Qiagen QIAamplifier 96 User manual

Sample to Insight__
March 2020
QIAamplifier™96
User Manual
For Molecular Biology Application. Not for use in diagnostic procedures.
QIAGEN GmbH, QIAGEN Strasse 1, D
-40724 Hilden
1120412

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Contents
1Introduction .................................................................................................. 6
1.1 About this user manual ........................................................................ 6
1.2 Conventions ....................................................................................... 7
1.3 Intended use of QIAamplifier 96 .......................................................... 7
1.4 Warranty and liability......................................................................... 8
2Safety Information......................................................................................... 9
2.1 Symbols and signal words used............................................................ 9
2.2 Safety markings on the QIAamplifier 96.............................................. 10
2.3 Technical condition ........................................................................... 11
2.4 Requirements for the operating personnel ............................................ 11
2.5 Safety instructions, transport, and installation ....................................... 12
2.6 Safety instructions – during operation.................................................. 12
2.7 Behavior during emergencies ............................................................. 14
3Technical Specifications............................................................................... 15
4Function and setup ...................................................................................... 16
4.1 High speed thermoblock.................................................................... 17
4.2 High Performance Smart Lid............................................................... 17
4.3 Display............................................................................................ 17
4.4 User-specific quick start of programs ................................................... 18
4.5 Easy programming............................................................................ 18
4.6 Linear gradient tool........................................................................... 18
4.7 GLP compliance................................................................................ 19
4.8 Open system philosophy.................................................................... 19
5Installation.................................................................................................. 20
5.1 Scope of delivery.............................................................................. 20
5.2 Unpacking and inspection ................................................................. 20
5.3 Setting the operating voltage.............................................................. 20
5.4 Commissioning................................................................................. 22

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6Control elements ......................................................................................... 23
6.1 QIAamplifier 96 front view ................................................................ 23
6.2 QIAamplifier 96 rear view................................................................. 24
6.3 High Performance Smart Lid (HPSL)..................................................... 25
6.4 The QIAamplifier 96 software ............................................................ 27
7Operation .................................................................................................. 36
7.1 Power on self-test .............................................................................. 36
7.2 Login screen..................................................................................... 36
7.3 Login............................................................................................... 37
7.4 Home screen.................................................................................... 39
7.5 Block status ...................................................................................... 40
7.6 Quick start function ........................................................................... 42
7.7 Incubation mode............................................................................... 44
8Creating, editing, and saving programs ........................................................ 46
8.1 Programming modes ......................................................................... 46
8.2 Creating a new program/using a program template............................. 48
8.3 Assigning program names ................................................................. 50
8.4 Setting the heated lid temperature....................................................... 50
8.5 Preheating the heated lid................................................................... 51
8.6 Editing steps..................................................................................... 52
8.7 Inserting a step................................................................................. 62
8.8 Deleting a step ................................................................................. 63
8.9 Saving the program .......................................................................... 63
9Starting, copying, and deleting programs ...................................................... 66
9.1 Starting a program ........................................................................... 66
9.2 Copying a program .......................................................................... 67
9.3 Copying all programs ....................................................................... 68
9.4 Deleting a program........................................................................... 69
9.5 Deleting all programs........................................................................ 70
10 Running, pausing, continuing, and stopping programs .................................... 71
10.1 Display during a run ......................................................................... 71

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10.2 Pausing a program ........................................................................... 73
10.3 Continuing the program .................................................................... 75
10.4 Skipping a step ................................................................................ 75
10.5 Stopping the program ....................................................................... 75
11 Tools ......................................................................................................... 77
11.1Configuration................................................................................... 78
11.2 User management............................................................................. 84
11.3 Documentation ................................................................................. 88
11.4 Service info file (SINF)....................................................................... 96
11.5 Backup ............................................................................................ 97
11.6 Cycler Info ....................................................................................... 98
11.7 Contact ......................................................................................... 100
12 Quick reference guide ............................................................................... 101
13 Troubleshooting ........................................................................................ 107
13.1 Administrator password forgotten ..................................................... 107
13.2 Slow heating and cooling................................................................ 107
13.3 Auto restart .................................................................................... 107
13.4 Auto restart without an apparent cause .............................................107
13.5 Adaptation of programs from other thermal cyclers.............................108
13.6 Loosening the lid wheel in case of blockage ......................................108
14 Maintenance and care .............................................................................. 109
14.1 Cleaning the housing ...................................................................... 109
14.2 Disinfecting the device..................................................................... 110
14.3 Firmware update ............................................................................ 110
15 Service .................................................................................................... 111
15.1 Device return information................................................................. 111
15.2 Packing the QIAamplifier 96............................................................ 112
16 Disposal................................................................................................... 113
Appendix A..................................................................................................... 114
Declaration of Conformity .......................................................................... 114
Certificates............................................................................................... 115

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Waste Electrical and Electronic Equipment (WEEE) ....................................... 116
Index .............................................................................................................. 118
Document Revision History................................................................................. 120

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1Introduction
The QIAamplifier 96 is intended for operation by qualified specialist personnel observing this
operating manual.
1.1 About this user manual
The operating manual contains information about the design and operation of the QIAamplifier 96
and provides personnel familiar with PCR technology with the necessary know-how for the safe
handling of the equipment and its components. The operating manual further includes notes on the
maintenance and service of the device and potential causes and remedies of any faults.
1.1.1 Technical assistance
At QIAGEN®, we pride ourselves on the quality and availability of our technical support. Our
Technical Services Departments are staffed by experienced scientists with extensive practical and
theoretical expertise in molecular biology and the use of QIAGEN products. If you have any
questions or experience any difficulties regarding QIAamplifier 96 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
support.qiagen.com.
1.1.2 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.
To produce useful and appropriate documentation, we appreciate your comments on this user
manual. Please contact QIAGEN Technical Services.

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1.2 Conventions
Instructions for action which occur in chronological order are numbered and combined into action
units and furnished with the corresponding results.
Lists,which are not in chronological order, are shown as itemized lists, sub-listings as bullet points.
Safety instructions are indicated by pictographs and signal words. The type and source of the
danger are stated together with notes on preventing the danger. The meaning of the pictographs
and signal words used is explained in the chapter Safety Information.
1.3 Intended use of QIAamplifier 96
The QIAamplifier 96 is an end-point thermal cycler. It is designed to amplify nucleic acids by
repeated cycles of heating and cooling using DNA polymerases in a PCR reaction.
The thermal cycler is developed for Molecular Biology Application (MBA).
The QIAamplifier 96 combines modern design with user-friendly software. The user interface
consists of a touchscreen with a graphical or spreadsheet display that shows the time, the status,
and the temperature program for each run. Using the touchscreen keyboard, information and
program parameters can be entered directly on the screen. Due to the high ramp rates, the
QIAamplifier 96 thermal cycler is suitable for fast PCR applications, thereby helping to shorten
program run times.

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1.4 Warranty and liability
The warranty duration and liability comply with the legal requirements and the provisions in the
general terms and conditions of QIAGEN.
Deviations from the intended use described in this manual result in limitations of warranty and
liability in the event of damage.
Warranty and liability claims are excluded for personal injury and property damage due to one or
several of the following causes:
Use of the QIAamplifier 96 other than intended
Improper commissioning, operation and servicing of the device
Modifications of the QIAamplifier 96 without prior consultation with QIAGEN
Unauthorized intervention in the QIAamplifier 96
Operation of the QIAamplifier 96 with faulty safety equipment
Use of other than original spare parts, wearing parts or consumables
Improper repairs
Improper transport and storage of the QIAamplifier 96
Faults due to the non-observance of this manual
Improper repairs
Improper transport and storage of the device
Faults due to the non-observance of this manual

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2Safety Information
For your own safety and to ensure error-free and safe operation of the QIAamplifier 96, please
read this chapter carefully before commissioning.
Besides the safety instructions in this user manual and the local safety regulations that apply to the
operation of the device, the general applicable regulations regarding accident prevention,
occupational health and safety, and environmental protection have to be observed and complied
with.
References to potential dangers do not replace the work protection regulations which must be
observed.
2.1 Symbols and signal words used
This manual uses the following symbols and signal words to indicate hazards or instructions. The
safety instructions are always placed before an action.
WARNING
Indicates a potentially hazardous situation which, if not prevented, can result in
death or most serious injuries (incapacitation).
CAUTION
Indicates a potentially hazardous situation which, if not prevented, can result in
light or minor injuries and material damage.
ATTENTION
Indicates a potentially hazardous situation which, if not avoided, can result in
damage to the product or items in its vicinity.

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Symbol for waste disposal in accordance with WEEE directive:
Do not dispose of in household waste
CE marking
China RoHS marking
2.2 Safety markings on the QIAamplifier 96
Damaged or missing safety symbols can cause incorrect actions leading to personal injury or
material damage.
Important: Do not remove safety symbols. Replace damaged safety symbols immediately.
The following safety symbols are attached to the inside of the heated lid and the rear of the device:
CAUTION!
Hazard area!
Proceed with due care when handling samples and working with the
QIAamplifier 96.
CAUTION!
Risk of burns!
There is a risk of burning at the heated lid, the thermal block, the samples, and
the rear of the device.

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ATTENTION! Keep ventilation slits clear!
Keep the ventilation slits on the underside and at the rear of the
device clear. Make sure that there are no objects underneath the
device (e.g., paper) that may be sucked a
gainst the ventilation slot
and thus interfere with ventilation.
2.3 Technical condition
The QIAamplifier 96 has been built and certified according to safety standard EN 61010-1. Do
not modify the device in any way. Any modification of the device will lead to a loss of warranty
and the EN 61010-1 certificate and poses a potential risk.
Observe the following:
The operator must only operate the device in a sound and operationally safe condition. The
technical condition must always comply with the legal requirements and regulations.
Prior to every use the device must be checked for damage and sound condition.
Any changes in the device affecting its safety must be reported by the operating personnel to
the operator without delay.
2.4 Requirements for the operating personnel
The QIAamplifier 96 must only be operated by qualified specialist personnel instructed in the use
of the device. The instructions also include imparting the contents of this manual.
In addition to the safety at work instructions in this operating manual, the generally applicable
safety and accident prevention regulations of the respective country of operation must be observed
and adhered to. The operator must ascertain the latest version of these regulations.
The operating manual must be accessible to the operating and service personnel at all times.

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2.5 Safety instructions, transport, and installation
Observe the following:
Drain the sample block before transporting the QIAamplifier 96. Make sure there are no
sample tubes in the block.
Only ship the QIAamplifier 96 in its original packaging with the transport lock installed.
Please verify that the delivery is complete on receipt of the QIAamplifier 96 and check for
possible transport damage. In case of claims, please contact QIAGEN.
The QIAamplifier 96 is intended for indoor use only. The QIAamplifier 96 is not designed for
installation and operation in an open or humid environment.
2.6 Safety instructions – during operation
2.6.1 General
The operator of the QIAamplifier 96 must make sure before each commissioning that the condition
of the device including the safety equipment is sound.
Observe the following:
Free access to the power switch on the back of the enclosure has to be ensured during
operation.
The ventilation fittings at the rear of the device must be unobstructed and operational.
Covered ventilation grilles or slits etc. may cause the device to break down or may cause
damage to it.
The use of oil between the samples and the sample block is not necessary to achieve an
improved heat exchange. However, if you still want to use oil, you should use mineral oil. Do
not use silicone oil.
Be careful to avoid crushing or pinching injuries when closing the device.
The QIAamplifier 96 may cause burns. Observe the following:
The thermal block, the samples and the heated lid reach high temperatures. There is a risk of
burns during contact.
Ensure that the lid is securely closed before starting the program. Do not touch the heated lid.

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The rapid heating of the thermal block can cause liquids to boil explosively. Always wear
safety goggles during operation.
Do not touch hot sample tubes or plates and do not open them or boiling liquid may escape.
Only use plates and tubes that are suitable for high temperatures (up to 100°C), fit well into
the thermal block (no shaking), and whose lids seal tightly.
2.6.2 Safety instructions – protection against explosion and fire
The QIAamplifier 96 must not be operated in an explosive environment.
The QIAamplifier 96 must not be operated with flammable, explosive, or volatile substances.
2.6.3 Safety instructions – electrical equipment
Work on the electrical components of the QIAamplifier 96 may only be performed by a qualified
electrical technician in accordance with the applicable electrical engineering rules. Life-threatening
electrical voltages may occur in the interior of the QIAGEN QIAamplifier 96.
Observe the following:
Any work on the interior of the device may only be carried out by the customer service of
QIAGEN and specially authorized technicians.
The electrical components must be checked regularly by a qualified electrician. Any defects,
such as loose connections and faulty or damaged cables, must be repaired without delay.
Before opening the device, it must be switched off at the power switch and the main plug must
be disconnected from the mains outlet.
The QIAamplifier 96 must be switched off immediately using the power switch (on the
equipment backplate) and the mains plug disconnected from the power supply if any faults
occur in the electric components.
Do not operate the device near sources of strong electromagnetic radiation (for example, an
unshielded, deliberately operated high frequency source), as these may affect proper
operation of the device.
2.6.4 Handling of samples, auxiliary, and operating materials
The operator is responsible for the selection of substances used in the process as well as for their
safe handling. This is particularly important for radioactive, pathogenic, infectious, poisonous,
corrosive, or otherwise dangerous substances. For details, contact the safety officer responsible for
your location. When handling dangerous substances, local safety codes and guidelines must be

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observed. The following general notes do not replace the specific local regulations or the regulations
in the EC safety data sheets of the manufacturers for the auxiliary and operating materials.
Observe the following:
Protective goggles and rubber gloves have to be worn when handing reagents.
If only a few samples are treated, an (empty) tube of the same height must additionally be
placed at each corner position of the block. If the number of samples in the block is too low,
there is a risk of the tubes being damaged and sample liquid leaking out.
For your own safety, observe the potential infectious qualities of the examined biological
material.
2.6.5 Safety instructions – service and repair
The QIAamplifier 96 is usually repaired by the service department of QIAGEN or its authorized
and trained specialist personnel. Unauthorized repairs can damage the device. Therefore, the
operator may generally only carry out the tasks listed in chapter Maintenance and care.
The following must be observed:
The exterior of the device may only be cleaned with a damp, not dripping, cloth after the
device has been switched off.
Do not use alcohol (e.g., methanol or ethanol), organic solvents, or abrasives to clean the
device.
Any maintenance on the device may usually only be carried out in the switched-off condition
(unless stated otherwise).
2.7 Behavior during emergencies
In case of danger or accidents, immediately switch off the QIAamplifier 96 using the main switch
on the equipment backplate. Disconnect the mains plug from the power supply.

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3Technical Specifications
Name QIAGEN QIAamplifier 96
Capacity 96 x 0.2 ml tubes, 96 well micro plates or 8 well strips
Block material Aluminum
Block coating Special alloy
Max. heating rate* 4.0°C/sec
Max. cooling rate* 3.3°C/sec
Avg. heating rate* 3.7°C/sec
Avg. cooling rate* 3.0°C/sec
Linear Gradient Tool Yes
Max./min gradient 20°C/0.1 °C
Gradient temperature range†20°C to 99 °C
Temperature uniformity 95°C: +/- 0,60°C after 15 s
72°C: +/- 0,30°C after 15 s
55°C: +/- 0,20°C after15 s
Temperature range 3°C to 99°C
Control accuracy +/- 0.1°C
Software User-specific quick start option for the five most recent programs; program
preview before start; option for toggling between programming table and graph
programming mode; Linear Gradient Tool1, service info file (SINF) generation;
expanded self-test; adjustable ramp rates; gradient temperature diagram view;
Program memory Total capacity of 350 programs in up to 90 user directories
Language English
Display 7” color touchscreen
Automatic restart after power failure Yes
HPSL technology Yes
Lid temperature range 30°C to 110°C
Power consumption 550 watt
Operating voltage 100, 115, 230 Volt ±10%, 50 – 60 Hz
Fuse 2 x 8AT (special type of fuse required)
Please contact QIAGEN technical services for assistance
Noise emissions Very low, max. 45 dBA
Interfaces†USB A, Ethernet
Environmental conditions 15°C to 35°C, max. 70% air humidity, max. 2,000 m above sea level,
overvoltage category II, pollution degree 2, IP20
Dimensions (WxDxH) 260 mm x 430 mm x 210 mm
Dimensions (WxDxH) with open lid 260 mm x 430 mm x 385 mm
Weight 11.5 kg
HPSL: High Performance Smart Lid. * Measured inside the block. †The network cable must be at least performance class Cat
5e and the cable configuration has to be STP

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4Function and setup
The QIAamplifier 96 thermal cycler is available with aluminum block and gradient function.
The device is controlled by a 7” touchscreen display and an easy-to-use user interface. PCR
protocols and run log files can be saved to a connected USB stick. By using the USB functions, PCR
protocols can be exchanged easily between devices and run log files can be stored for
documentation reasons on a PC.
Figure 1. The QIAamplifier 96 Thermal Cycler.
The QIAamplifier 96 thermal cycler features an automatic restart. If a power failure occurs during
the run, the device will continue the run as soon as power is restored. In case of long-term power
failure (longer than 30 minutes), the device will keep the sample block at 4°C (freeze step) and the
user can decide to repeat the run with the same samples or to discard them.
The gradient function can be used for the optimization of new primer pairs. The Linear Gradient
Tool allows the programming of gradients with a defined temperature difference between the rows
or columns of the sample block.

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This manual provides information on how to use the QIAamplifier 96 Thermal Cycler most
effectively.
4.1 High speed thermoblock
All blocks of the QIAamplifier 96 thermal cycler are made of aluminum and offer high ramp rates
for fast protocol run times. A rubber seal on the heated lid forms an encapsulated space around
the sample block as soon as the lid is closed. The closed space serves to improve the temperature
uniformity of the sample block and avoids the formation of condensed water at the final PCR cooling
step. Furthermore, all blocks are perfectly sealed to prevent condensed water from penetrating into
the Peltier elements underneath the sample block and other parts of the electronics. The sealing
protects the Peltier elements and prolongs the lifetime of the device.
4.2 High Performance Smart Lid
The QIAamplifier 96 heated lid has been optimized to shorten protocol run times. Moreover, the
heated lid fulfills two other important functions: It prevents the formation of condensation at the
reaction tube portion located above the block surface level, and it ensures reliable contact between
the reaction tubes and the thermoblock by applying constant pressure. Thanks to the integrated
clutch mechanism, the pressure applied to the reaction tubes is always the same, regardless of the
plasticware height. The combination of the heated lid shape and the reliable contact pressure
ensures even temperature distribution between samples, thus significantly improving temperature
uniformity.
With one press on the front button, the heated lid gently swings open and locks in its end position.
This mechanism ensures that the lid cannot fall and the heated lid is out of the radius of action while
the user inserts PCR tubes or plates. This prevents any risk of injury from crushing or hot surfaces.
4.3 Display
The QIAamplifier 96 thermal cycler features a 7” state-of-the-art color touchscreen user interface.
The touchscreen is built-in at a flat angle to ensure reflection-free viewing and ergonomic
programming. For programming PCR protocols, the software incorporates QIAGEN spreadsheet
and alternatively offers graphical programming. One touch of a button leads from the spreadsheet
to the alternative graphical programming mode. This makes the creation of new programs or editing
existing programs fast and easy.

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4.4 User-specific quick start of programs
Many other thermal cyclers offer a so-called “List of latest programs used”. In the list of latest
programs used, a certain number of PCR programs is collected and offered for quick start. The list
is typically ordered only by date and the user has to search for the desired program. In contrast,
the QIAamplifier 96 software creates a user-specific list and only the latest programs started by the
currently logged-in user are offered for quick start. Even if a lab member does not use the device
for a longer time, the information on the latest programs started by this user will not get lost.
For maximum convenience, the QIAamplifier 96 software additionally features a program preview.
Before the start of a program the protocol steps are summarized in a clearly arranged table by the
program preview tool. The preview therefore provides a comprehensive overview of the protocol
structure without the need to access programming screens. The program preview is also available
before the quick start of programs.
4.5 Easy programming
Creating new PCR programs takes a lot of time if for each single step all parameters have to be set
manually. The QIAamplifier 96 software offers several pre-installed program templates for different
applications. The program templates provide a general protocol structure that can be easily
adapted for the current experiment.
4.6 Linear gradient tool
For optimizing new primer pairs in a single run, the QIAamplifier 96 is equipped with a gradient
function. Finding the best primer annealing temperature is crucial for the specificity and efficiency
of PCR reactions. Often the optimization of experiments is conducted to a limited extent only,
leading to unspecific byproducts or reduced PCR sensitivity. By using the gradient function, new
primer pairs with unknown annealing temperatures can be tested quickly and optimized in a very
short time.
For maximum convenience, the QIAamplifier 96 offers the Linear Gradient Tool. For most other
devices, the temperature difference from row to row or from column to column in a gradient step
varies across the sample block. The QIAamplifier 96 Linear Gradient Tool enables the programming
of gradient steps with a defined temperature increment between the columns or rows. The Linear
Gradient Tool option enables the comfortable creation of gradient steps and thus the best annealing
temperature can be easily transformed to a non-gradient protocol.

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4.7 GLP compliance
The software can manage up to 30 user accounts. With each system start, the QIAamplifier 96
performs an initial self-test and additionally, the software offers an extended self-test that can be
initiated by the user. The results of the extended self-test are summarized in a protocol and stored
by the device. In addition to the self-test functions, the device creates and stores log files for each
single run. For long-term storage, the log files and extended self-test protocols can be exported as
a proprietary file format.
4.8 Open system philosophy
The QIAamplifier 96 is an open system regarding consumables and reagents. Depending on the
sample block, the system can be used with single tubes, strips, or plates. PCR plates can be standard
profile or low profile and they can be skirted, half-skirted, or non-skirted. The QIAamplifier 96 can
handle all kinds of plates and the plasticware can be sealed with domed lids, flat lids, sealing foil,
or other technologies. Regardless of the sealing method used, thanks to the HPSL technology, (see
chapter 4.2) the same pressure is always applied to the consumables for absolutely reproducible
conditions.
The QIAamplifier 96 thermal cycler is not limited to reagents from a specific vendor and can be
used with any kind of polymerase. Regardless of whether isothermal, hot start, or non-hot start
polymerases are used, the QIAamplifier 96 will produce reliable results. By programming a pause
step for the initial denaturation for example, the system can be used for manual hot start
applications. After inserting the samples into the heating block, the PCR protocol can be started just
by pressing Continue.

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5Installation
5.1 Scope of delivery
Thermal cycler
Mains cable
Operating instructions
Please keep the original packaging in case the device needs to be returned. The shipping box for
the QIAamplifier 96 thermal cycler contains a specially developed foam system for the transport of
high-quality electronic devices.
5.2 Unpacking and inspection
Unpack and carefully check the device. Immediately report any damage to QIAGEN. Do not
attempt to operate the device if there is any visible damage.
Keep the original packaging for possible return. The QIAamplifier 96 must always be transported
in its original packaging. If the packaging is no longer available, please contact QIAGEN.
5.3 Setting the operating voltage
WARNING
Danger of electric shock!
Before commissioning the device, make sure that the voltage selector setting on
the underside of the device corresponds to the mains voltage in your laboratory.
The QIAamplifier 96 can be operated at 100, 115, or 230 volts.
Note: Set the operating voltage by turning the dial on the underside of the QIAamplifier 96 to the
desired voltage. You can do so with a coin.