Analytik Jena qTOWER3 User manual

Operating manual
qTOWER3auto / qTOWER384 auto
Real-time PCR thermal cycler

Analytik Jena GmbH
Konrad-Zuse-Str.1
07745 Jena Germany
Phone + 49 3641 77 70
Fax + 49 3641 77 92 79
Email [e-mail]
Biometra GmbH
Rudolf-Wissell-Str. 30
37079 Göttingen Germany
Phone + 49 551 50 68 610, -12 or -14
Fax + 49 551 50 68 666
E-mail [e-mail]
Analytik Jena GmbH
Konrad-Zuse-Str. 1
07745 Jena Germany
Phone + 49 3641 77 9460
Fax + 49 3641 77 946
E-mail [e-mail]
http://www.analytik-jena.com
10-3107-082-23
A (01/2021)
Analytik Jena GmbH
© Copyright 2021 Analytik Jena GmbH
Manufacturer
Technical Service
Application Support
General Information
Documentation number
Edition
Technical documentation
made by:

Contents
Contents
1Basic information ....................................................................................................... 5
1.1 Notes on this operating manual....................................................................................... 5
1.2 Purpose.............................................................................................................................. 6
1.3 Warranty and liability........................................................................................................ 7
2Safety and warning instructions ................................................................................ 8
2.1 General notes .................................................................................................................... 8
2.2 Safety markings................................................................................................................. 8
2.2.1 Safety symbols................................................................................................................... 8
2.2.2 Symbols ............................................................................................................................. 9
2.3 Requirements for the operating personnel.................................................................... 10
2.4 Safety instructions - Transport and installation............................................................. 10
2.5 Safety instructions: during operation ............................................................................. 11
2.5.1 Summary of safety instructions ...................................................................................... 11
2.5.2 Safety instructions – protection against explosion and fire........................................... 11
2.5.3 Safety instructions – electrical equipment ..................................................................... 11
2.5.4 Handling of samples, auxiliary and operating materials ............................................... 12
2.6 Behavior during emergencies ......................................................................................... 13
2.7 Safety instructions – maintenance and repair ............................................................... 13
3Layout and function ................................................................................................. 14
3.1 Layout.............................................................................................................................. 14
3.1.1 qTOWER³ auto ................................................................................................................ 16
3.1.2 qTOWER3auto power module........................................................................................ 18
3.2 Function........................................................................................................................... 19
3.2.1 Fluorescence spectrometer ............................................................................................. 19
3.2.2 PCR thermal cycler .......................................................................................................... 21
3.2.3 Lid heating ...................................................................................................................... 21
3.2.4 Plastic .............................................................................................................................. 21
3.3 Type plate........................................................................................................................ 22
4Installation and commissioning ............................................................................... 23
4.1 Power supply ................................................................................................................... 23
4.2 Unpacking and inspection............................................................................................... 24
4.3 Installing and connecting the device .............................................................................. 25
5Operation.................................................................................................................. 27
5.1 Switching on the qTOWER³ auto.................................................................................... 27
5.2 Switching off the qTOWER³ auto.................................................................................... 27
5.3 Real-time PCR analysis ................................................................................................... 28
5.3.1 Safety instructions........................................................................................................... 28
5.3.2 Preparing samples........................................................................................................... 28
6Maintenance and repair........................................................................................... 29
6.1 Cleaning the housing ...................................................................................................... 30
6.2 Checking the drawer ....................................................................................................... 30
6.3 Disinfecting the device.................................................................................................... 31
6.4 Replacing the fuse........................................................................................................... 32
7Error messages ......................................................................................................... 33
7.1 General ............................................................................................................................ 33
7.2 Information on errors or malfunctions........................................................................... 33
8Transport and storage.............................................................................................. 35
8.1 Transport......................................................................................................................... 35
8.1.1 Inserting the transport lock............................................................................................. 35
8.1.2 Moving the qTOWER³ auto in the laboratory ................................................................ 35
8.1.3 Device return information............................................................................................... 36

Figures
8.2 Storage............................................................................................................................. 37
9Disposal .................................................................................................................... 38
10 Specification ............................................................................................................. 39
10.1 Technical data ................................................................................................................. 39
10.1.1 qTOWER3auto ................................................................................................................ 39
10.1.2 Power module ................................................................................................................. 40
10.2 Environmental conditions ............................................................................................... 41
10.3 Standards and directives ................................................................................................. 42
Figures
Fig. 1 Device components............................................................................................15
Fig. 2 qTOWER³ auto (front view)...............................................................................16
Fig. 3 qTOWER3auto with extended drawer..............................................................17
Fig. 4 qTOWER³ auto (rear view) ................................................................................17
Fig. 5 Power module (front view)................................................................................18
Fig. 6 Power module (rear view) .................................................................................18
Fig. 7 Schematic representation: fluorescence spectrometer.....................................19
Fig. 8 Schematic representation: light beam course through filter color module .....20
Fig. 9 qTOWER3auto type plate ..................................................................................22
Fig. 10 qTOWER3auto power module type plate .........................................................22
Fig. 11 Connecting the qTOWER3auto .........................................................................25
Fig. 12 Connections at rear ............................................................................................26
Fig. 13 Fuse compartment at the back of the qTOWER³ auto power module.............32

Basic information
5
1Basic information
1.1 Notes on this operating manual
These operating instructions describe the following thermal cycler models:
qTOWER3auto
qTOWER384 auto
Note: In the text below, these devices are collectively called qTOWER3auto. If differ-
ences between the models exist, they are explained in the corresponding sections.
The automated real-time PCR thermal cyclers are only intended for use by qualified spe-
cialist personnel observing these operating instructions. In addition, these instructions
include the description of the qTOWER3auto power module, which supplies the thermal
cycler with power.
The operating manual contains information about the design and function of the device
and provides operating personnel familiar with PCR technology with the necessary
know-how for the safe handling of the equipment. The operating manual further con-
tains notes on the maintenance and servicing of the device, as well as potential causes
and remedies of any faults.
Instructions in chronological sequence are numbered, grouped into blocks of instruc-
tions and the expected result is indicated.
Safety instructions are indicated by pictographs and signal words. The type, source and
consequences of the danger are stated together with notes on preventing the danger.
The meaning of the pictograms and signal words used is explained in section 2 “Safety
and warning instructions”.
The operating manual uses the following symbols and signal words to indicate hazards
or instructions. 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.
Contents
Conventions
Symbols and signal words
used

Basic information
6
1.2 Purpose
The qTOWER³ auto is a thermal cycler developed for real-time PCR experiments which
amplify DNA by way of the polymerase chain reaction (PCR), while using fluorescence
spectroscopy for the highly sensitive detection of target sequences. The signal from the
fluorescent dyes excited by a light source correlates, in terms of quantity, with the PCR
product and may be shown in real-time.
Thanks to a modular design that has been specially adapted to meet the requirements
of automation technology, the device can be used for all relevant real-time PCR applica-
tions, for example for the detection of pathogens, gene expression analysis, SNP geno-
typing or mutation detection, as well as for experimental studies with increased sample
throughput.
Optimized for the area of gene expression and genotyping, the real-time PCR cycler al-
lows for multiplex analyses depending on the fluorescence properties of the dyes and
sensors, as well as the available filter modules – proof of several target sequences in a
single PCR reaction. Analytik Jena offers a number of color or FRET modules here, up to
six of which can be installed simultaneously in the device.
In addition to the optical components for the detection of real-time signals, the amplifi-
cation of the target sequences plays a central role. With Peltier technology and the use
of high-quality block materials, the qTOWER3auto boasts a superb thermal homogene-
ity, maximum speed and accuracy.
The qTOWER³ auto is fully controlled from the PC using the qPCRsoft auto application
software. The control software is simple and intuitive, and guides the user on a step-by-
step basis through the programming, data acquisition and analysis menu items. Further-
more, the software offers a wide spectrum of free analysis tools which allow for the
quick and reliable evaluation of comprehensive analyses:
Absolute and relative quantification
ΔΔCt – Analyses with/without PCR efficiency
DNA melting curves
SNP genotyping
End point analyses
Further information on the various qPCRsoft auto software functions can be found in
the software user manual.
We recommend the following scientific publication for an intensive introduction into the
real-time PCR analysis techniques and applications:
LOGAN, Julie; EDWARDS, Kristin; SAUNDERS, Nick (ed.): Real-Time PCR – Current Tech-
nology and Application. Norfolk UK: Caister Academic Press, 2009

Basic information
7
ATTENTION
The device is intended for
general laboratory use. The license is limited to applications
outside of vitro diagnostics (research use only).
The device may only be used for the applications described in these operat
ing instruc-
tions.
The manufacturer does not accept liability for any other use.
1.3 Warranty and liability
The warranty duration and liability comply with the legal requirements and the provi-
sions in the general terms and conditions of Analytik Jena.
Deviations from the intended use described in this operating manual result in limitations
of warranty and liability during a damage event. Warranty and liability claims are ex-
cluded for personal injury and property damage due to one or several of the following
causes:
Improper use of the qTOWER³ auto.
Improper commissioning, operation and maintenance of the device.
Modifications of the equipment without prior consultation with Analytik Jena.
Operation of the device with defective or faulty safety equipment.
Use of parts other than the original spare parts, wearing parts, or consumables.
Repairs that have not been carried out correctly.
Improper transport and storage of the device.
Errors due to the non-observance of this operating manual.

Safety and warning instructions
8
2Safety and warning instructions
2.1 General notes
For your own safety and to ensure error-free and safe operation, please read this
section carefully before commissioning.
Observe all safety instructions in these operating instructions.
References to potential dangers do not replace the work protection regulations
which must be observed.
The device meets all EMC requirements for commercial and industrial use and for
use in small businesses!
2.2 Safety markings
2.2.1 Safety symbols
Damaged or missing safety symbols can cause incorrect actions leading to personal in-
jury or material damage. Do not remove safety symbols! Replace damaged safety sym-
bols immediately!
The following safety symbols are attached to the front of the power supply unit or to the
rear of the device:
Safety symbol Meaning
Risk of electric shock! Do not touch!
General warning sign
Warning about hot surface
Disconnect the plug before opening the device
Do NOT dispose of this device as municipal waste! To ensure
optimum protection of the global environment and minimize
pollution, valuable raw materials can be recovered. Please re-
cycle this device.
Alternatively, dispose of the electronic components as elec-
tronic waste in accordance with valid regulations.

Safety and warning instructions
9
The device contains substances subject to regulation (accord-
ing to regulation SJ/T 11363-2011). Analytik Jena guarantees
that the substances will not leak within the next 25 years and,
therefore, will not cause any environmental danger or health
risk within this period of time if the device is used as intended.
2.2.2 Symbols
The following symbols are used on the device and/or its packaging:
Symbol Meaning
CE marking
Manufacturer and address
Year of manufacture
Order number
Temperature limit
Serial number
Note
Observe the operating manual!
Caution
In combination with the symbol above:
Attention! Observe accompanying documents!

Safety and warning instructions
10
2.3 Requirements for the operating personnel
The qTOWER³ auto may only be operated by qualified specialist personnel instructed in
the use of the device. The instruction also includes imparting the contents of this oper-
ating manual.
In addition to the work safety instructions in this operating manual, the generally appli-
cable 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 has to be accessible to the operating and maintenance per-
sonnel at all times! Operation or maintenance of the device by individuals under the
influence of alcohol, drugs or medication is not permitted.
It must be ensured that only authorized personnel work at the device. The operating
personnel must be familiar with the dangers arising from samples and excipients.
Suitable personal protection equipment must be worn.
Prior to pauses or at the end of the work, appropriate skin cleaning and protection
measures must be carried out.
Eating, drinking and smoking at the installation location of the device is prohibited!
The device must be handled with the appropriate care and kept clean in accordance
with laboratory standards to prevent contamination of the device. Observance of
these laboratory rules reduces the risk of being contaminated with potentially infec-
tious material and the risk of cross-contamination of the samples. Wear protective
gloves and take other safety measures if there is a chance that your skin may come
into contact with infectious material when handling the device.
The operator must decontaminate the device if the housing or the sample block has
been contaminated with hazardous substances – suitable disinfectants and methods
are described in the section “Disinfecting the device” on page 31.
ATTENTION
Disinfectants other than those specified may
only be used following prior consultation
with Analytik
Jena.
2.4 Safety instructions - Transport and installation
The device may only be transported with the transport locks in place and in its original
packaging. Always ensure that the device is empty and no sample vessels are in the
sample block. Further information can be found in separate packing instructions.
The qTOWER³ auto can be installed by the Analytik Jena Customer Service or specialist
personnel trained and authorized by Analytik Jena.
Observe the guide values and adhere to the legally mandated limits for lifting and carry-
ing without auxiliary means!
For safety reasons, 2 persons are required to transport the device.

Safety and warning instructions
11
Since the device does not have handles, grip the device firmly with both hands at the
lower end, lifting it simultaneously.
2.5 Safety instructions: during operation
2.5.1 Summary of safety instructions
The operator of the qTOWER³ auto must make sure before each commissioning that the
condition of the device including the safety equipment is sound. The technical condition
must always comply with the legal requirements and regulations.
Free access to the power switch on the back of the enclosure has to be ensured dur-
ing operation.
The ventilation fittings at the rear and the bottom of the device must be free and op-
erational. Covered ventilation grilles or slots etc. may cause the device to break down
or may cause damage to it.
Risk of crushing when moving the drawer.
The thermal block, the samples, and the heated lid reach high temperatures.
There is a risk of burns during contact.
Wear safety goggles during operation!
The rapid heating of the thermal block can cause liquids to evaporate explosively.
Only use plates and tubes that are suitable for high temperatures (up to 110 °C)!
Do not touch hot sample tubes or plates and do not open them or boiling liquid may
escape!
2.5.2 Safety instructions – protection against explosion and fire
Do not operate the qTOWER³ auto with flammable, explosive or volatile substances.
Do not operate the qTOWER³ auto in a potentially explosive environment.
The operating personnel must be familiar with the location of the fire-fighting
equipment in the operating room of the device.
2.5.3 Safety instructions – electrical equipment
The qTOWER³ auto meets the requirements for interference emission and resistance de-
fined in the corresponding standards series – for further information, see the “Standards
and directives” section on page 42.
Assess the electromagnetic environment before operating the device. Do not operate
the device near sources of strong electromagnetic radiation (for example, an un-
shielded, deliberately operated high frequency source), as these may affect proper
operation of the device.
The device may only be connected to power sources whose nominal voltage is the
same as that on the rating plate of the device.

Safety and warning instructions
12
The electrical components must be checked regularly by a qualified electrician. Any
defects, such as loose connections, faulty or damaged cables must be repaired with-
out delay.
The qTOWER3auto must be switched off immediately using the power switch (on
the equipment backplate) and the power supply disconnected from the mains if
there is any interference with the electric components.
Before opening, the device must be isolated from all circuits!
Work on the electrical components of the qTOWER3auto may only be performed by
Analytik Jena Customer Service employees and specially authorized technicians ac-
cording to the valid electrotechnical regulations. Life-threatening voltages may be
applied within the device! There is a risk of electric shock if contact is made with live
components, which may lead to serious injury or death.
Make sure the correct fuses are used and replace these if necessary. To do this, sepa-
rate the device from the mains supply.
The device may only be used with the power cable supplied or a power cable with the
same specification. The use of other power cables is not permitted.
Wipe spilled samples or reagents immediately with an absorbent cloth or piece of
paper. Do not allow any liquid to enter the device.
Do not use the power supply unit in environments with extreme humidity (> 95%) or
in locations in which condensation may occur.
2.5.4 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, infec-
tious, poisonous, corrosive, or otherwise hazardous substances. For details contact the
safety officer responsible for your location.
When handling hazardous substances local safety codes and guidelines must be ob-
served. 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.
Protective goggles and rubber gloves have to be worn when handing reagents.
For your own safety, please observe the potential infectious qualities of the exam-
ined biological material.
Observe all notices on the cleaning and decontamination of the device. The use of
other cleaning or decontamination procedures is only permitted following prior con-
sultation with Analytik Jena.
When using operating materials, always observe the appropriate regulations and the
notes in the EC safety data sheets of the manufacturer with regard to their storage,
use and disposal.
Never place auxiliary and operating materials in containers or vessels for food. The
approved containers for the relevant material are to be used and these have to be la-
beled accordingly. The notes on the labels have to be observed!

Safety and warning instructions
13
Auxiliary and operating materials as well as their containers may not be disposed of
as domestic waste or enter the sewage system or the soil. The applicable regulations
for disposal of these materials must be observed.
Ensure good room ventilation in working rooms.
2.6 Behavior during emergencies
In case of danger or accidents, immediately switch off the qTOWER³ auto at the main
switch.
Disconnect the power plug from the power supply!
Because a rapid response can save lives during an emergency, the following has to be
ensured:
The operating personnel must be familiar with the locations of safety equipment, ac-
cident and danger alarms as well as first-aid and rescue equipment as well as its use.
The operator is responsible for the respective training of the operating personnel.
All equipment for first aid (first-aid kit, eyewash bottles, stretcher, etc.) as well as
equipment for firefighting (fire extinguishers) must be within reach and easy to ac-
cess. All equipment has to be in a sound condition and should be checked regularly.
2.7 Safety instructions – maintenance and repair
On principle, maintenance of the qTOWER³ auto is performed by the customer service
department of Analytik Jena or by specialist personnel that has been authorized and
trained by Analytik Jena. Unauthorized maintenance can damage the device.
Therefore, the operator may generally only carry out the tasks listed in section “Mainte-
nance and repair” p. 29.

Layout and function
14
3Layout and function
3.1 Layout
The qTOWER3auto boasts a modular design concept, comprising a block cycler unit with
fluorescence spectrometer and a power module unit (controller). Depending on the
block system used, 96 or 384 samples may be processed per run. The qTOWER3auto is
suitable for use in a robotic system, whereby up to 4 devices can be controlled simulta-
neously using a PC. A CyBio Composer or .dll can be used to integrate the devices.
The movable drawer provides maximum flexibility for system integrators. With easy ac-
cess to the extended drawer, the sample carrier (microtiter plate) can be easily posi-
tioned on the drawer without any problems.
The patented high-performance optics, comprising a fiber-optic shuttle system and
unique light source, guarantee a superb homogeneous excitation and illumination of all
individual samples. The light source comprises 4 high-performance LEDs with a broad
spectrum reaching deep into the red. In combination with specially optimized filter mod-
ules comprising one emission and one excitation filter, a broad spectrum of fluorophores
can be specifically excited and detected. Depending on the application, up to 6 filter
modules may be mounted in one device, whereby the simultaneous analysis of up to 6
target sequences may take place in a well.
A recalibration of the system after replacing the filter modules is not necessary here.

Layout and function
15
Fig. 1 Device components
1 qTOWER³ auto
2 qTOWER³ 84 auto
3 qTOWER3auto power module
1
2
3

Layout and function
16
3.1.1 qTOWER³ auto
The qTOWER³ auto combines a PCR thermal cycler with a patented fluorescence pho-
tometer. The status LED on the front of the qTOWER³ auto informs the user about the
current status of the device (active/inactive). Furthermore, the device has a movable
drawer which can be moved in and out, depending on the operating state of the device.
Fig. 2 qTOWER³ auto (front view)
1 Upper part with fluorescence photometer
2 Status LED (indicates whether the device is switched on or off)
3 Drawer
4 Block cycler unit
The drawer serves to hold the sample carrier (micro titer plate). Once a sample carrier
has been positioned on the drawer and moved into the device, this is positioned above
the thermal block and the front flap closes and locks automatically.
ATTENTION
Never attempt to pull the drawer out or push it in manually.
All movements of the drawer (moving in/out) are exclusively controlled by the software
commands in the qPCRsoft auto program or using an external communication software.
1
2
3
4

Layout and function
17
Fig. 3 qTOWER3auto with extended drawer
1 Drawer
2 Guide tracks of the drawer
The connections described in Fig. 4 are attached to the rear side of the qTOWER³ auto,
beside the fans.
Fig. 4 qTOWER³ auto (rear view)
1 USB port for PC connection
2 Type plate
3 Fan grating
4 Electrical connections
– Data 1 connection (lid heating – communication lines)
– Data 2 connection (connection of thermal block sensors)
– Power line connection (power)
1
2
3
4

Layout and function
18
3.1.2 qTOWER3auto power module
The qTOWER3auto power module is used to provide the automated real-time PCR
qTOWER³ auto thermal cycler with power. The external solution allows for flexibility
with regards to installation or integration in automation systems.
The operating status (on/off) is indicated by the status LED on the front of the device.
The connections for Data 1, Data 2 and Power are also located here.
Fig. 5 Power module (front view)
1 Status LED (indicates whether the device is switched on or off)
2 Power connection
3 Data 1 connection (lid heating – communication lines)
4 Data 2 connection (for connecting the sensors of the thermal block)
A mains connection socket, the fuse compartment and the power switch are located at
the back of the qTOWER³ auto, in addition to the service connection.
Fig. 6 Power module (rear view)
1 Type plate
2 Warning note
3 Service connection
4 Ethernet port
5 On/Off switch
6 Fuse compartment
7 Mains connection socket

Layout and function
19
3.2 Function
3.2.1 Fluorescence spectrometer
The detector unit is a patented 8-channel epi-fluorescence photometer with fiber multi-
plexer and mechanical scanning device.
The detector unit is a patented 16-channel epi-fluorescence photometer with fiber mul-
tiplexer and mechanical scanning device.
The fluorescence spectrometer comprises the following components – see the following
schematic representation:
Fig. 7 Schematic representation: fluorescence spectrometer
A long-life, sturdy four-color LED (blue, green, white and red) in the qTOWER³ auto is
used as an excitation light source for the emission of fluorescent dyes. The LEDs allow
for a sensitive excitation of various dyes across a very broad wavelength spectrum that
goes deep into red, whereby the light source does not require any warm-up period (Fig.
7).
The light is passed through optic fibers to collimator lenses, bundled and then trans-
ferred to the excitation filter of the color modules fitted to a rotating filter wheel. The
light is deflected via a beam divider and passed through additional optical fibers to a
lens array in a shuttle system scanning the sample block in columns (Fig. 7: Multi-
plexer).
The fluorescent dyes are specifically excited in the reaction mix thanks to the light and
emit light of a longer wavelength. Using the lenses in the shuttle system, the emitted
light is bundled and passed back to the color modules via the optical fibers (Fig. 7:
Measuring head).
In the color modules, the light passes the beam divider followed by two emission filters
and is then transferred to the photomultiplier (CPM) for detection.
Starting from the light source, the light beam course is represented in the following dia-
gram by the blue and green arrows.
qTOWER3auto
qTOWER384 auto
Light source
Multiplexer
Measuring head
Photomultiplier
(PMT)

Layout and function
20
Fig. 8 Schematic representation: light beam course through filter color module
The filter wheel of the photometer can be populated freely with a choice of filter mod-
ules. In addition, filter modules can be retrofitted at any time, extending the application
spectrum of the device. The product portfolio from Analytik Jena comprises a total of 12
different filter modules (6 color modules for the most frequently used fluorescent dyes,
from the blue to the red excitation range; 5 filter modules specially optimized for FRET
applications and 1 protein module for melting curve analysis). A retrofitting or replace-
ment of the installed modules may be carried out by the Analytik Jena Service team at
any time.
ATTENTION
If you intend to extend the application spectrum of the device with regard to using filter
modules, always contact the service department because extensions
– to be performed
by the operator himself
– are not intended by the manufacturer.