.1.2 Create an experiment using a template
To create an experiment based on an available template, click the template listed under Favorite
Templates.
Alternatively, open the drop-down menu associated with the template and select Create experiment
from template.
To work with a template not in the Favorite Templates list, click Create from other template and
select the template file in the resulting dialog.
A new experiment opens, with all settings stored in the template file.

6.1.1.3 Create an experiment based on an existing experiment
To create an experiment based on a previously executed experiment, open the drop-down menu
associated with the experiment and select Create experiment from experiment.
Note: The Recent Experiments list is initially empty and then populated automatically with the 11
experiments that were last saved or run. For more information, see View recent experiments.
A new experiment is created with the following settings from the chosen experiment:
General experiment information (comments, kit information, template name)
Rotor type and reaction volume
Thermal profile
Acquisitions
Sample information (names, colors, line styles, group and target information, sample types, units,
concentrations)
Analysis settings
6.1.2 Define general information
If not active, switch to the General step by clicking General (1) in the Step Marker.

The screen of the General step is arranged into 4 areas, where you can enter information about the
experiment that should appear in the report.
Note: All data entered here is informational only. The data do not influence how an experiment is
created, executed or analyzed.

Comment (1) Enter relevant information about the experiment in the comment field.
Experiment By default, this field contains the user name of the operator currently logged
operator (2) into the Q-Rex software. Edit the operator if necessary.
Creation date These are read-only fields that are prefilled if information is available.
Assay setup file
Note: If the experiment was created from a setup file or worklist, the name of
or worklist
the file or worklist is displayed. If the experiment was created from a
Template (3)
template, the name of the file is displayed.
Kit information This table summarizes specifications of QIAGEN kits for the experiment.
(4) Click Add QIAGEN kit to add kit information (see Add kit information), which
will then appear in the table.
The Lot Number column is editable. The column Product Number cannot
be edited and is filled only if a QIAGEN kit was selected from the library.
The Kit Expiry Date column can be set to any valid date.
Click to delete a kit from the list.

Note: if not using QIAGEN kits, use the Comment field to save relevant
information. Information entered in the Comment field appears on the
experiment report.

6.1.2.1 Add kit information
Click Add QIAGEN Kit to enter the product number, expiration date and lot number of a kit.
A dialog opens where information about one or more QIAGEN kits can be entered.
To select a kit from the predefined list (1):
1. Scroll the QIAGEN Kits list to find the needed kit. The list can be filtered by application, start
material, detection chemistry, kit name or catalog/product number.
Combine filter options to narrow down the list.
2. Choose a kit from the list and confirm by clicking Select. Selected kit(s) are displayed in the
lower part of the window.
3. Enter Lot Number and Kit Expiry Date if desired.

To scan a kit bar code (2):
1. Click Scan kit barcode to open the input dialog.
2. Either scan the bar code or type the bar code number into the Kit barcode field. Product
number, kit expiry date and kit lot number are automatically added to their respective fields.
3. Click OK to confirm your kit selection. All selected kits will be listed in the Kit Information
Table.
Note: Lot number and expiration date of a kit can be changed in the Kit Information Table.
6.1.3 Define the run profile
If not active, switch to the Run Profile step by clicking Run Profile (1) in the Step Marker.

The screen for the Run Profile step is divided into three areas: Basic profile settings (1), Thermal
profile (2) and Acquisitions (3). Start by defining the basic profile settings and then continue with the
thermal profile definition. Finally, add an acquisition and adjust all related settings.
6.1.3.1 Define basic profile settings
Select a Rotor Type from the drop down menu (1) and enter a Reaction Volume (2).
You may also import a previously defined run profile by clicking Import Run Profile (3).

Information about the permitted and recommended reaction volume range are displayed next to the
reaction volume entry field. If the entered reaction volume is not within the recommended range, a
warning symbol ( ) appears. If the entered volume is not within the permitted range, the field is
highlighted yellow and marked as invalid. The entered value must be corrected before the run can
be started.
Note: The first time you select a rotor type, the reaction volume field is populated with a default
reaction volume corresponding to the recommended volume. This volume should be adjusted to
meet specific experimental conditions.
Import a run profile
You can import a run profile from another Q-Rex Software experiment or template. Information like
rotor type, thermal profile and acquisitions are imported and overwrite all settings, both default and
those which may have already been defined. File types available for import are .qret and .qrex files.
6.1.3.2 Define the thermal profile
In the Thermal Profile editor, you can define a thermal profile by dragging profile phases from a
Toolbox (1) onto the Profile area (2). The Profile area is linked to the Run preview (3), which
displays the profile over the complete run and the estimated run time. The profile area is also linked
to the Acquisitions table, as long as the currently selected profile phase is highlighted in the Run
preview.

One or more profile phases can be selected from the toolbox to the right of the profile area to
design a cycling profile:
Hold Hold at a specific temperature
(see Define a hold phase)
2-Step Cycling Define 2 temperatures, hold times, number of cycles and

acquisitions
(see Define a cycling phase)
3-Step Cycling Define 3 temperatures, hold times, number of cycles and

acquisitions (see Define a cycling phase)
Melt Define an increasing temperature range and an acquisition for melt

experiments (see Define a melt phase)
HRM Define an increasing temperature range and an acquisition for

HRM experiments (see Define an HRM phase)
Hybridization Define a decreasing temperature range and an acquisition for melt

experiments (see Define a hybridization phase)
HRM Define a decreasing temperature range and an acquisition for HRM

Hybridization experiments (see Define an HRM hybridization phase)
To add a phase to a profile, drag the corresponding icon into the Profile area. For example, to add
a Hold phase, click the Hold icon and hold the mouse button down (1 ), then drag the icon into the
Profile area (2 ) and release the mouse button. The Hold phase becomes a step of the profile (3 )
and appears in the Run preview.
You can also change the position of an implemented phase by drag and drop. Click and hold the
header of the profile phase, move it to the desired position in the profile and then release.
Profile phases can be deleted by clicking X in the phase header and confirming the resulting
message.

Newly inserted profile phases include default values that should be adjusted to meet experimental
setup requirements:
1. To change a temperature, do one of the following:

Roll the mouse pointer over the temperature you wish to change. A field with the current
temperature becomes visible. Click the temperature field and edit the value as needed.
Roll the mouse pointer over the temperature bar of the relevant step. The mouse pointer
changes to a double-headed arrow. Click and hold the bar, and move it up or down to adjust
the temperature. As the bar is adjusted, the changing temperature is displayed and the adjusted
profile is reflected in the run preview.
2. To adjust a hold time, roll the mouse pointer over the hold time you wish to change. A field with
the current time becomes visible. Delete the field contents and enter a new hold time for the
step. The time entry must be formatted as hh:mm:ss.

Define a hold phase
A hold phase instructs the Rotor-Gene Q to remain at a specified temperature for a defined
duration.
Note: Data acquisition is not possible during a Hold phase.
To add a hold phase to a thermal profile:
1. Drag the Hold icon from the Toolbox and drop it into the Profile area.
2. Enter the temperature for the Hold (see Define the thermal profile).
3. Set the time interval for which the temperature should remain constant (see Define the thermal
profile).
Note: For details about technical specifications of the Rotor-Gene Q, refer to the Rotor-Ge ne Q Use r
M anual.
Define a cycling phase
A PCR cycles multiple times through user-defined temperature changes that enable denaturation and
enzymatic amplification of DNA. Each cycle is defined by cycling phases that define the temperature
of the reaction and the length of time spent at that temperature.
A 2-step Cycling phase consists of 2 cycling steps.

A 3-step Cycling phase consists of 3 cycling steps.
Each step includes default values that should be adjusted to meet specific experimental setup
requirements.
To set up a cycling phase:
1. Drag the 2-step Cycling or 3-step Cycling icon from the Toolbox and drop it into
the Profile area.
2. In the Cycles entry field, enter the number of times that the cycling phase should be
performed.
3. Add an acquisition to 1 or more cycling steps (see Add an acquisition).
4. Optional: you can further adjust the cycling phase in the following ways:
Modify the cycling phase by adding or removing a cycling step (see Add or remove a cycling
step)
Adjust the temperature for each cycle (e.g., add a touchdown/up to a cycle). For details, see
Vary hold temperature per cycle.
Adjust the hold time for each cycle (e.g., add an extended or shortened hold time). For
details, see Vary hold time per cycle.

Advanced: Add/remove a cycling step
A cycling step is a portion of a cycling phase. You can add or remove cycling steps to a defined 2-
step or 3-step Cycling phase.
To add a step to a defined cycling phase:
1. Select a step and right-click to open the context menu.
2. Select Add step to the left (1) or Add step to the right (2) to insert a new cycling step before
or after the selected step.
3. Adjust the time and temperature of the newly inserted step (see Define the thermal profile).
To remove a step from a cycling phase:
1. Select the step to be deleted and right-click to open the context menu.
2. Select Remove step.
Advanced: Vary hold temperature per cycle
The temperature of a step can be raised or lowered over a defined number of cycles using the
Touchdown and Touchup option.
The Touchdown function is used to decrease the hold temperature of a given step over a defined
number of cycles. Conversely, the Touchup function is used to increase the hold temperature of a
step over a defined number of cycles.

To add one of these options to a cycling phase:
1. Select the step you wish to modify and right-click to open the context menu.
2. Select Use touchdown/up (1) to open the options window.
3. Select Touchdown or Touchup.

4. Indicate the desired temperature change and the number of cycles for the touchdown or
touchup and click OK.
Note: Temperatures should remain within the recommended range of 35-99°C.
Start hold temp. displays the hold temperature at which the touchdown or touchup will start.

The End hold temp. shows the hold temperature that will be used for the remaining cycles of
the phase after touchdown or touchup. Both fields are read-only.
The modified cycling step will be labeled in the thermal profile with an arrow corresponding to
the modification.
A downward arrow next to the temperature field indicates touchdown.
An upward arrow next to the temperature field indicates touchup.
To remove a Touchdown or Touchup:
1. Select the step to be modified and right-click to open the context menu.
2. The context menu shows a tick mark next to Use touchdown/up.
3. Click the tick mark to remove the function from the cycling step. The cycling step will no longer
display a touchdown or touchup icon.
M anual.

Advanced: Vary hold time per cycle
You can increase or decrease the hold time of a step over a defined number of cycles with the
Extend/Shorten hold time option.
To extend or shorten a cycling step over a defined number of cycles:
2. Select Extend/shorten hold time (1) to open the options window.
3. Select Extend hold time or Shorten hold time.

4. Define the change in time and the number of cycles for the hold time extension or shortening
and click OK.

Start hold time displays the length of the first cycle of the extension or shortening. End hold
time shows the hold time that will be used for the remaining cycles of the phase after the
extension or shortening. Both fields are read-only.
Extend or shorten hold time icons will be displayed next to the time field.
An upward arrow next to the time field indicates an extended hold time.
A downward arrow next to the time field indicates a shortened hold

time.
To remove an extended or shortened hold time:
2. The context menu shows a tick mark next to Extend/shorten hold time.
3. Click the tick mark to remove the function from the cycling step. The cycling step will no longer
display an extend or shorten time icon.
M anual.

Define a melt phase
A melt phase is used as a quality check after a PCR with intercalating dyes or to determine the
melting point of a sample. The temperature is steadily increased so that amplified products dissociate
at a certain temperature, depending on their length and sequence composition.
A melt phase is a ramp between 2 temperatures, from low to high. The recommended temperature
range is 35–99ºC.
A melt phase includes the option to perform gain optimization just before the melt begins. For
details, see Advanced: Adjust gain settings.
To set up a melt phase:
1. Define a cycling phase with an acquisition (see Add an acquisition) on the same channel as
planned for the melt phase.
Note: A cycling phase with a defined acquisition must precede a melt phase. Otherwise, no
acquisition channel can be chosen.
2. Drag a Melt icon into the Profile area, to the right of the cycling phase.
Note: A newly inserted melt phase includes default values that should be adjusted to meet
experimental setup requirements.
3. Specify the start temperature (1) and the end temperature (2) for the melt phase. Roll the
mouse pointer over the values displayed in the Profile area and click the entry field that
appears. Enter the desired value.

4. Define the temperature increments (3) and the length of time for which each increment should
be held (4). Roll the mouse pointer over the values displayed in the Profile area and click the
entry field that appears. Enter the desired value.
5. Add one or more acquisitions for the melt phase by clicking (5 ). The acquisition channel
must match an acquisition defined in the preceding cycling phase. For more information, see
Add an acquisition.
M anual.
Define a hybridization phase
A hybridization phase is used to hybridize nucleic acids. The reaction temperature is steadily
decreased so that single-stranded nucleic acids associate to form double-stranded molecules at a
certain temperature, depending on their length and sequence composition. The hybridization curve
shows an increase in fluorescence from intercalating dyes, which peaks at the association time point.
A Hybridization is a ramp between 2 temperatures, from high to a low.
To set up a hybridization phase:
1. Define a cycling phase with an acquisition (see Add an acquisition) on the same channel as
planned for the hybridization phase.
Note: A cycling phase with a defined acquisition must precede a hybridization phase.
Otherwise, no acquisition channel can be chosen.

2. Drag a Hybridization icon into the Profile area, to the right of the cycling phase.
Note: A newly inserted hybridization phase includes default values that should be adjusted to
meet experimental setup requirements.
3. Specify the start temperature (1 ) and the end temperature (2 ) for the hybridization phase. Roll
the mouse pointer over the values displayed in the Profile area and click the entry field that
appears. Enter the desired value.
4. Adjust the temperature declines (3 ) and the length of time for which each decline should be
held (4 ). Roll the mouse pointer over the values displayed in the Profile area and click the
5. Add one or more acquisitions for the hybridization phase by clicking (5). The acquisition
channel must match an acquisition defined in the preceding cycling phase. For more
information, see Add an acquisition.
M anual.
Define an HRM phase
High resolution melt (HRM) analysis is used to characterize double-stranded DNA samples based on
their dissociation (melting) behavior. HRM is similar to classical melting curve analysis, but affords
more accuracy with smaller temperature change steps and provides more information for a wider
range of applications. Samples can be discriminated according to sequence, length, GC content or
strand complementarity down to single base-pair changes.
HRM analysis can only be performed on instruments with installed HRM hardware. Fluorescence
signals must be collected with extremely high optical and thermal precision. Thus, data are acquired
using specialized HRM sources and detectors.
The target sequence must be amplified to a high copy number before performing HRM analysis. This
is usually done by PCR in the presence of a dsDNA intercalating fluorescent dye.
An HRM phase includes the option to perform gain optimization just before the melt begins. For
details, see Advanced: Adjust gain settings.
Note: An HRM phase can be analyzed only with the corresponding plug-in.

To set up an HRM phase:
1. Define a cycling phase with an acquisition in the Green channel (see Add an acquisition).
Note: A cycling phase with an acquisition in the Green channel must precede an HRM phase.
The HRM channel is not available under other setups for the cycling phase.
2. Drag an HRM icon into the Profile area, to the right of the cycling phase.
Note: A newly inserted HRM phase includes default values that should be adjusted to meet
experimental setup requirements.
3. Specify the start temperature (1) and end temperature (2) for the HRM phase. Roll the mouse
pointer over the values displayed in the Profile area and click the entry field that appears.
Enter the desired value.
4. Adjust the temperature increments (3) and the length of time for which each increment should
be held (4). Roll the mouse pointer over the values displayed in the Profile area and click the
5. Add one or more acquisitions for the HRM phase by clicking (5). For more information,
see Add an acquisition.
Note: When the HRM channel is selected for acquisitions, no other channel can be used for
additional acquisitions.
M anual.

Define an HRM hybridization phase
A hybridization phase is used to hybridize nucleic acids. The reaction temperature is steadily
decreased so that single-stranded nucleic acids associate to form double-stranded molecules at a
certain temperature, depending on length and sequence composition. The hybridization curve shows
an increase in fluorescence from intercalating dyes, which peaks at the association time point.
An HRM Hybridization is a ramp in small steps between 2 temperatures, from high to low.
To set up an HRM hybridization phase:
1. Define a cycling phase with an acquisition in the Green channel.

Note: A cycling phase with an acquisition in the Green channel must precede an HRM
hybridization phase. The HRM channel is not available under other setups for the cycling phase
2. Drag an HRM Hybridization icon into the Profile area, to the right of the cycling phase.
Note: A newly inserted HRM hybridization phase includes default values that should be adjusted
to meet experimental setup requirements.
3. Specify the start temperature (1 ) and the end temperature (2 ) for the HRM hybridization phase.
Roll the mouse pointer over the values displayed in the Profile area and click the entry field
that appears. Enter the desired value.

4. Adjust the temperature declines (3 ) and the length of time for which each decline should be
held (4 ). Roll the mouse pointer over the values displayed in the Profile area and click the
5. Add one or more acquisitions to the HRM hybridization phase by clicking (5). For more
information, see Add an acquisition.
Note: When the HRM channel is selected for acquisitions, no other channel can be used for
additional acquisitions.
M anual.
6.1.3.3 Add an acquisition
Data can be acquired at almost every step of a thermal profile. The only exception is a hold phase,
which cannot be combined with a data acquisition.
Data acquisition for a selected thermal profile step can be set up in two ways: in the Thermal Profile
editor or in the Acquisitions Table.
To add acquisitions in the Thermal Profile editor:
1. Click the camera icon at the bottom of a profile step.

All QIAGEN channels, including examples of fluorophores that can be detected in each
channel, are displayed. These are default channels and cannot be modified.

2. Click the check box next to the desired channel for the acquisition and confirm with OK. More
than one acquisition can be added to the step by selecting more than one channel.
Note: Only one acquisition per channel for a given step can be defined using this method. To
add multiple acquisitions in the same channel, use the Acquisitions Table (see below).
Upon selecting one or more channels, the camera icon in the Profile area changes to a dark
background and adjacent color bars indicate which channels you selected (1). Additionally, a
blue dot appears at the corresponding step in the Run preview (2) and the Acquisitions
Table is populated with corresponding information (3).
The Acquisitions table summarizes the acquisitions for an experiment, including chosen channels
and gain settings. The table is synchronized with the Thermal Profile editor and displays only the
acquisitions of a selected profile step. If no profile step is selected, the table appears empty.
To add acquisitions in the Acquisitions Table:
1. Select a profile phase and click Add Acquisition below the Acquisitions Table.
All QIAGEN channels, including examples of fluorophores that can be detected in each
channel, are displayed. These are default channels and cannot be modified.
Note: You can add multiple acquisitions in the same channel via the Acquisitions Table. Such
a setup is useful when performing a multiassay run in which different gain settings are defined.
2. Click Edit Channels to work with advanced options, such as defining custom channels with a
specific combination of excitation and emission wavelengths, adding or removing experiment
channels, or moving experiment channels to the list of custom channels.

3. Click the duplicate or remove icons located in the Actions column of the
Acquisitions Table to duplicate or delete acquisitions.
4. Use the options in the Gain method column to adjust gain settings.
Advanced: Define custom channels
You can create new channels and define the combination of excitation and emission wavelengths
using the Custom Channels feature.
To set up a custom channel:
1. Click the Run Profile step of the experiment in the Step Marker.
2. Click in the Acquisitions table.
3. Click Add custom channel (1) for a new row in the Custom Channels area.

4. Enter a unique name in the Channel Name entry field (2 ) and choose the Excitation (3 ) and
Emission (4 ) wavelengths from the respective drop-down menus. This information is required.
Excitation specifies the wavelength of the source LED. Possible wavelengths are:
Emission specifies the detection wavelength and filter type (nm=band pass, hp=high pass).
Possible wavelengths are:
5. Optional: Change the displayed color for the acquisition channel. This will be shown, for
example, next to the camera icon in the Profile area. Use the Example of fluorophores entry
field to record dyes that are compatible with the specifications of the created channel.
6. Click OK to confirm your entries. The channel is saved and made available to all users as a
custom channel.
Note: If the custom channel is saved in a template or has been used in an experiment, it will
appear as an Experiment Channel when opened on another computer. Experiment
channels are not editable. To edit one, first transfer the channel to the custom channels by
clicking the arrow icon in the Experiment Channels table.

Advanced: Adjust gain settings
Gain optimization ensures that all data are collected within the dynamic range of the detector. If the
gain is too low, the relevant signal is lost in background noise. If the gain is too high, all signals will
appear off-scale (saturated).
Gain settings are defined per acquisition and are set on Auto-gain by default.
Note: When running a reaction for the first time, we recommend preparing a test sample containing
all reaction components, placing it in the Rotor-Gene Q and using gain optimization to determine the
best gain setting. If the gain results in a poor signal, the target sample ranges should be increased. If
the gain results in a signal that is saturated, then the target sample ranges should be decreased.
To adjust gain settings:

1. Click the cell in the Gain Method column of the Acquisitions table corresponding to the
acquisition you wish to edit.
2. Choose your preferred gain method in the dialog that appears: Auto-gain or Fixed.
Auto-gain By default, Auto-gain is set based on the fluorescence of all filled tubes to
optimize the gain value. Auto-gain uses the median of all tubes.
As an advanced option, you can manually define which tubes should be used
to determine auto-gain in the Sample Layout step.
This gain method measures the fluorescence in one or more tubes specified
in the sample layout. If no targets are assigned, 1 tube is sufficient to
determine the gain. If different targets are assigned, select at least 1 tube for
each target group. The final gain will be the lowest of the individual gain
values.
For more details, see define the auto-gain tubes manually.
Fixed Fixed allows you to define a fixed gain value for the selected acquisition.

3. If you select Auto-gain, adjust the Gain method (1 ) and Auto-gain settings (2 ) to meet
experimental setup requirements. Define the minimum and maximum fluorescence ranges to
use during gain optimization. Check, and if necessary, change the Generic Settings (3).
Note: The Generic Settings will be used for all cycling acquisitions in a thermal profile.
4. If you select Fixed, define the gain value.

Melt and HRM analysis also include the option to perform gain optimization just before melting
begins.
To define gain adjustment for a Melt or HRM phase:
1. Click the Gain Method column in the Acquisitions table. Click the check box if you want to
perform an auto-gain optimization before melt or HRM analysis (1 ).
2. Adjust the Maximum fluorescence value (2 ) if necessary.

The software will search for the optimal gain setting so that the measured fluorescence value
just before the melt phase is as high as possible, but not higher than this value.

6.1.4 Define a sample layout
Specifications about samples and targets, as well as how these are displayed, are defined in the
Sample Layout step of the Experiments environment.
Click the Sample Layout step in the Step Marker. The Sample Table is visible in the main area.
Sample information is added and edited in the table. A second area, the Drawer, is usually closed
when you first open the Sample Layout step. Click the Drawer icon in the top right corner of the
screen to open or close the Drawer. In the Drawer you can define additional sample
information.
When you first open the Sample Layout step in a new experiment, all cells in the Type column
display Not in use and are highlighted in yellow. You must include at least 1 sample with Type
defined as something other than Not in use to start a run.
In the Sample Layout step, you can:

Define sample details
Define targets
Define sample groups
Configure concentration number format
Assign well names to tubes
Import sample information

6.1.4.1 Define sample details
The Sample table in the Sample Layout step includes several columns to define information about
the samples of an experiment.
Column Label Description
Tube Displays the position of the tube in the rotor.
Color Indicates the color used to display the associated fluorescence data.
Style Indicates the line style used to display the associated fluorescence data.
Name Allows you to enter a sample name.
Type Defines the type of sample (Not in use, Sample, PC, NTC, NC, Standard).
Acquisition Indicates the channel and phase in which data are acquired.
Target Displays the name of the acquisition or target, if defined.
Conc. Allows you to enter a given concentration. You can also configure the number
format used.
Unit Indicates the concentration unit used (None, copies/µl, copies/ml, copies/
reaction, %, IU/µl, IU/ml, ng/µl, µg/µl, ng/reaction, pg/µl, %mut, µM).
Depending on settings, the following additional columns may appear in the table.
Well Defines the position of the tube as a well name.
Sample Groups If defined, displays the sample group(s) to which a sample has been
assigned. You can assign a sample to multiple groups.

To define sample Type, select one or more samples (see Selecting samples), right-click the Type
column and choose a sample type from the context menu. The selected type will be applied to all
highlighted samples as well as cells with the same sample name.
To define Color and line Style, select one or more samples (see Selecting samples), right-click the
Color or Style columns and choose a color or line style from the respective context menu. The
selected color or style will be applied to all highlighted samples.

To enter sample names, you can:
Click a cell in the Name column and enter the sample name in the active cell.
Right-click the cell to open the context menu and use cut, delete, copy and paste functions.
Select one or more samples (see Selecting samples) and paste a name copied to the clipboard
using Ctrl+V.
Import sample information.
6.1.4.2 Define targets
Define specific targets for an experiment in the Drawer of the Sample Layout step. If not open,
click the Drawer icon in the upper right corner of the screen.
Check the Define Targets box and enter a name in the Target column.
You can also choose a target type from a drop-down menu in the Type column. The target types
Test, IC (internal control) and RG (reference gene) are available in the Q-Rex Software.
Additional target types may be available with future plug-ins.

To add 2 or more targets to the same acquisition, click Add Target and select the acquisition for
which an additional target is needed.
Once you have defined the targets, you can assign a target to a sample. Right-click the
corresponding cell in the Target column of the Sample table in the main area and select a target
from the context menu.
6.1.4.3 Define sample groups
Define sample groups for an experiment in the Drawer of the Sample Layout step. If not open,
click the Drawer icon in the upper right corner of the screen.
Check the Define Sample Groups box and enter a name for the sample group in the Name field.
To define more than one group, click Add Group to add rows to the table.
Once you have defined the sample groups, you can assign a sample to one or more groups. Right-
click the corresponding cell in the Sample Groups column of the Sample table in the main area
and select the group name(s) from the context menu.
Note: The Sample Groups column appears in the Sample table only if the Define Sample
Groups box is checked in the Drawer.

6.1.4.4 Configure concentration number format
To define the number format used to display concentration values in an experiment, open the
Drawer by clicking the Drawer icon in the upper right corner of the Sample Layout screen.
Under Concentration number format, choose Decimal format or Scientific notation. Also
define the number of decimal places from the drop-down menu.
A preview of your selected setting will appear.
6.1.4.5 Assign well names to tubes
To make it easier to convert the sample layout from a plate-based format (e.g., 96-well plate) to the
Rotor-Gene Q rotor-based format, you can assign well names to tube positions.
Open the Drawer by clicking the Drawer icon in the upper right corner of the Sample Layout
screen. Check the Assign well names to tubes box.
Click row by row to assigned well names by rows (A1, A2, A3, A4,... starting at rotor position 1).
Click column by column to assigned well names by columns (A1, B1, C1, D1,... starting at rotor
position 1).
6.1.4.6 Manually define auto-gain tubes
This gain method measures the fluorescence in one or more tubes specified in the sample layout. If
no targets are assigned, 1 tube is sufficient to determine the gain. If different targets are assigned,
select at least 1 tube for each target group. The final gain will be the lowest of the individual gain
values.

To manually define auto-gain tubes, open the Drawer by clicking the Drawer icon in the upper
right corner of the Sample Layout screen. Check the Manually define auto-gain tubes box.
Having checked this option, an Auto-G ain column appears in the S ample table:
Any tube in use (ie., sample type is anything other than Not in use ) can be selected individually to
include in the gain measurement.
6.1.4.7 Import sample information
You can import a sample file (*.smp) containing relevant information such as sample names, sample
types, line color and concentration values. This sample file can be saved from the Edit Samples
menu in the Rotor-Gene Q Software.
Sample files are always based on 1 rotor format (e.g. Rotor-Disc 72) and this information is saved
with the file. Thus, the tube positions defined in a Q-Rex Software experiment should match the
rotor format of the imported sample file. If you create an experiment for a 100-well rotor but load a
sample file for a 72-well Rotor-Disc, only 72 samples will be imported. The remaining samples in
the experiment will remain unchanged. Conversely, if a sample file contains information for more
tube positions than defined in a Q-Rex Software experiment, the information will be added to all
tubes defined in the experiment and you will receive a warning message indicating that the
remaining sample information from the file was not imported.
Note: If importing an *.smp file containing multiple pages, only information from the first page will
be imported.

To import sample information:
1. Click Import sample information at the bottom of the Drawer in the Sample Layout.
2. Click SMP file import to open a file browser and navigate to the location where the sample file
is saved. Click the file to import it.

6.2 Set up an experiment via wizard
Dedicated wizards allow you to set up a new experiment in the Q-Rex Software from a QIAgility
result file or from a QIAGEN kit.
To access these wizards, go to the My Q-Rex environment where you will find two icons in the
Create Experiment field.
Activates a wizard that helps use information from a previously
executed QIAgility Setup Manager run to create a new experiment,
including thermal profile assignment and sample layout definition.
Activates a wizard that helps you choose the thermal profile
template corresponding to the QIAGEN kit used in your experiment,
and to save the experiment as a template or start a run.
6.2.1 Set up an experiment from a QIAgility result file
Create a new experiment based on a QIAgility result file (.xml format, created with the QIAgility
Setup Manager) using the QIAgility Wizard.
1. Click QIAgility Wizard in the Create Experiment field of the My QRex environment.
The wizard opens in a new window.

2. To select a QIAgility result file, open the file browser (1) and navigate to the location where the
result file is saved.
A summary of the information in the run file will be displayed in the QIAgility run summary
field.
3. Select Next to open the Kit & Template step of the wizard.
The Kit information Table displays the imported kit information.
4. Select a template for the kit. If a QIAGEN kit was used and a corresponding template is
available in the template library, the template will be preselected in the Select QIAGEN
template file list. If more than one template is suitable, all templates will be listed.
If no template matches the kit information, choose a file by opening the file browser under Use
custom template.
A short template summary will be shown in the lower part of the window.
In case no template is available, you can define the thermal profile after the QIAgility wizard
has prepared the new experiment.
Note: Targets defined with the QIAgility can only be imported if a Q-Rex Software template
with matching acquisitions has been defined.

5. Select Next to open the Targets step of the wizard.
Target name, Fluorophore , Acquisition and Target type are displayed in a table
summarizing the target information stored in the QIAgility result file.
6. Assign targets to acquisitions. The Acquisition column contains a drop-down list of acquisitions
that match each target defined in the template, that is, all acquisitions with channels that match
the fluorophore of a target based on emitter and receptor wavelengths. If only one acquisition
matches a target, the acquisition is preselected.
If a Target type was not recognized by the Q-Rex Software, the target type Test is assigned.
7. Once all required information is defined, finalize the import by clicking the enabled Finish
button. You can save the experiment as a template or start a run.

6.2.2 Set up an experiment from a QIAGEN kit
Create a new experiment based on a QIAGEN kit using the QIAGEN Kit Wizard.
1. Click QIAGEN Kit in the Create Experiment field of the My Q-Rex environment.
The wizard opens in a new window with the QIAGEN Kits step.
2. Select a QIAGEN kit from the predefined list (option 1). Alternatively, you can scan the kit bar
code (option 2). For instructions, skip to step 5.
The list can be filtered by application, start material, detection chemistry, kit name or catalog/
product number.
Combine filter options to narrow down the list.
3. Confirm your selection by clicking Select. The selected kit is displayed in the lower part of the
wizard.
4. Enter Lot Number and Kit Expiry Date, if desired.

5. Alternatively, you can scan the kit barcode. Click Scan kit barcode to open the input dialog.
6. Either scan the bar code or type the bar code number into the Kit barcode field. Product
number, kit expiry date and kit lot number are automatically added to their respective fields.
Note: you can add multiple kits in the QIAGEN kit wizard.
7. Click Next to proceed to the Templates step.

8. The wizard identifies 1 or more templates that match the selected kit(s). Choose a template
from the drop-down list.
A Template Summary is displayed.
9. If the wizard could not find a matching template in the library or you wish to use a custom
template, check the Use different template box. Click Select to find the template file.
10. Optional: Check the Add to favorite templates box if you wish to add this template to the
Favorite Templates list in the My Q-Rex environment.

Run an experiment
7 Run an experiment
You can start a run after defining the Run Profile and Sample Layout of an experiment. This
section describes how to:
Start a run
View running experiment
View fluorescence curves during a run
View profile progress
Stop a run
7.1 Start a run

To start a run once you have defined all required information:
1. Click Start Run.

2. Save the experiment. Enter a file name and use the file browser to navigate to the location
where you want to save the file. Click OK.
3. A dialog opens, listing details about the run operator, the available cycler and an estimated run
time.
Note: If required, you can change the run operator.
4. Confirm that a locking ring is attached to your rotor by checking the corresponding box. You
cannot start a run until this is confirmed.

5. Click Start Run.
7.2 View a running experiment

You can view the progress of a run by clicking Run (1) in the Step Marker of the Experiments
environment.
On the screen of the Run step, you can follow fluorescence curves, a temperature graph and the
run progress, which are all updated in real-time. You can also see sample and run information.

The fluorescence plot at the top of the screen displays the fluorescence curves of all samples
activated in the tube selector on the right side of the screen. For more details, see View
fluorescence curves during run.
The temperature graph, with temperature on the vertical and time on the horizontal axis, displays
the course of the temperatures defined for the cycling. During a run, the graph does not reflect the
actual temperature measurement in the cycler. When the run is finished, this area displays the
temperature history of the run.
The run preview at the bottom of the screen shows the run progress and allows you to add cycles,
skip run phases and raise the end temperature of a melt or HRM phase. For more information on
using these options, see View profile progress.
The run information area summarizes general information about the run and shows the estimated
run time.
The tube selector lists information about the samples in the analysis and allows you to activate or
deactivate samples to be displayed in the fluorescence plot.
7.3 View fluorescence curves during a run
The fluorescence plot (1) in the Run step is continuously updated throughout a run. The displayed
curves are the fluorescence signals detected by the cycler for all activated samples. The horizontal
axis of the plot shows the total number of cycles defined in the run profile for a selected cycling
phase. The scale of the vertical axis adapts to always display the fluorescence curves with best
resolution.
Note: You cannot zoom in or out of the fluorescence plot.
Use the tube selector (2) on the right side of the screen to activate a sample so its fluorescence
curve is displayed in the plot. Clicking a tube activates it, highlighting it in dark blue. Click an
activated sample to deactivate it and remove it from the plot.
Note: Activating or deactivating sample tubes during a run does not impact data acquisition of the
experiment. This option is only relevant for visualization in the plot.
Use the drop-down list (3) in the upper left corner to change the plot view between different profile
phases. The list includes all phases containing an acquisition, as defined in the thermal profile.

All acquisitions of a selected phase (4) are displayed next to the drop-down list. The acquisitions are
labeled with their corresponding channel name and, if a cycling step has multiple acquisitions, they
will all be displayed. Click the acquisition you would like to populate the fluorescence plot. The active
acquisition will be highlighted in dark grey.
Note: If you select a melt phase from the drop-down list, acquisition(s) will be displayed, but none
will be active. Click an acquisition to populate the fluorescence plot.
If multiple acquisitions were defined for the same channel in a step, they will also be displayed.
7.4 View profile progress

As in the Run Profile step, a Run preview is also included at the bottom of the screen in the Run
step. The Run preview is a graphical representation of the programmed thermal profile, with blue
dots indicating points of data acquisition.
In the Run step, a gray background appears behind the phases of the thermal profile that have been
completed.
From the Run preview, you have options to modify the run. For more information, see Adjust run
duration.
7.4.1 Adjust run duration
During a run, you have a few options to adjust its progress.

Whenever a cycling phase is active in a run, you can add 5 cycles to the programmed thermal
profile by clicking Add 5 cycles.
The run preview and the number of cycles in the Run Profile step are automatically updated. The
estimated run time is also recalculated and the addition of 5 cycles is recorded in the experiment
audit trail.

You can skip the current phase and proceed with the next phase programmed in the thermal profile
by clicking Skip current profile phase. If the run is in the final phase, the run will end.
Skipping a profile phase is also recorded in the experiment audit trail.
To modify a Melt or HRM phase by 5°C, click Add 5 degrees. The end temperature of the melt or
HRM phase will rise by 5°C while hold time and temperature change at each cycle will remain as
defined in the Run Profile step.
The change to the Melt or HRM phase is recorded in the experiment audit trail.
Melt and HRM phases cannot be extended if the end temperature exceeds 95°C.
7.4.2 View auto-gain optimization progress
You can optimize the gain for an experiment at the start of a run or directly before the first
acquisition, depending on the setup of the thermal profile. For more information on acquisitions and
gain optimization, see Add an acquisition.
If you chose auto-gain optimization while defining the thermal profile of an experiment, a pop-up
window with information about the progress of the gain optimization appears during the run.
The window will remain on the screen until it is closed by clicking OK.
A table in the window lists the acquisitions defined for the profile phase. During gain optimization, the
Q-Rex Software varies gain values at the target temperature until the signal lies within the defined
target range. The table will list status descriptions such as Too low or Too High until the gain value
is optimal. Then the status appears as Finished.
Gain information is recorded in the experiment audit trail as they are measured in the experiment.

7.5 Stop a run
If necessary, you can stop a running experiment at any time. Click Stop Run and confirm with OK.
The Rotor-Gene Q will stop and cool down the rotor before releasing the instrument lid.
Upon stopping a run, the text "Run stopped by user" with date and time appears in the Run
information table and the action is recorded in the experiment audit trail.

Analyze an experiment
8 Analyze an experiment
Different analyses of an experiment are available through plug-ins. This section describes general
use concepts for analyses. For detailed instructions on the setup and analysis of specific experiments,
read the descriptions specific to each plug-in (see the Q-Rex plug-in user manuals).
Add an analysis
Analysis overview
View fluorescence plots
Select tubes for analysis
Define analysis parameters
View results
Remove an analysis
Note: Some of the described methods and functionalities may not apply to future plug-ins.
8.1 Add an analysis

To add an analysis, click the menu icon in the Analysis step of the Step Marker in the Experiments
environment. Select Add analysis to reveal a list of all the installed analyses plug-ins and select the
analysis type you want to add.
You can add up to 8 analyses to your experiment, including the same analysis multiple times.

8.2 Analysis overview
The screen of the Analysis step in the Experiments environment displays fluorescence curves,
analysis parameters and results in one overview.
The main area in the center of the screen (1) contains 2 Fluorescence plots (2) at the top (see
View fluorescence plots) and a Result table (4) at the bottom (View results). You can adjust the size
of the panels in the main area by moving the drag handles (3).
The Drawer (5) is closed when you first open the Analysis step. Click in the upper right corner
of the screen to open it. Clicking closes the Drawer.
The Analysis tab of the Drawer allows you to define the analysis parameters for a selected target
(see Define analysis parameters). The target and parameters displayed correspond to the active
fluorescence plot, which is highlighted with a darker plot background. The displayed parameters will
also differ depending on the analysis plug-in you are using.
In the Tube Selector tab, you can select and deselect tubes to be included in the analysis (Select
tubes for analysis).

8.3 View Fluorescence plots
A typical Fluorescence plot has the following elements:

A Plot Selector (1)
A Target Selector (2)
A button to maximize and minimize the plot window (3)
A toolbar to modify the display of the plot (4). See Modify plot view.
The plot area (5). This area has a darker background color when the plot is active.
A legend (6)

To analyze an experiment based on fluorescence curves:
1. Select the plot type you want displayed in the active plot. Click the drop-down menu of the Plot
Selector to display the available plot types and select one.
The plot types available will depend on the analysis. You can define a different type for each of
the Fluorescence plots in the analysis overview.
Note: The active plot is highlighted in darker blue and determines the analysis parameters
displayed in the Analysis tab of the Drawer.
2. Select a target for the analysis. Open the Target Selector (1) to view targets sorted by their
corresponding acquisition and select one.
You can browse through a list of targets using the Forward and Back buttons (2).
The target selected in the active Fluorescence plot is displayed in the Analysis tab of the
Drawer.
Note: You can view multiple targets at the same time in a single plot window. In this case, the
analysis parameters, which always refer to a single target, are inactive.

3. To view details about a particular curve in the active Fluorescence plot, roll the mouse pointer
over the curve.
The curve is highlighted and details appear in a tooltip.
4. To modify how the plot is displayed, see Adjust plot view.

5. Optional: you can also copy the graph and use it in other applications. See Copy plot to
clipboard.
For any analysis, you can select which tubes to include (see Select tubes for analysis), you can define
the parameters of the analysis (see Define analysis parameters) and you can obtain detailed results
in tabular form (see View results).
8.3.1 Modify plot view
The toolbar at the top of each Fluorescence plot includes icons that allow you to alter the way in
which data in the Fluorescence plot are displayed. The icons are grouped by function and only one
icon per group can be active at a given time (the icon is highlighted in darker blue).
Scaling
Scale to 100% (1) The icon is enabled only for raw data and displays the complete range of
acquired fluorescence data.

Auto-scale (2) Automatically scales the plot to use space optimally. Both axes are
restricted to available minimum and maximum values.
Shift zoomed region Clicking this icon allows you to shift the visible area of the plot (to pan)
(3) when you are zoomed in on a specific region. Click and drag the plot in
the desired direction.
Axes
Log scale (4) Click this icon to change the axis scale to a logarithmic scale
(base 10).
Linear scale (5) Click this icon to make the axis scale linear.
Curves
Replicate mean (6) Click this icon to display the arithmetic mean of replicates instead of
individual replicate curves. The mean is calculated for each cycle as the
mean fluorescence value of all tubes with the same sample name and
selected target.
Note: this option is not available for melt plots.
You can also zoom, select and deselect curves directly in the plots. Left-click the plot area and, while
holding down the mouse button, drag a rectangle across an area of interest. Upon releasing the
mouse button, a context menu appears with the option to zoom in on the framed area, select the
curves included in the framed area, or deselect the curves included in the framed area (see Select
tubes for analysis).

8.3.2 Copy plot to clipboard
To copy a plot into another application:
1. Right click the plot you want to copy and select Copy graph to clipboard from the context
menu.
This copies the plot to the clipboard.
2. Paste the copied plot into an appropriate application.

Graph and legend will be inserted.
8.4 Select tubes for analysis

You can select or deselect tubes for an analysis in the Results Table, the Tube Selector tab of the
Drawer and in an active Fluorescence plot.
Selections made in any of these areas are synchronized in other areas. So, for example, selections
made in the Results Table are updated in the Tube Selector and the Fluorescence plot.
To select or deselect tubes in the Results Table, simply check or uncheck the corresponding box in
the left-most column.

In the Tube Selector, you can quick select or deselect multiple tubes:
The cell of a selected tube appears dark blue, while that of a deselected tube appears light blue.
Select or deselect a single tube by clicking the corresponding row.
Select or deselect a group of adjacent tubes by clicking the first tube in the group and dragging
the mouse to the last tube.
You can also define the tubes to be included in an analysis by selecting or deselect the corresponding
curves in the active fluorescence plot. Click the plot area and drag a rectangle across the area
containing the curves you wish to select or deselect. Upon releasing the mouse button, a context
menu gives you the option to:
Select Curves: selects the tubes corresponding to the curves contained in the rectangle and
deselects all other tubes.
Deselect Curves: Deselects all tubes corresponding to the curves contained in the rectangle. All
other selected tubes remain selected.
Note: The selection status of a tube is saved with the experiment.

Note: Deselecting one or more tubes removes the respective data from any further calculations
(e.g., mean Cq in Replicates or Group Result tables).
For more information, see Selecting samples.

8.5 Remove an analysis
To remove an analysis from an experiment, click the menu icon of the Analysis step of the Step
Marker in the Experiments environment. Select Remove analysis and the analysis you want to
remove from the resulting menus.

8.6 Define analysis parameters
Define analysis parameters in the Analysis tab of the Drawer.
The Target selected for the analysis is visible at the top (1) and definable analysis parameters are
listed below. This is the target selected in the active fluorescence plot. If multiple targets are selected
in the plot, the Target field remains empty and the analysis parameters cannot be edited.
Default values are defined for most of the listed parameters, but some parameters require input and
are highlighted in yellow (2). As long as the required input fields remain empty, the parameter is
shown as invalid and results cannot be displayed. The example in the screenshot above shows that
the Cq threshold has not been defined, which is required to calculate Cq values.
Note: If an invalid input field is hidden, the surrounding parameter group, the Analysis tab or even
the Drawer itself are shown as invalid.
Define the following parameter groups for a basic analysis:
Filter data
Normalize curves
Define Cq threshold
Analyze melt curves

8.6.1 Filter data
The parameters in this group are optional. Use them with caution as they directly impact your raw
data.
You can define the following parameters:

Parameter Description
Degree of data Change the digital filter used in the fluorescence plot to smoothen data
smoothing (Dig. filter): based on a sliding window of points. Available options are None, Light,
(1) Medium and Heavy.
Remove non- Check this option to remove certain curves from the data based on one of
amplified curves with two filter criteria (see 2a or 2b).
(2)
Note: This parameter is called Outlier Removal in the Rotor-Gene Q
Software.
fluorescence change Enter a value in this field to remove curves with a percental fluorescence
< X % (2a) change that is less than the value entered relative to the curve with the
largest fluorescence change from the first to the last cycle. Values
between 0 and 30 can be entered.
Example: The sample with the largest fluorescence change has a
fluorescence of 2 in cycle 1 and 47 in the last cycle. In this case, 45
fluorescence units represent 100%. A cut-off of 10% would remove any
sample with a change in fluorescence of less than 4.5.
reaction efficiency Enter a value in this field to remove curves with a reaction efficiency that
< X % (2b) is less than the value entered. Values between –100 and 100 can be
entered.
A value of 0% indicates that no reaction took place during the exponential
phase. 100% indicates that a completely efficient reaction took place.
Negative percentages indicate that the fluorescence signal declined
during the exponential phase.

Crop cycles (3) Check this option to remove raw data prior to normalization based one of
two filter criteria (see 3a or 3b).
Remove data before Data acquired prior to the cycle number entered are removed.
cycle: X (3a)
Remove data after Data acquired after the cycle number entered are removed.
cycle: X (3b)
8.6.2 Normalize curves
The parameters in this group are optional and depend on the use of Dynamic tube normalization.
Use these parameters with caution.

Dynamic tube (1) Check this option to normalize curves based on the average value of
all data points before amplification becomes visible. When unchecked,
Q-Rex Software uses the average of the first 5 values.
Use noise slope Check this option to use a line-of-best-fit to determine the fluorescence
correction (2) noise level and normalize curves to that line. When unchecked, Q-
Rex Software uses the average.
Note: Noise slope correction can improve data if sample baselines
are noticeably sloped, but can lead to undesired effects if the slope is
not steady or if the initial cycles show a significant increase or
decrease compared to the remaining curve.
Ignore first cycles: X (3) The entered number of cycles at the start of the run are ignored and
not used to normalize the fluorescence data.

Adjust take-off points (4) Check this option to define a minimum length of baseline to be used for
normalization, based on two criteria (see 4a and 4b).
If take-off point < X (4a) If the calculated take-off point is below the entered cycle number (4a),
use take-off cycle: Y (4b) the cycle defined in 4b is used.
8.6.3 Define Cq threshold
Cq values can only be calculated if a Cq threshold is defined. You can define a specific Cq threshold
by entering a value in the Analysis tab of the Drawer or by creating a threshold line in the
Normalized data fluorescence plot.
To define a specific Cq threshold in the Analysis tab of the Drawer:
1. Under Threshold start cycle, enter the cycle where the calculation threshold should begin.
Any fluorescence signal crossing the threshold prior to the threshold start cycle will not be
included in the results.
2. Enter the Cq threshold into the Threshold field.
To define a specific Cq threshold directly in the Normalized data fluorescence plot:
1. Click in the plot area where the Cq threshold should be positioned. A solid horizontal line
appears. Click and drag the line up or down to adjust the Cq threshold.

2. Define the threshold start cycle by rolling the mouse pointer over the left border of the active
Normalized data fluorescence plot. When the mouse pointer changes to a double-headed
arrow, click and drag the resulting vertical line to the desired threshold start cycle. A tooltip will
show the threshold start cycle value (1). Click and drag the line to adjust the threshold start
cycle.
8.6.4 Analyze melt curves
To calculate melt peak values, you must define a Peak threshold and a Tm threshold. The Flip
sign of dF/dT and Determine melt peaks options for melt peak analysis are checked by default.
Calculated melt peak values are displayed in the Tubes View of the Results Table.

Flip sign of dF/dT (1) Before defining peaks, use this option to ensure that the dF/dT sign is
correct for the dataset and will give positive peaks.
Determine melt peaks When checked, Q-Rex Software calculates for each sample melt
(2) peaks above a defined threshold and temperature (see 2a and 2b).
Note: Activating this option renders the analysis invalid until Peak and
Tm thresholds are defined. As a result, functions requiring a valid
experiment status (e.g., adding the analysis to a report) are not
available.
Peak threshold: X (2a) Enter the threshold above which melt peaks should be calculated.
Tm threshold: X °C (2b) Enter the temperature threshold above which melt peaks should be
calculated.
Once set, the Peak threshold (2) appears as a horizontal line in the Melt peak fluorescence plot
and can be adjusted by dragging it up or down. Similarly, the Tm threshold (1) appears as a
vertical line and can be adjusted by dragging it left or right.

8.7 View results
Once all required analysis parameters are defined, the Results Table in the lower half of the
Analysis screen displays the results in 3 different views. Click the tabs at the top of the Results
Table to access each view.
Tubes: This view shows results for each tube in the experiment, with all acquisitions listed next to
each other in a single row (Tubes View).
Replicates: Reports results for all replicates of a sample. Typical results, such as Cq values, are
reported as the arithmetic mean and the standard deviation of all sample replicates (Replicates
View).
Groups: Similar to the Replicates view, the Groups view shows aggregated results. In this case,
results are reported for sample groups (see Groups View).

8.7.1 Tubes View
The Tubes View of the Results Table shows results for each tube, laid out in a row.
For all analyses, the Tubes View always includes the following columns:
– The first column contains a check box to select or deselect a tube for
analysis. The selection is synchronized with data in the Tube Selector and
the fluorescence plots (see Select tubes for analysis).
Tube Indicates the tube position in the rotor.
– The third column displays the color used for the corresponding curve in a
fluorescence plot.
Style Indicates the line style used for the corresponding curve in a fluorescence
plot.
Sample name Lists the sample name.
Sample groups Optional: If you defined sample groups, this column displays all groups to
which a sample is assigned (see Define sample groups).
Sample type Lists the assigned sample type (Sample, Standard, PC, NTC or NC).
Comment Allows you to enter comments relevant to each sample.

Further columns may be added to the Results Table, depending on the analysis. For the basic
analysis, you will find results data for each acquisition in the following columns:
Target Lists the target assigned to the tube for the specific acquisition (Define
targets).
Cq Shows the Cq value calculated for the tube.
Take-off Indicates the take-off point, the cycle where the run transitioned into the
exponential phase.
Eff. Displays the reaction efficiency of the tube, which is calculated based on
the 4 data points following the take-off point.
Tm °C Optional: If the run profile included a melt phase, the detected melt peak
temperature is also listed.
8.7.2 Replicates View
The Replicates View of the Results Table shows results for each technical replicate, laid out in a
row. Results from tubes with the same name, acquisitions and targets are aggregated as a technical
replicate.

For all analyses, the Replicates View always includes the following columns:
– The first column contains a check box to select or deselect a sample with its
technical replicates. The selection is synchronized with data in the Tube
Selector and the fluorescence plots (see Select tubes for analysis).
Sample name Lists the sample name.
Sample groups Optional: If you defined sample groups, this column displays all groups to
which a sample is assigned (see Define sample groups).
Sample type Lists the assigned sample type (Sample, Standard, PC, NTC or NC).
Target Displays the target assigned to replicate tubes for the specific acquisition
(Define targets).
Rep. Cq Lists the arithmetic mean of the Cq values of tubes with the same sample
name and target.
Cq SD Provides the standard deviation of the listed Cq values of tubes with the
same sample name and target.
Note: A technical replicate will have multiple rows, if tubes of the sample have multiple target
assignments.
Note: If a melt phase is part of the experiment, melt peak temperatures are only displayed in the
Tubes View.

8.7.3 Groups View
The Groups View of the Results Table shows results for each defined sample group and
acquisition, laid out in a row. Results are calculated from all tubes assigned to the same sample
group.
For all analyses, the Groups View always includes the following columns:
Sample groups Indicates the groups defined for the samples of the experiment (see Define
sample groups).
Target Lists the target assigned to the sample group for the specific acquisition
(Define targets).
Cq mean Displays the arithmetic mean of the Cq values of all samples with the same
sample group and target assignment.
Cq SD Provides the standard deviation of the listed Cq values of all samples with
the same sample group and target assignment.
Note: A sample group will have multiple rows, if samples of the group have multiple target
assignments.

Reports and exports
9 Reports and exports
The Q-Rex Software has report and export capabilities which you can access by clicking the Report/
Export step of the Step Marker in the Experiments environment.
Access the different functionalities by clicking on the corresponding tab:
Reports
Exports
Experiment audit trail
Copy and paste
9.1 Reports
Reports allow you to save or print formatted experiment information and results. A report includes
information for a single experiment only.
Each report consists of a header with general information about the experiment, and one or more
user-defined sections with information about the analyses performed.
To generate a report of an experiment:

1. Click the Report tab.
2. Select the level of detail for all sections in the report with the Select report type radio-buttons,
either Standard, Short or Detailed.

Information about the report appears in the Report content field.
Note: You cannot select different levels of detail for different report components.
3. To include analysis results in the report, select the analysis from the list in the Select analysis
to be included section.
Only valid analyses can be added to a report. The checkbox of an analysis containing errors
(indicated by a yellow Analysis step in the Step Marker) will be disabled.
4. Click Generate report.

5. Enter a file name for the report and the location where it should be saved. The Q-Rex Software
uses date and experiment name as a default file name.
6. Click OK to save the report file. Reports are saved as *.pdf files.

9.2 Exports
Exports allow you to use experiment information and analysis results in other applications for further
processing. The Q-Rex Software exports data to a number of different formats. You can also create
customized export formats. To do so, please contact QIAGEN Technical Service.

To export information and results of an experiment:
1. Click the Export tab.

2. Select an export format.
Format Description
RGQ Absolute Creates one quantitation analysis template file (*.qut) with
Quantification Analysis absolute quantification analysis parameters for each target.
Data
Note: Crop cycles data are not exported.
Fluorescence data Creates a *.csv file with basic experiment information and
export tables containing the raw fluorescence values. The file
includes 1 table per acquisition, including melt acquisitions.
RGQ Experiment Creates an experiment file (*.rex) for the Rotor-Gene Q

Software.
Note: The use of multiple concentration units in one
experiment, of touchup in the thermal profile or of duplicate
acquisitions within a single cycling step is not exported.
RGQ Quantitation Creates 1 quantitation analysis template file (*.qut) with basic
Analysis Data analysis parameters for each target.
Note: Crop cycles data are not exported.
RDML v1.2 Report Exports the experiment in RDML-compliant format.
RGQ Template Creates a template file (*.ret) for the Rotor-Gene Q Software.
3. Click Export.

4. Enter a file name for the export and the location where it should be saved. The Q-Rex Software
uses the export format as a default file name.
5. Click OK to save the export file.
Note: Only information that is stored with the Q-Rex Software can be exported. The Q-Rex Software
uses data structures that differ from those of older Rotor-Gene software. Consequently, not all the
information of a Q-Rex Software experiment can be exported to use in older software and several
data fields in *.rex experiment files will appear unpopulated (see description of the RGQ Experiment
export format).
Please contact QIAGEN Technical Service if you have questions.

9.3 Experiment audit trail
An experiment audit trail lists all events relevant to an experiment. These events are saved along with
the experiment and always available by opening the experiment and selecting the Audit Trail tab
under the Report/Export step.
You can set the language used for an experiment audit trail to the system language or to English.
The system language is the language chosen for the Q-Rex Software in the Configuration
environment, not the language of the operating system.

To create an Audit Trail file:
1. Click Export at the bottom right of the Audit Trail tab.

2. Enter a file name for the audit trail and the location where it should be saved.
3. Click OK to save the audit trail file. Audit trails are saved as *.txt files.
9.4 Copy and paste

The Q-Rex Software supports copy-paste functionality to enable the easy transfer of setup
information to and from other software. Sample layout information can be copy-pasted from other
applications, such as Microsoft Excel®, into the Q-Rex Software and vice versa. Analysis results can
be copied from the Q-Rex Software and pasted into other applications.
To copy data from the Q-Rex Software:
1. Select the data to be copied in the Sample Layout or Result table. For instructions on how to
select data cells see Selecting samples.

2. Press Ctrl+C to copy the selected cell(s). In the Sample Layout, you can also right-click the
selected data to reveal a context menu with the option to copy.
The copied data are now available in the clipboard (see Microsoft Windows documentation for
more details on the clipboard).
3. Paste the data into another application (e.g., Excel) following instructions specific to that
application. For many applications, you can select the destination and either press Ctrl+V or
select Paste from the Edit menu.
To paste data into the Sample Layout table in the Q-Rex Software:
1. Copy data in the source application to the clipboard (e.g., a list of sample names from Excel).
In many applications, you can select the data and either press Ctrl+C or select Copy from the
Edit menu.
2. Select the area of the Sample Layout table in the Q-Rex Software where the copied data will
be added.
Note: Make sure to select an area of the same size as the data copied to the clipboard. For
example, if the data in the clipboard consists of 1 column with 23 rows, select 1 column x 23
rows of the destination table in the Q-Rex Software.
3. Paste the data from the clipboard by pressing Ctrl+V. Alternatively, right-click the destination
area in the table and select Paste from the context menu.
For additional information, see Selecting samples, Select tubes for analysis, and Working with tables.

Administrative tasks
10 Administrative tasks
This section describes administrative tasks, such as user and cycler management, as well as how to
customize general software settings and view the system audit trail.
View the system audit trail
Manage users
Manage cyclers
Customize settings
10.1 View the system audit trail

View the system audit trail in the Service environment.
Select the System Audit Trail tab to reveal a screen with 2 sections:
A list of events in the lower half of the screen

Options to filter the events list in the upper half

Use the filter options to limit the list of events and corresponding messages to those you need (by
date, time, user, Message ID or context) and press Apply filter.
Click Reset filter settings to reset all filter settings to their default values.
Click Export to file to save the filtered events list to a file. The events list will be saved as a text file
with tab separated columns.
You can set the language used for messages to the system language or to English. The system
language is the language chosen for the Q-Rex Software in the Configuration environment, not the
language of the operating system.
10.2 Manage users

You can manage user accounts for the Q-Rex Software in the Configuration environment.
1. Click the User Management tab (1) to see a table of Registered users.
From this table you can configure settings for all Q-Rex Software users.
2. Click (2) to edit an account, such as the admin account.

3. You can change the name of the person with the admin account and add an e-mail address.
We highly recommend changing the password to secure settings and work in the Q-Rex
Software.
Note: the User ID of the admin account used to log in cannot be changed. You can, however,
add additional Administrator, Operator and Service user accounts (see User roles).
If a user enters a wrong password 5 times, his or her account will be deactivated. To re-activate
users:
1. Log in with an Administrator or Service user account.

2. Click the User management tab in the Configuration environment.
By default, you will only see active users. To reveal deactivated users, uncheck the
option. Deactivated user profiles are labeled with a icon.
3. Click to edit the user profile and check the option in the dialog.
4. Define a temporary password for the user to log into the system again.
When the user logs in again, he or she will be required to define a new password.

10.3 Manage cyclers
You can manage cyclers connected to the Q-Rex Software in the Configuration environment.
Click the Cycler management tab to see a list of registered cyclers.
Each registered cycler is listed with a user-defined name, manufacturer-assigned serial number and
date of last verification.

To add and set up a new cycler:
1. Click Add cycler.

2. Enter the required information in the resulting dialog.
Name Assign a name to the cycler

Serial number Enter the serial number of the instrument. If the cycler is
connected, the serial number is visible below the instrument
icon in the Main toolbar. See Main toolbar.
Last verification date Optional: enter the date of the cycler's last optical
temperature verification (OTV).
3. Click OK. The new instrument will appear in the list of registered cyclers.
To edit details of a registered cycler, click in the row of list corresponding to the cycler you
want to edit. You can also delete a cycler directly from the list by clicking .

10.4 Customize settings
To define general settings for the Q-Rex Software, click the Settings tab in the Configuration
environment. Here you can define the display language, enter information about the mail server for
e-mail notifications, set the number format for concentration values, and manage password options.
You can also add images to the header of reports and end of reports.
Language
Select the language for the Q-Rex Software from the drop-down list. All text in the software appears
in the selected language. Click Reset to revert the language selection to the default English (United
States).

Reporting
You can add a header image, such as a logo, as well as a concluding image (footer image) to all
reports generated with the Q-Rex Software.
To select an image, click and select the image in the resulting dialog. All images in formats *.
bmp, *.jpg and *.png are supported. The chosen image will appear in the preview field.
Note: The maximum image size for the header is restricted to 1900 x 300 pixels and for the
concluding image is 1900 x 828 pixels. The Q-Rex Software will resize larger images down to this
maximum size.
You can remove images by clicking .
Concentration number format
Use this option to define the format in which concentration values are displayed throughout the
software. This notation is also used as the number format setting for newly created experiments.
Choose between decimal format or scientific notation. For either setting, you can define the number
of decimal places (between 0 and 10) to display.

User Management
Under User management, you can set password criteria.

Password renewal interval Enter the time interval after which users must define a new
password. Passwords will not expire if you enter 0 or if you
leave the field blank.
Password strength You can set the password strength to:
Simple: Use this option if authentication of users is not required.
This policy allows you to use short passwords, or use an empty
password field. The password may have 0–40 characters..
Medium: Use this option if authentication of users is required.
The password must have 8–40 characters.
Strong: Use this option if high security authentication is
required. The password must have 8–40 characters, contain a
minimum of 2 lower case letters, 2 upper case letters, 2
numbers and 2 special characters.

Email Notification
In the event that you need assistance from QIAGEN Technical Service, you can streamline
troubleshooting by sending them support packages. For details about support packages, see
Troubleshooting.
General network settings of your mail server must be provided to enable sending support packages.
To obtain the needed information, please contact your network administrator.

Troubleshooting
11 Troubleshooting
This section provides assistance in managing errors that might occur when using the Q-Rex Software.
Resolving error messages and warnings

Error messages and warnings are displayed when unexpected events or behavior occur during use.
All messages have a Message ID, which is displayed at the end of the error message. Several
errors may be combined in one message. Refer to the listed Message IDs whenever an error
message or warning appears.
The sections System setup, Operation and Error messages and error codes include lists and
explanations of error codes. If an error message or warning appears that is not listed or cannot be
resolved, note the Message ID, the message text and the steps leading to the error. Then contact
QIAGEN Technical Service.
Note: In addition to the Message ID, information about the steps and dialog boxes leading to an
error help QIAGEN Technical Service Specialists resolve the error. Make sure to note details. For
problems with a specific experiment, create a support package and send it to QIAGEN Technical
Service.
Creating a support package

Support packages are folders containing multiple files that help QIAGEN Technical Service to
analyze entries and events that may contribute to an error or issues with an experiment or
instrument.
Note: Support packages that are older than 90 days are deleted automatically.
To send a support package to QIAGEN Technical Service:

1. Enter the Service environment and click the Support Package tab to reveal a list of available
support packages for the experiments run on the selected cycler.
Note: You must configure the e-mail settings in the Configuration environment to send
support packages to QIAGEN Technical Service. Refer to Customize settings for further
assistance.
2. Select the checkbox of the experiment(s) in which the error occurred.

3. An e-mail dialog appears where you can enter a subject and a message describing your
problem. Also enter an e-mail address in the Reply to (1) field, so QIAGEN Technical Service
can respond to your inquiry.
4. Click Send support package(s) (2) to send the e-mail.
Note: Always send support packages from the computer that was connected to the Rotor-Gene Q
when the error occurred. This ensures that all relevant information is included in the support
package.

To send the support package of an experiment run on a computer without internet connection:
1. Go to the folder %ProgramData%/QIAGEN/QRex/SupportPackage/.

2. Find the support package that was generated. Support package files are named according to
the following scheme:
[Date]_[Time]_[Experiment name]_[Status].support-package, where the information in brackets
corresponds to each file generated, e.g.,
20151002_053705pm_SYBRGreenTestRun_RunFinished.support-package.
3. Send the file as an e-mail attachment to QIAGEN Technical Service. Use the e-mail address
corresponding to your region:
Europe: Techservice-eu@qiagen.com
North America: Techservice-NA@qiagen.com
Japan: Techservice-jp@qiagen.com
Asia Pacific: Techservice-ap@qiagen.com
Other: Techservice-eu@qiagen.com
11.1 Error messages and error codes

The general structure of an error message is:

The Message ID uniquely indicates the source of an error and helps QIAGEN Technical Services to
identify the error.The following list includes the most common error messages that might occur while
using the Q-Rex Software and troubleshooting suggestions.
In case you need to contact QIAGEN Technical Service, provide the Service Specialist:
Steps and events leading to the error message
The Message ID
Message ID Error text Comments and suggestions

1010016 User name is unknown or User name, password or both are incorrect. Up
password is incorrect. Enter to 5 wrong password attempts are allowed.
user name and password
again.
1040012 This user was deactivated Five wrong attempts to enter a password
because the password has been deactivates a user account. A user with
entered wrong too many times. Administrator rights must log in and reactivate
Contact your local the account.
administrator. The current
session will be closed.
20050027 File is used by another instance The file you wish to open is being used by
of the Q-Rex Software. another instance of the Q-Rex Software, e.g.,
on another computer through a network drive.
If that is not the case:
1. Close the Q-Rex Software.

2. Go to the directory where the experiment
file is located and find a file with same
name but with the ending .lock (e.g., find
pcr_test.lock for pcr_test.qrex).
3. Delete the .lock file.
4. Try to open the experiment file again.
20050029 The file was created using a A file created with a newer version of the Q-Rex
newer version of Q-Rex, do Software may still be opened with an older
you want to load it risking data version. It is possible that some data is lost in the
loss? loaded file. Check the file results for data
consistency.
20050003 Error during experiment A file cannot be loaded because, e.g., it is
loading. The experiment cannot corrupted, it cannot be found or is not
be created. accessible in the selected directory. Check that
the file is not corrupted and that it is accessible.

20046007 The signature of the experiment The file has been altered, either manually or
is not valid. It might have been with another application. The data in the
altered outside of the experiment might be corrupted. Check the file
application. Do you want to results for data consistency.
proceed with loading of the
experiment?
20050002 Errors occurred while loading Information stored in the experiment was
the template file. Information changed by the Q-Rex Software using default
within the template was values because the file was corrupted,
changed. incompatible or manually altered. Check the file
results for data consistency.
20050040 Errors occurred while loading The analysis being loaded is not compatible with
the template file. Information the installed plug-in version. Make sure that the
within the template was installed plug-in is compatible with the file being
changed. loaded.
20050024 Information could not be loaded Plug-in data in the file could not be loaded
from the file because a plug-in because a plug-in is not installed. Make sure
was not found. Do you want to that the relevant plug-ins are installed.
continue loading?
20046013 There are unsaved changes in Always make sure that no data are discarded
the experiment. If you continue, when closing a Q-Rex Software experiment.
these unsaved changes will be Save your experiments to prevent data loss.
discarded.
1240021 For each Melt or HRM Files from the Rotor-Gene Q Software are not
acquisition there has to be a compatible with the Q-Rex Software and cannot
corresponding acquisition on be imported. If the Rotor-Gene Q Software file
the same channel in a cycling has a melt or HRM phase, it must also include a
phase. corresponding acquisition in the same channel.
340000 The file has an invalid The Rotor-Gene Q Software file may be
document format. Contact corrupted and cannot be loaded into the Q-Rex
QIAGEN Technical Services. Software. Check for data consistency in the
Rotor-Gene Q Software file.
330007 The Rotor-Gene Software file The Rotor-Gene Q Software file was altered
signature is invalid, do you want outside of the Rotor-Gene Q Software. Data
to continue loading the file? might be corrupted or lost after loading. Check
the file results for data consistency.
1650024 There was a communication Make sure the Rotor-Gene Q lid is properly
problem with the device. closed and that the cable connection between
the Rotor-Gene Q and the computer is not loose
or faulty. Reconnect or replace the cable. Use
only dedicated cables and accessories supplied
by QIAGEN. Switch the Rotor-Gene Q off and
on again. Close and restart the Q-Rex Software.

20011000 Multiple concentration units are Various concentration units are defined in the
not supported by the Rotor- Q-Rex Software file. To export such a file to the
Gene Q Software. Rotor-Gene Q Software format, use the same
concentration units for all tubes.
20011002 Duplicate acquisition channels The Q-Rex Software file includes duplicated
are not supported by the Rotor- acquisitions, i.e., acquisitions in the same
Gene Q Software. channel and profile step. The file cannot be
exported to a Rotor-Gene Q file after the
experiment has been executed.
20011007 Experiment not run and cannot Only experiments that have been run can be
be exported. exported to the Rotor-Gene Q Software.
11.2 System setup

The following errors might occur while setting up the Q-Rex Software.
Error description Comments and suggestions

Computer or Rotor-Gene Q does not Check the power connection. The power cable might be
turn on. loose or faulty. Reconnect or replace the cable.
The Q-Rex Software cannot Make sure the cable connection between the Rotor-Gene
communicate with the cycler. Q and the computer is not loose or faulty. Reconnect or
replace the cable. Use only dedicated cables and
accessories supplied by QIAGEN.
Switch the Rotor-Gene Q off and on again. Close and
restart the Q-Rex Software.
Note: The Q-Rex Software supports communication
between instrument and computer only via a USB cable.
The Q-Rex Software does not start
because:
a) The Q-Rex Software is not installed Install the Q-Rex Software.
b) The computer is running an old The Q-Rex Software can only be operated with Windows
version of Microsoft Windows 7 or Windows 8.1.

11.3 Operation
This section includes information about errors that might occur while using the Q-Rex Software and
troubleshooting suggestions.
Operation errors
The plot background prints Some printer drivers are configured in a way that the transparent
in black background colors used in the Q-Rex Software plots are printed in
black. Refer to the manual of your printer to change this
configuration.
To ensure that the results displayed in plots are exactly the same as
the printed reports, the background colors must be transparent.
General errors
Incorrect rotor loading Load tubes and Rotor-Discs into the rotor of the Rotor-Gene Q in the
correct orientation, ensuring that each tube sits correctly in place.
Samples will not align optimally over the detection system if
positioned incorrectly in the rotor, which can reduce the acquired
fluorescence signal and detection sensitivity.
Missing locking ring Always attach the dedicated locking ring to the rotor of the Rotor-
Gene Q before starting a run. The locking ring ensures that caps
remain on tubes during a run and that tubes and Rotor-Disc are
positioned correctly.
Rotor not completely filled To achieve maximum temperature uniformity in the chamber of the
Rotor-Gene Q, each position in the rotor must contain a tube. Filling
all positions in the rotor ensures even airflow to every tube. Keep a
set of empty capped tubes available that can be used to fill any
unused positions.
The bar code of a Make sure that the handheld bar code scanner is correctly
QIAGEN kit cannot be connected to the computer and configured properly, e.g., data will
read using the handheld be sent after pressing Enter. Try to read other bar codes with the
bar code scanner scanner. Ensure that all bar codes can be easily read.
Login error Check that the user name is correct.
Make sure to enter the correct password.
Note that after 5 unsuccessful login attempts, the user account will
be locked. In that case, a registered user with administrator role
must reactivate the user account.

Glossary
12 Glossary
Glossary terms in alphabetical order
A
Acquisition Acquisition is the collection of fluorescence data. Each acquisition (set of
fluorescence data) from a channel is displayed in the software as
unanalyzed data in a raw data fluorescence plot. These data can be
analyzed using the options in the Analysis menu.
Auto-gain Methods to determine an appropriate gain value for a run. The goal is
to select the gain so that the signal does not drive into saturation but is
significantly different from background fluorescence.
B
Baseline The virtual line that represents an amplitude of zero in measured data.
C
Channel A channel consists of a light emitting diode (LED) with an excitation filter
paired with an emission filter. The LED and excitation filter excite
samples at a given wavelength. Fluorescence emitted by samples is
passed through the emission filter, before being detected by a
photomultiplier.
Cq Quantification cycle. The fractional cycle at which a curve reaches a

predefined normalized fluorescence threshold.
Custom channels The Q-Rex Software allows you to create new excitation/detection
wavelength combinations that can be saved as custom channels.
Cycle step Multiple cycling steps create a cycling phase. At a minimum, a step
consists of a defined temperature and time.
D
E
Efficiency Efficiency of the qPCR. See Reaction efficiency.
Experiment channels The experiment channels are channels created and saved in other
experiments and are only available in the active experiment. These
channels are not editable. To edit them, move them to custom channels.
They can also be removed from the experiment.
F
Fluorophore A molecule that is excited by specific wavelength(s) of light and emits
photons, becoming fluorescent.

G
Gain The Rotor-Gene Q uses a photomultiplier to collect fluorescence
photons and convert them to electronic signals. The gain is a setting that
determines the sensitivity of the photomultiplier and is set so that the
signal does not drive into saturation but is significantly different from
background fluorescence.
Gain optimization The aim of gain optimization is to ensure that all data are collected
within the dynamic range of the detector. The gain is optimized so that
the signal does not drive into saturation but is significantly different from
background fluorescence.
GUI Graphical User Interface.
H
Hybridization The temperature in a thermal profile is steadily decreased so that
double-stranded nucleic acids (DNA, cDNA) associate at a certain
temperature, depending on their length and sequence composition. The
hybridization curve shows the fluorescence increase when using
intercalating dyes and has a peak at the association time point.
I
J
K
L
M
Melt analysis An analysis method used as quality check after PCR with intercalating
dyes or to determine the melting point of a sample. The temperature is
steadily increased so that amplified products dissociate at a certain
temperature, depending on their length and sequence composition. The
melt curve shows the fluorescence decrease and has a peak at the
dissociation time point.
Multiassay run Running more than one assay in one rotor. In this case, the thermal
profile of both assays must be identical. This feature is supported by the
option to add multiple acquisitions on the same acquisition channel. This
way the acquisitions can be individually set up for gain optimization.
N
Normalization A preprocessing of fluorescence curves that is intended to normalize the
amplitude of the fluorescence values (compensate for variations in the
amount of dye). This is typically combined with the removal of
background fluorescence (baseline correction) and some smoothing of
the data.

O
OTV Optical temperature verification (OTV) is a method that verifies the in-
tube temperature in a Rotor-Gene Q.
P
PCR Polymerase chain reaction.
Profile phase A thermal profile consists of one or more profile phases. Possible profile
phases are Hold, Cycling, Melt, Hybridization, HRM and HRM
Hydridization.
Q
QIAGEN channel QIAGEN default channels are Blue, Green, Yellow, Orange, Red,
Crimson, HRM. Their availability always depends on the optical
configuration of the Rotor-Gene Q.
qrex file Q-Rex experiment file format used by the Q-Rex Software.
qret file Q-Rex experiment template format used by the Q-Rex Software.
Quantification cycle The fractional cycle at which a curve reaches a predefined normalized
(Cq) fluorescence threshold. Other terms, that are not used in the Q-Rex
Software are CT (Cycle Threshold) or Cp (crossing point).
qut file Quantitation analysis parameter file format as used by Rotor-Gene Q

Software and the Rotor-Gene Assay Manager.
R
Reaction efficiency The efficiency of the PCR amplification. Efficiency can be reported
either as a percentage (where 100% means that the number of DNA
strands double in each cycle) or as a factor (where 2.0 means that the
number of DNA strands double in each cycle).
Replicate See technical replicate.
ret file Rotor-Gene experiment template file used by the Rotor-Gene Q

Software.
rex file Rotor-Gene experiment file format used by the Rotor-Gene Q

Software.
S
smp file Sample template file format used by the Rotor-Gene Q Software.

T
Take-off point The cycle where the second derivative of the amplification curve
reaches 25% of its maximum value. Take-off point indicates the
transition from background noise to the exponential phase.
Target The nucleic acid target sequence that is detected by a specific qPCR.
Technical replicate Multiple reactions (tubes) with the same sample (nucleic acid template)
and measuring the same target(s).
Template An experiment file without raw and processed data. It can consist of
sample layout, a run profile, an analysis profile and export parameters.
Thermal profile The temperature/time profile for a run. The thermal profile is part of
the run profile and typically consists of different profile phases.
Threshold Predefined fluorescence value used to calculate the quantification cycle

(Cq) of a curve.
Tm Melting temperature
Touchdown/Touchup The temperature for one cycling step is increased (touchup) or

decreased (touchdown) in each cycle for a defined number of cycles.
U
V
W
X
Y
Z

Appendices
13 Appendices
13.1 Appendix A – Supported file types

The Q-Rex Software uses the following special file types:
Extension Usage
.qrex Q-Rex experiment
.qret Q-Rex experiment template
.rex Experiment file used by Rotor-Gene Q Software
.ret Experiment template used by Rotor-Gene Q Software and the Rotor-Gene
Assay Manager
.smp Sample definition file as used by Rotor-Gene Q Software
.qut Quantitation analysis parameter file as used by Rotor-Gene Q Software
and the Rotor-Gene Assay Manager
Please contact QIAGEN for all requests concerning technical details of the file formats. Please note
that QIAGEN may choose not to disclose parts or all of the technical details of the file formats.

13.2 Appendix B – License terms
QIAGEN’s Q-Rex Software License Agreement
TERMS AND CONDITIONS of an LEGAL AGREEMENT (the "Agreement") by and between QIAGEN
GmbH, QIAGEN Strasse 1, D-40724 Hilden, Germany, ("QIAGEN") and you (either an individual
or a legal entity), the licensee of the software (hereinafter referred to as "SOFTWARE")
By installing, having installed and using the SOFTWARE you are agreeing to be bound by the terms
of this Agreement. If you do not agree to the terms of this Agreement, promptly return the software
package(s) and the accompanying items (including written materials) to the place you obtained them
for a full refund of the costs of the SOFTWARE.
1. GRANT OF LICENSE
Scope. Subject to the terms and conditions of this agreement, QIAGEN grants you a worldwide,
perpetual, non-exclusive, and nontransferable license to use the SOFTWARE solely for your internal
business purposes.
You shall not:
- modify or alter the whole or any part of the SOFTWARE nor merge any part of it with another
software nor separate any components of the SOFTWARE from the SOFTWARE nor, save to the
extent and in the circumstances permitted by law, create derivative works from, or, reverse
engineer, decompile, disassemble or otherwise derive source code from the SOFTWARE or
attempt to do any of these things
- copy the SOFTWARE (except as provided above)
- assign rent, transfer, sell, disclose, deal in, make available or grant any rights in the Software
Product in any form to any person without the prior written consent of QIAGEN;
- remove alter, obscure, interfere with or add to any proprietary notices, labels, trademarks, names
or marks on, annexed to, or contained within the SOFTWARE;
- use the SOFTWARE in any manner that infringes the intellectual property or other rights of
QIAGEN or any other party; or
- use the SOFTWARE to provide on-line or other database services to any other person.
Single-Computer Use. This Agreement permits you to use one copy of the SOFTWARE on a single
computer.
Trial versions. Trial versions of the SOFTWARE may expire after a period of 30 (thirty) days without
prior notice.
Open Software/Third Party Software. This Agreement does not apply to any other software
components identified as subject to an open source license in the relevant notice, license and/or
copyright files included with the programs (collectively the "Open Software") Furthermore, this
Agreement does not apply to any other software for which QIAGEN is only granted a derived right to
use ("Third Party Software"). Open Software and Third Party Software may be supplied in the same
electronic file transmission as the SOFTWARE, but are separate and distinct programs. The
SOFTWARE is not subject to the GPL or any other open source license.

If and insofar QIAGEN provides Third Party Software, the license terms for such Third Party
Software shall additionally apply and prevail. If Open Software is provided, the license terms for
such Open Software shall additionally apply and prevail. QIAGEN shall provide you with the
corresponding source code of relevant Open Software, if the respective license terms of the Open
Software include such obligation. QIAGEN shall inform if the SOFTWARE contains Third Party
Software and/or Open Software and make available the corresponding license terms on request.
2. UPGRADES
If the SOFTWARE is an upgrade from a previous version, you are granted a single license to both
copies, and you may not separately transfer the prior version(s) except as a one-time permanent
transfer to another user of the latest upgrade and all prior versions as allowed in Section 4 below.
3. COPYRIGHT
The SOFTWARE, including any images, and text incorporated in the SOFTWARE, is copyrighted and
is protected by German copyright laws and international treaty provisions. You may not copy any of
the printed materials accompanying the SOFTWARE.
4. OTHER RESTRICTIONS
You may not rent or lease the SOFTWARE, but you may transfer the SOFTWARE and accompanying
written materials on a permanent basis to another end user provided you delete the setup files from
your computer, and the recipient agrees to the terms of this Agreement. You may not reverse
engineer, decompile, or disassemble the SOFTWARE. Any transfer of the SOFTWARE must include
the most recent upgrade and all prior versions.
5. LIMITED WARRANTY
QIAGEN warrants that the SOFTWARE will perform substantially in accordance with the
accompanying printed materials for a period of ninety (90) days from the date of receipt. Any
implied warranties on the SOFTWARE are limited to ninety (90) days. Some states/jurisdictions do
not allow limitations on duration of an implied warranty, so the above limitation may not apply to
you.
6. CUSTOMER REMEDIES
QIAGEN's entire liability and your exclusive remedy shall be, at QIAGEN's option, either (a) return
of the price paid or (b) repair or replacement of the SOFTWARE that does not meet QIAGEN's
Limited Warranty and that is returned to QIAGEN with a copy of your receipt. This Limited Warranty
is void if failure of SOFTWARE has resulted from accident, abuse or misapplication. Any
replacement of SOFTWARE will be warranted for the remainder of the original warranty period or
thirty (30) days, whichever is longer.

7. LIMITED LIABILITY
In no event shall QIAGEN or its suppliers be liable for any damages whatsoever (including, without
limitation, damages for loss of business profits, business interruption, loss of business information, or
other pecuniary loss, unforeseeable damage, lack of commercial success, indirect damage or
consequential damage - in particular financial damage – or for damage resulting from third party
claims) arising out of the use or inability to use the SOFTWARE, even if QIAGEN has been advised
of the possibility of such damages.
The above restrictions of liability shall not apply in cases of personal injury or any damage resulting
from willful acts or gross negligence or for any liability based on the Product Liability Act
(Produkthaftungsgesetz), guarantees or other mandatory provisions of law.
The above limitation shall apply accordingly in case of:
- delay,
- compensation due to defect,
- compensation for wasted expenses.
8. NO SUPPORT
Nothing in this agreement shall obligate QIAGEN to provide any support for the SOFTWARE.
QIAGEN may, but shall be under no obligation to, correct any defects in the SOFTWARE and/or
provide updates to licensees of the SOFTWARE. You shall make reasonable efforts to promptly
report to QIAGEN any defects you find in the SOFTWARE, as an aid to creating improved revisions
of the SOFTWARE.
Any provision of support by QIAGEN for the SOFTWARE (including network installation support), if
any, shall solely be governed by an according separate support agreement.
9. TERMINATION
If you fail to comply with the terms and conditions of this Agreement, QIAGEN may terminate this
Agreement and your right and license to use the SOFTWARE. You may terminate this Agreement at
any time by notifying QIAGEN. Upon the termination of this Agreement, you must delete the
SOFTWARE from your computer(s) and archives.
YOU AGREE THAT UPON TERMINATION OF THIS AGREEMENT FOR ANY REASON, QIAGEN
MAY TAKE ACTIONS SO THAT THE SOFTWARE NO LONGER OPERATES.
10. GOVERNING LAW, VENUE

This Agreement shall be construed and interpreted in accordance with the laws of Germany, without
giving effect to conflict of laws provisions. The application of the provisions of the UN Sales
Convention is excluded. Notwithstanding any other provision under this Agreement, the parties to this
Agreement submit to the exclusive jurisdiction of the Dusseldorf courts.

Third Party Software License Information
This Product contains or makes use of the following third party components: Log4Net, Stateless
(Apache License v.2.0), DotNetZip, Plossum (zip/libpng license), Mog (BSD license) NHibernate
(GNU Lesser General Public License).

13.3 Appendix C – Liability clause
QIAGEN shall be released from all obligations under its warranty in the event repairs or
modifications are made by persons other than its own personnel, except in cases where the
Company has given its written consent to perform such repairs or modifications.
All materials replaced under this warranty will be warranted only for the duration of the original
warranty period and in no case beyond the original expiration date of original warranty unless
authorized in writing by an officer of the Company. Read-out devices, interfacing devices, and
associated software will be warranted only for the period offered by the original manufacturer of
these products. Representations and warranties made by any person, including representatives of
QIAGEN, which are inconsistent or in conflict with the conditions in this warranty shall not be binding
upon the Company unless produced in writing and approved by an officer of QIAGEN.

13.4 Appendix D – Important notes
This section lists known software limitations and/or items that may be important for troubleshooting.
Please read this section carefully.
Lock files
The software creates files with the file extension .lock to mark experiment files as being in use. In
case the software is terminated unexpectedly (for instance a power failure), these lock files may
remain on the file system and prevent access to the experiment. If you encounter problems when
opening an experiment, please check whether there are files with the extension .lock in the same
directory as the experiment file. If the Q-Rex Software is not running, these lock files can safely be
deleted.
Multi-Cell Paste
When pasting multiple cells into a table (for instance when editing sample information), you must
select the target area before pasting. The target area must have the same dimensions as the pasted
content (height and width).
Melt threshold when importing .rex files

When .rex files containing a melt phase are imported into the Q-Rex Software, no default threshold
(temperature and amplitude) is set when the .rex file contains no thresholds.
Handling of pages when importing .rex files

When .rex files containing multiple pages are imported, sample information is imported only for the
first page because multiple pages can contain information about the same tube in a .rex file. This
structure is not compatible with the Q-Rex Software data model.
Multiple attached cyclers

If multiple cyclers are connected to the computer running the Q-Rex Software, please switch off all
cyclers except for the one you are using. The Q-Rex Software does not currently support the use of
multiple cyclers in parallel.
Software updates
Do not attempt to execute a Q-Rex Software run while the operating system is installing updates. The
installation of software updates may consume the system resources needed for Q-Rex Software to
maintain exact timing of a run.

Anti-virus and anti-spyware scan
We strongly recommend to disable file system scans of anti-spyware and anti-virus software during
Q-Rex Software runs. The execution of such scans may consume the system resources needed for
Q-Rex Software to maintain exact timing of a run.
Encryption
Please note that experiment and template files are not encrypted. Anyone with sufficient technical
knowledge can extract the information in an experiment or template file.
Administrative OS rights
We do not recommend using the Q-Rex Software with administrative rights for the operating system.
While this will not cause the software to malfunction, Q-Rex Software relies on the operating system
for access restrictions to experiments. Access restrictions will not be available when using the
software with administrative OS rights.

13.5 Copyright information
Trademarks
QIAGEN®, QIAgility®, Rotor-Gene® (QIAGEN Group); Adobe®, Reader ® (Adobe Systems

Incorporated); Core™, Intel® (Intel Corporation); Excel®, Microsoft®, Windows® (Microsoft
Corporation). Registered names, trademarks, etc. used in this document, even when not specifically
marked as such, are not to be considered unprotected by law.
© 2015 QIAGEN, all rights reserved.

1099000 10/2015 HB-2006-001

www.qiagen.com
Technical Support
www.support.qiagen.com
1099000 10/2015 HB-2006-001

HB-2006-001 1099000 UM IAS RGQ QRexBasic 1015 WW

Uploaded by

Document Information

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

HB-2006-001 1099000 UM IAS RGQ QRexBasic 1015 WW

Uploaded by

Copyright:

Available Formats

October 2015

Q-Rex Software User

For use with the Rotor-Gene® Q instruments

2.6 Waste disposal

Q-Rex Software User Manual 10/2015 2

Q-Rex Software User Manual 10/2015 3

Define the .............................................................................6-12

Q-Rex Software User Manual 10/2015 4

8.2 Analysis overview

Q-Rex Software User Manual 10/2015 5

Q-Rex Software User Manual 10/2015 6

1.1 Provided user manuals

Q-Rex Software User Manual 10/2015 1-2

1.3 General information

1.3.1 Technical assistance

Q-Rex Software User Manual 10/2015 1-3

1.3.3 Version management

1.3.4 Intended use

Q-Rex Software User Manual 10/2015 1-4

Using the Q-Rex Software Help

Q-Rex Software User Manual 10/2015 1-5

Name Icon Description

Back Returns to the previous screen.

Forward Returns to the screen displayed before clicking Back.

Print Allows you to print:

The navigation panel contains the following tabs:

Search Search for specific help topics.

Favorites Save and manage shortcuts to specific help topics.

Q-Rex Software User Manual 10/2015 1-6

Safety information for the Rotor-Gene Q

Q-Rex Software User Manual 10/2015 2-2

WARNING/ Risk of personal injury and material damage [W1]

WARNING/ Risk of personal injury and material damage [W2]

WARNING/ Risk of personal injury and material damage [W3]

CAUTION Damage to the instrument [C1]

Q-Rex Software User Manual 10/2015 2-3

WARNING/ Risk of personal injury and material damage [W5]

WARNING/ Risk of personal injury and material damage [W6]

WARNING/ Risk of personal injury and material damage [W7]

CAUTION Damage to the instrument [C2]

Q-Rex Software User Manual 10/2015 2-4

WARNING Electrical hazard [W8]

To ensure satisfactory and safe operation of the Rotor-Gene Q:

WARNING Electrical hazard [W9]

Q-Rex Software User Manual 10/2015 2-5

WARNING Explosive atmosphere [W10]

WARNING Risk of explosion [W11]

CAUTION Damage to the instrument [C3]

2.4 Biological safety

Q-Rex Software User Manual 10/2015 2-6

WARNING Samples containing infectious agents [W12]

* OSHA: Occupational Safety and Health Administration (United States of America).

Q-Rex Software User Manual 10/2015 2-7

WARNING Hazardous chemicals [W13]

* OSHA: Occupational Safety and Health Administration (United States of America).

WARNING Risk of fire [W14]

2.5.1 Toxic fumes

2.6 Waste disposal

Q-Rex Software User Manual 10/2015 2-8

WARNING Moving parts [W15]

WARNING/ Risk of personal injury and material damage [W16]

CAUTION Damage to the instrument [C4]

CAUTION Damage to the instrument [C5]