Analytik Jena qTOWER3 User manual

Operating manual
qTOWER3/ qTOWER3G
Real-Time PCR Thermal Cycler

Analytik Jena AG
Konrad-Zuse-Str.1
07745 Jena Germany
Phone + 49 3641 77 70
Fax + 49 3641 77 9279
Email [e-mail]
Biometra GmbH
Rudolf-Wissell-Str. 30
37079 Göttingen Germany
Phone + 49 3641 77 7407
Fax + 49 3641 77 7449
Email [e-mail]
Analytik Jena AG
Konrad-Zuse-Str. 1
07745 Jena Germany
Phone + 49 3641 77 9460
Fax + 49 3641 77 9279
Email [e-mail]
http://www.analytik-jena.com
Microsoft and Windows are registered trademarks of Microsoft Corp.
The identification with ® or TM is omitted in this manual.
10-3107-002-23
03.19
Analytik Jena AG
© Copyright 2019 Analytik Jena AG
Manufacturer
Technical Service
Application Support
General Information
Copyrights and
Trademarks
Documentation number
Output
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made by:

Contents
qTOWER3/ qTOWER3G Edition 03.19 1
Contents
1Basic Information.................................................................................3
1.1 Notes on the manual ...................................................................................... 3
1.2 Intended use................................................................................................... 3
1.3 Warranty and liability ...................................................................................... 5
2Safety instructions ...............................................................................6
2.1 Symbols and signal words used..................................................................... 6
2.2 Safety symbols on the qTOWER³ .................................................................. 8
2.3 Technical condition......................................................................................... 8
2.4 Requirements for the operating personnel..................................................... 9
2.5 Safety instructions, transport and installation............................................... 10
2.6 Safety instructions - operation...................................................................... 10
2.6.1 General......................................................................................................... 10
2.6.2 Safety instructions - Protection against explosion and fire .......................... 11
2.6.3 Safety instructions - electrical equipment..................................................... 11
2.6.4 Handling of samples, auxiliary and operating materials............................... 12
2.6.5 Safety instructions - service and repair ........................................................ 13
2.7 Behavior during emergencies ...................................................................... 14
2.8 Standards and directives.............................................................................. 15
3Technical data ....................................................................................17
4Installation conditions .......................................................................19
4.1 Environmental conditions ............................................................................. 19
4.2 Energy supply............................................................................................... 19
4.3 Space requirement ....................................................................................... 20
5Function and setup ............................................................................21
5.1 Fluorescence spectrometer.......................................................................... 21
5.2 PCR thermocycler ........................................................................................ 22
6Commissioning ..................................................................................24
6.1 Connections and control elements............................................................... 24
6.2 Setting up the qTOWER3............................................................................. 27
7Operation ............................................................................................29
7.1 Switching the qTOWER³ on ......................................................................... 29
7.2 Switching off the qTOWER³ ......................................................................... 29
7.3 Inserting samples / Starting the PCR analysis ............................................. 30

Contents
2 Edition 03.19 qTOWER3/ qTOWER3G
8Maintenance and care ....................................................................... 32
8.1 Cleaning the housing.................................................................................... 32
8.2 Cleaning the sample block ........................................................................... 32
8.3 Disinfecting the device ................................................................................. 33
8.4 Exchanging fuses ......................................................................................... 34
8.5 Installing color modules ................................................................................ 34
9Troubleshooting ................................................................................ 39
10 Transport and storage ...................................................................... 40
10.1 Transport ...................................................................................................... 40
10.2 Placing the transport lock ............................................................................. 40
10.3 Return ........................................................................................................... 41
10.4 Moving the qTOWER³ in the laboratory ....................................................... 41
10.5 Storage ......................................................................................................... 42
11 Disposal ............................................................................................. 42
12 Index ................................................................................................... 43
Figures
Fig. 1 Layout of the qTOWER³ ......................................................................................... 21
Fig. 2 Schematic structure of the Epi fluorescence photometer....................................... 22
Fig. 3 qTOWER³ front view............................................................................................... 24
Fig. 4 qTOWER³, open ..................................................................................................... 24
Fig. 5 qTOWER³ rear view................................................................................................ 25
Fig. 6 Type plate ............................................................................................................... 26
Fig. 7 Voltage selector switch on the bottom of the qTOWER³ ........................................ 26
Fig. 8 Mains and connection cable ................................................................................... 27
Fig. 9 Position of additional vessels for measurements with few samples....................... 30
Fig. 10 Position A1 on the sample block ............................................................................ 31
Fig. 11 Fuse holder on the rear of the device..................................................................... 34
Fig. 12 Transport lock in the qTOWER3............................................................................. 40

Basic Information
qTOWER3/ qTOWER3G Edition 03.19 3
1 Basic Information
1.1 Notes on the manual
The user manual describes the following two models of the qTOWER3series:
qTOWER3
qTOWER3G
In the text below these devices are collectively called qTOWER3. Differences between
the models are explained in the corresponding section.
The qTOWER³ is intended for operation by qualified specialist personnel observing this
user manual.
The manual informs about the design and function of the unit and provides personnel
familiar with PCR technology with the necessary know-how for the safe handling of the
equipment. The manual also provides notes on the servicing and caring for the unit.
Conventions
Instructions for action which occur in chronological order are numbered and com-
bined 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 notes 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 section "Symbols and signal words
used" p. 6.
The elements of the control and analysis program are indicated as follows:
Program terms are identified with SMALL CAPS e.g., Menu FILE.
Menu items are separated by arrows (), e.g. FILE NEW.
Buttons are marked with square brackets, e.g. [ADD].
1.2 Intended use
qTOWER³ is a thermal cycler for amplifying DNA by way of the polymerase chain reac-
tion (PCR) licensed for real-time PCR experiments. The license is limited to applications
outside of vitro diagnostics (research use only).
The integrated detector enables the measurement of the sample fluorescence in up to
six spectral channels during the PCR, with the filters used in the color or FRET modules
being exactly matched to the properties of the most frequently used fluorescence dyes,
thereby permitting a sensitive and selective detection of fluorescent PCR products.

Basic Information
4 Edition 03.19 qTOWER3/ qTOWER3G
Analytik Jena AG offers a number of color or FRET modules of which up to six can be
installed simultaneously in the device. Replacement and retrofit of color or FRET mod-
ules can be easily accomplished.
qTOWER³ is an open platform for real-time PCR and supports both intercalating dyes
as well as individual samples and kits of various manufacturers. qTOWER³ can be used
in different applications, such as expression analyses, genotyping and the detection of
pathogens.
qTOWER³ is fully controlled from the PC using the program qPCRsoft. qPCRsoft pro-
vides the following functions
Device control and monitoring
User administration
Context-sensitive help functions
Design of real-time PCR experiments and their evaluation
Storage of methods (templates) and measuring results (projects)
Planning and evaluation of
−Absolute quantifications
−Relative quantifications
−ΔΔCt – analyses
−DNA melting curves
−Genotyping
−End point analyses
Results printout
Results export to MS EXCEL or as CSV file
Results export to extended programs for the analysis of real-time PCR data
(e.g. GenEx, qBASE)
A detailed description of the program qPCRsoft is available in the software 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 Technol-
ogy and Application. Norfolk UK: Caister Academic Press, 2009

Basic Information
qTOWER3/ qTOWER3G Edition 03.19 5
1.3 Warranty and liability
The warranty and liability periods comply with the legal requirements and the provisions
in the General Terms and Conditions of Analytik Jena AG.
Deviations from the intended use described in this manual result in limitations of warran-
ty 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 qTOWER³ other than intended
improper commissioning, operation and servicing of the device
modifications of the equipment without prior consultation with Analytik Jena AG
unauthorized intervention in the equipment
operation of the device with faulty safety equipment
use of other than original spare parts, wearing parts or consumables
improper repairs
improper transport and storage of the device
faults due to the non-observance of this manual

Safety instructions
6 Edition 03.19 qTOWER3/ qTOWER3G
2 Safety instructions
2.1 Symbols and signal words used
This manual uses the following symbols and signal words to indicate hazards or in-
structions. The safety instructions are always placed before an action.
WARNING
Indicates a potentially hazardous situation.
If it is not prevented death or most serious injuries (incapacitation) can result.
CAUTION
Indicates a potentially hazardous situation.
Unless avoided light or minor injuries may result.
CAUTION! Hot surface!
Touching the hot surface can cause burns.
WARNING! Danger of electric shock if touched!
Electrical voltages present a danger of ele
ctrical shock.
BIOLOGICAL HAZARD
This symbol indicates that precautions must be taken when working with potentially infectious
material.
NOTICE
Indicates a potentially hazardous situation which might cause material or environmental dam-
age.

Safety instructions
qTOWER3/ qTOWER3G Edition 03.19 7
In this manual, on the product itself, and on the packaging, the following symbols are
used to present important information to the customer, regardless of which language
they speak.
CE marking
Manufacturer of the product, including address
Manufacturing date of the product
Order number of the product
Temperature limit
Serial number of the device
Observe operating instructions
Caution
In combination with the symbol above:
Attention
! Note the accompanying documents
Symbol for
waste disposal in accordance with WEEE directive:
Do not dispose of in household waste

Safety instructions
8 Edition 03.19 qTOWER3/ qTOWER3G
2.2 Safety symbols on the qTOWER³
The qTOWER³ is fitted with safety symbols, the content of which must always be ob-
served. Damaged or missing safety symbols can cause incorrect actions leading to
personal injury or material damage! The safety symbols must not be removed! Dam-
aged safety symbols must be replaced without delay!
The following safety symbols are attached to the qTOWER³ and accessories:
Warning symbol
Mandatory action signs
(on heatable lid)
(on equipment backplate)
Warning against a
hazard location
Warning against
hot surface
Before opening the device al-
ways disconnect the mains plug
The following notice sign is attached to the rear of the qTOWER3:
2.3 Technical condition
The qTOWER³ corresponds in its design and construction to the current state of the art
technology. Unauthorized modifications or changes, especially such that affect the safe-
ty of the staff and the environment, are generally not allowed.
Observe the following:
Any manipulation of the safety equipment is prohibited! In case of an accident
manipulations of the safety equipment will be interpreted as deliberate!
The operator must only operate the device in a sound and operationally safe
condition. The technical condition must always comply with the legal require-
ments 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.

Safety instructions
qTOWER3/ qTOWER3G Edition 03.19 9
2.4 Requirements for the operating personnel
The qTOWER³ 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 manual the generally applicable safe-
ty 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 regu-
lations.
The operating and service personnel must have access to the manual at any time!
Observe the following:
The device must only be commissioned, operated and serviced by trained per-
sonnel instructed in technical safety.
The operation or servicing of the device by minors or individuals under the influ-
ence of alcohol, drugs or medication is not permitted.
It must be ensured that only authorized personnel works at the device. The op-
erating 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 protec-
tion measures must be carried out.
Eating, drinking and smoking at the location of the device is prohibited!
The device must be handled with the appropriate care and kept clean in ac-
cordance with laboratory standards to prevent contamination of the device (e.g.
on the heatable lid). Observance of these laboratory rules reduces the risk of
being contaminated with potentially infectious material and the risk of cross-
contamination of the samples. Wear protective gloves and/or take other safety
measures if there is a chance that your skin may come into contact with infec-
tious material when handling the device.
The operator must decontaminate the device if the housing or the sample block
were contaminated with hazardous substances. For suitable disinfection agents
and procedures see "Disinfecting the device" p. 33. Other disinfection agents
that are not included in the list shall only be used after consultation with Analytik
Jena AG.

Safety instructions
10 Edition 03.19 qTOWER3/ qTOWER3G
2.5 Safety instructions, transport and installation
Observe the following:
Only transport the device in its original packaging and with the transport lock in
place! Make sure that the device is empty and no sample vessels are in the
sample block.
Please verify that the delivery is complete on receipt of the qTOWER³ and
check for possible transport damage. If the delivery is incomplete or the device
was damaged during transport, please contact Analytik Jena AG.
To prevent health damage the following must be observed when moving the
device in the laboratory (lifting and carrying):
−For reasons of safety 2 persons are required to transport the device and
must position themselves on both sides of the equipment.
−Since the device does not have handles, grip the device firmly with both
hands at the lower end, lifting it simultaneously.
The guide values and statutory limits for lifting and carrying loads without
auxiliary equipment must be observed and adhered to.
The qTOWER³ can be installed by the Analytik Jena AG customer service or trained
specialist personnel authorized by Analytik Jena AG.
2.6 Safety instructions - operation
2.6.1 General
The operator of the qTOWER³ 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 op-
erational. Covered vents or ventilation slits etc. may cause the device to break
down or may cause damage to it.
Be careful to avoid crushing or pinching injuries when closing the device.

Safety instructions
qTOWER3/ qTOWER3G Edition 03.19 11
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.
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!
The rapid heating of the thermal block can cause liquids to boil explosively. Al-
ways wear safety goggles during operation!
Do not touch hot sample vessels or plates and do not open them or boiling liq-
uid may escape!
Only use plates and vessels 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 qTOWER³ must not be operated in an explosive environment.
The operating personnel must be familiar with the location of the fire-fighting equipment
in the operating room of the device.
The qTOWER³ must not be operated with flammable, explosive or volatile substances.
2.6.3 Safety instructions - electrical equipment
Work on electrical components of the qTOWER³ may only be carried out by a qualified
electrician in accordance wit the applicable electrical engineering rules. Life-threatening
electrical voltages may occur in the interior of the qTOWER³!
Observe the following:
Any work on the interior of the device may only be carried out by the customer
service of Analytik Jena AG and specially authorized technicians.

Safety instructions
12 Edition 03.19 qTOWER3/ qTOWER3G
The electrical components must be checked regularly by a qualified electrician.
Any defects, such as loose connections, faulty or damaged cables, must be re-
paired without delay.
Do not replace the removable mains cable of the device by a mains cable that
does not meet the specifications (without protective ground conductor).
Before opening the device it must be switched off from the power switch and the
mains connector must be disconnected from the mains outlet!
The qTOWER³ must be switched off immediately using the power switch and
the power supply disconnected from the mains if there is any interference with
the electric components.
The qTOWER³ fulfills the corresponding requirements for interference emission
and resistance from the IEC 61326 series. Assess the electromagnetic envi-
ronment of the device before operation.
Do not operate the device near sources of strong electromagnetic radiation (e.g.
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, infec-
tious, 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 observed. The following general notes do not re-
place 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:
The relevant regulations and the notes in the EC safety data sheets of the man-
ufacturers have to be observed and complied with regards to storage, handing,
use and disposal for all auxiliary and operation materials used during the opera-
tion of the device.
Auxiliary and operation materials may never be placed in containers or vessels
for food. The approved containers for the relevant material are to be used and

Safety instructions
qTOWER3/ qTOWER3G Edition 03.19 13
these have to be labeled accordingly. The notes on the labels have to be ob-
served!
Protective goggles and rubber gloves have to be worn when handing reagents.
Auxiliary and operating materials as well as their containers may not be dis-
posed in domestic waste or enter the sewage system or the soil. The applicable
regulations for disposal of these materials must be meticulously observed.
Ensure good room ventilation in working rooms.
If only a few samples are treated, an (empty) vessel 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 vessels being damaged
and sample liquid leaking out.
For your own safety, please observe the potential infectious qualities of the ex-
amined biological material.
2.6.5 Safety instructions - service and repair
On principle, maintenance of the qTOWER³ is performed by the customer service de-
partment of Analytik Jena AG or its authorized and trained specialist personnel. Unau-
thorized maintenance can damage the device. Therefore, the operator may generally
only carry out the tasks listed in chapter "Maintenance and care" p. 32.
The following has to 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).

Safety instructions
14 Edition 03.19 qTOWER3/ qTOWER3G
2.7 Behavior during emergencies
In case of danger or accidents, immediately switch off the qTOWER³ using the main
switch on the equipment backplate. 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 staff must be familiar with the location of safety equipment, acci-
dent and danger alarms as well as first aid and rescue equipment as well as
their handling.
The operator is responsible for the respective training of the operating staff.
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 access. All equipment has to be in a sound condition and should be checked
regularly.

Safety instructions
qTOWER3/ qTOWER3G Edition 03.19 15
2.8 Standards and directives
Safety class and safety type
The qTOWER³ features protection class I.
The casing features protection type IP 20.
Device safety
The qTOWER³ complies with the safety standards
EN 61010-1:2010
UL 61010-1:2012
CAN/CSA-C22.2 No. 61010-1-12:2012
EMC compatibility
The qTOWER³ has been tested for radio interference suppression and interference
resistance and meets the requirements of
EN 61326-1:2013
EN 61326-2-6:2006
The qTOWER³ complies with the applicable requirements of EMC directive 2014/30/EU
and low voltage directive 2014/35/EU.
Environmental compatibility
The qTOWER³ has been tested for environmental compatibility and meets the require-
ments of
DIN ISO 9022-2:2015-06
DIN ISO 9022-3:2015-08
DIN EN 60068-2-64:2009-04
DIN EN 60068-2-27:2010-02
DIN EN 60068-2-31:2009-04
EU directives
The qTOWER³ is designed and tested in accordance with standards meeting the re-
quirements of EU directives 2014/35/EU and 2014/30/EU. The device leaves the manu-
facturer in a pristine and technically safe state.
Federal Communications Commission Advisory (U.S. only)
This device complies with Part 15 of the FCC Rules. Operation is subject to the follow-
ing two conditions: (1) this device doesn´t cause harmful interference, and (2) accepts
any interference (including interference that may cause undesired operation). This de-
vice complies with Part 18 of the FCC Rules.
Interference-causing Equipment Standards (Canada only)
This device complies with Canadian ICES-001 / NMB-001.

Safety instructions
16 Edition 03.19 qTOWER3/ qTOWER3G
Guidelines for China
The qTOWER³ contains restricted substances (according to directive "Management
Methods for the Restriction of the Use of Hazardous Substances in Electrical and Elec-
tronic Products"). Analytik Jena guarantees, that those hazardous substances may not
leak out during the next 25 years when the instrument is used in accordance with its
intended purpose.
To ensure safe operation, the operator must strictly observe the safety and operating
instructions contained in this manual. For accessories which have also been supplied,
and system components from other manufacturers, their operating instructions should
be referred to.
Besides the safety instructions in this manual and the local safety regulations that apply
to the operation of the qTOWER³ 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.

Technical data
qTOWER3/ qTOWER3G Edition 03.19 17
3 Technical data
Block format
96 wells
Sample volume
10 – 80 µL
Lid temperature
30 – 110 °C
Temperature gradient
40°C (qTOWER3 G only)
Max. heating rate*
max. 8°C/s,
Ø
7°C/s
(depending on consumables used)
Max. cooling rate*
max. 6 °C/s,
Ø
5.5°C/s
(depending on consumables used)
Heating rate adjustment
min. 0.1 °C/s
Temperature uniformity
(15 s after starting the clock)
±0.15 °C at 55 °C
±0.25 °C at 72 °C
±0.50 °C at 95 °C
Temperature range
3 °C – 99 °C
Control accuracy
± 0.1 °C
Temperature increments
min. 0.1 °C/cycle
Time increments
min. 1 s/cycle
Heated lid
Manual opening mechanism, automatic contact
pressure
Heated lid contact pressure
30 kg, automated
Dimensions
(H x W x D)
59 cm x 27.5 cm x 27.5 cm
70 cm x 27.5 cm x 50 cm when opened
Mass
30 kg
Noise level
45 dB
Energy supply
Operating voltage
Line frequency
100 V, 115 V, 230 V
50 – 60 Hz
Power consumption (max.)
max. 850 W
Instrument fuses
2 x 10 AT / 250 V
Safety circuits
Monitoring of the closing mechanism of the device
(lock with handle), over-temperature protection in
the heated lid
Operating conditions
Air pressure: 0.7 bar to 1.06 bar
Max. permissible altitude: 2000 m
Humidity: max. 70 %
Operating temperature: +15 °C to +35 °C

Technical data
18 Edition 03.19 qTOWER3/ qTOWER3G
Supported plastic products
96-well micro titer plates with optical film
8-well strips 0.2 ml with optical lids
0.2 ml individual vessels with optical lids
Sensitivity
1 nmol/l FAM at 30µl sample volume in a 96-well
PCR plate
Measuring time
96-well plate (single measurement, 6 colors) ap-
prox. 6 s
Measuring range
±130 000 (±17 bit)
Dynamic range
10 log stages
Light source
Four high-intensity LEDs (blue, green, white, red)
Detector
Photo Multiplier (PMT)
Color filter modules
Color modules for all frequently used real-time
PCR dyes
Color module 1 (470 nm/520 nm)
Color module 2 (515 nm/545 nm)
Color module 3 (535 nm/580 nm)
Color module 4 (565 nm/605 nm)
Color module 5 (630 nm/670 nm)
Color module 6 (660 nm/705 nm)
Protein color module 1 (490 nm/580 nm)
FRET filter combinations:
FRET module 1 (470 nm/580 nm)
FRET module 2 (470 nm/670 nm)
FRET module 3 (470 nm/705 nm)
FRET module 4 (515 nm/670 nm)
FRET module 5 (470 nm/605 nm)
Software and PC
qPCRsoft
Control and analysis program
Analysis methods
Absolute quantification, relative quantification,
ΔΔCt method, allelic discrimination,
efficiency calculation, DNA melting curves,
POS/NEG analysis in the end point
Export functions
Excel, CSV, LIMS, GenEx, qBase
Data connection
USB
PC software requirements
Minimum Pentium IV, > 1 GHz
Operating system
Win 7 / Win 8 / Win 10