VWR XT96 User manual

Instruction manual
VWR®PCR Thermal Cycler XT96 / XTender96
EU cat. no US cat. no
XT96 732-1359 76452-151
XT96 Gradient 732-3428 76452-153
XTender96 732-3657 76452-155
XTender96 Gradient 732-3658 76452-157
___
Version 2 Issue 17 October 2021

2vwr.com I Instruction manual VWR®PCR Cycler XT96
Legal address of Manufacturer
Europe
VWR International bv,
Researchpark Haasrode 2020
Geldenaaksebaa
n 464 B-3001
Leuven
[phone]
be.vwr.com
UK Importer:
VWR International Ltd
Hunter Boulevard, Magna Park
Lutterworth, Leicestershire, LE17 4XN
uk.vwr.com
United States
VWR International LLC
100 Matsonford Rd
Radnor, PA 19087
[phone]
www.vwr.com
Country of Origin : GERMANY

3vwr.com I Instruction manual VWR®PCR Cycler XT96
CONTENTS
INTRODUCTION 4
GENERAL WARNING 4
SAFETY INSTRUCTIONS 4
LICENCE NOTICE 5
DELIVERY CONTENTS 6
UNPACKING 6
SPECIFICATIONS 7
CONNECTIONS 8
INSTALLATION OF THE PCR CYCLER XTENDER96 9
OPERATING THE PCR CYCLER XT96 10
Main Menu 12
Change User 13
Incubation Mode 14
Run dialogue 15
Run dialogue: Overview – “Simple Mode” 15
Run dialogue: Overview – “Expert Mode” 16
Program Dialogue 22
Deleting a command from the program 25
Available commands (program steps) 26
GLPs dialogue 28
Explorer dialogue 30
Diagnose dialogue32
System dialogue 33
MAINTENANCE 41
Cleaning, maintenance and repair of the thermal cycler 41
Returns only in original packaging 41
Temperature check-up 41
Calibration 41
ORDERING INFORMATION 42
TECHNICAL SERVICE 42
WARRANTY 42
COMPLIANCE WITH LOCAL LAWS AND REGULATIONS 42
DISPOSAL INSTRUCTION 43
LOCAL VWR OFFICES IN EUROPE AND ASIA PACIFIC 44

4vwr.com I Instruction manual VWR®PCR Cycler XT96
INTRODUCTION
The VWR thermal cyclers are the ideal PCR devices for all molecular biological and biochemical
laboratories working in the field of basic research or routine diagnostics. The 250°C HTR (High
Temperature Range) Peltier technology allows quick changes in temperature up to 4 °C/sec (max). The
individual monitoring and controlling of each of the eight Peltier elements per block equipped with
'Long Life Technology' ensure the tightest correlation of target and actual temperature across the
entire thermal plate leading to highest reproducibility of the results. To avoid condensation each block
is equipped with a heated lid.
The VWR thermal cyclers are equipped with a touch-sensitive, graphic coloured TFT display of the
newest generation, allowing operation of the device by simply touching symbols and graphic elements
on the screen. This leads to easy and intuitive handling and programming of the device. Additionally,
a mouse can be connected via USB.
Furthermore, an Ethernet port is available to connect the devices with Microsoft Windows®or Linux
networks. It is therefore possible to use an external server for archiving programs and GLP reports
which will be available globally in the network (e.g. for other thermal cyclers).
Transfer of data can be done by using commercially available USB memory sticks enabling a nearly
unlimited saving space for programs and GLP reports, which can be printed using a printer connected
to the thermal cycler via the network.
Notice: The USB ports support only standard cable mice and standard USB sticks.
The maximum acceptable length of the connecting cable of the port is 3 m!
GENERAL WARNING
The PCR Cycler XT96 has been designed for laboratory use and it should not be used at temperature
below 15 °C. If the instrument is at a temperature below 10 °C place it in a warmer room and wait at
least two hours before using it. Before plugging the instrument into a power supply, check that the
voltage and frequency on the label matches the power supply specifications. Before any operation
ensure that the ventilation grids are not obstructed.
SAFETY INSTRUCTIONS
The PCR Cycler XT96 is designed with function, reliability, and safety in mind.
Before using the PCR Cycler XT96 please read this entire manual and strictly follow the safety
instructions!
Intended use of the PCR Cycler XT96: Working environment for DNA amplification during a Polymerase
Chain reaction (PCR).
Safety and protection of the user cannot be ensured if the PCR Cycler XT96 is used in any manner that
is not specified in these instructions. Special notice must be taken of the following:
Returns only in original packaging
Please use the manufacturer's original package to ensure a safe return.

5vwr.com I Instruction manual VWR®PCR Cycler XT96
Caution: Dangerous voltage
Ensure that the voltage requirements of the PCR Cycler XT96 exactly match your local
AC power supply.
Only use the original AC cable supplied with the PCR Cycler XT96.
Caution: Liquids
Ensure that no liquids can enter the device. Reaction tubes must be filled outside of the
thermal cycler.
Caution: Dangerous explosive material
Do not use reactive or explosive substances in the PCR Cycler.
Caution: Damage
Check for transport damage and completeness of the accessories upon arrival. If any
damage is noticed, contact your distributor or manufacturer immediately. If you detect
any damage of the PCR Cycler XT96 or one of its accessories, do not connect the PCR
Cycler to the AC wall outlet and do not use the device in any manner!
Caution: Hot surfaces
The thermal plate, the heated lid and the reaction tubes quickly reach temperatures
above 50 ºC / 122 ºF. There is danger of burning! Keep the lid closed until the temperature
reaches 30 °C / 86 ºF or less. Only use materials (tubes, tube caps, plates and sealing
films) which are heat resistant to 120 ºC / 248 ºF.
Caution: Environment
The ventilation of the device must not be covered.
Danger: Line voltage
Incorrectly grounded products can be extremely hazardous in the event of a fault.
Use only a 3-conductor power cable (3x 0.75 mm2) with protective ground. The power
connector may only be plugged into a socket with a protective ground. The protection
must not be nullified by an extension cable without protective ground.
LICENCE NOTICE
This instrument is licensed for research and development and for uses other than human in vitro
diagnostics under one or more of the following patens of Applera Corporation: U.S. Patent Nos.
5,656,493, 5,038,852, 5,333,675, 5,475,610 (claims 1-159 and 164-166), 6,703,236 (claims 7-10) and
7,238,517 or corresponding claims in their non-U.S. counterparts. No right is conveyed expressly, by
implication or by estoppels under any other patent of Applera, including but not limited to U.S. Patent
No. 6,814,934 and its non-U.S. counterparts, which describe and claim thermal cyclers capable or real-
time detection.

6vwr.com I Instruction manual VWR®PCR Cycler XT96
DELIVERY CONTENTS
After receipt of the system, please check if the following items are included in the shipment. If any
transport damage is noticed, contact your distributor or manufacturer immediately.
IMPORTANT NOTICE: IF YOU FIND ANY DAMAGE OF THE DEVICE, DO NOT USE THE DEVICE!
1 Thermal cycler
1 Power cord
1 Instruction manual
1 Link PC-software VWR 'PCR Cycler XT Software'
UNPACKING
Remove the instrument from its packaging and inspect it for signs of damage. If any are
discovered, inform your supplier immediately
The instrument must be placed on a stable, level surface and positioned such that air can
circulate freely around the casing
Ensure your proposed installation site conforms to the environmental conditions for safe
operation
There should be enough space to make sure that the ventilation grills on the front and back
are not covered and sufficient ventilation is provided. The accessibility of the power switch
must not be hindered. There should be a distance of at least 25 cm (10 inch) to the wall or the
next device. Two thermal cyclers should not be placed back-to-back or back to front.
The instrument is designed for indoor use only, temperature range of 10 to 35 °C and
humidity of 35 to 70% are recommended
If the instrument has just been unpacked or has been stored in a cold environment, it should
be allowed to come to room temperature for 2 – 3 hours in the laboratory before switching
on. This will prevent calibration failure because of internal condensation
The instrument must be connected to the power supply with the power cord supplied.
It is recommended that users should thoroughly read this manual prior to use
Contact your supplier if you experience any difficulties with this instrument

7vwr.com I Instruction manual VWR®PCR Cycler XT96
SPECIFICATIONS
VWR PCR Cycler XT96
•8 Peltier elements with Long-Life-technology and 8 control circuits with Pt 1000 temperature
sensors
•Maximal heating and cooling rate: 4 °C/s
•Block uniformity (at 72 °C): ± 0.35 °C
•Temperature range thermoblock: 4 to 105 °C
•Control accuracy thermoblock: ± 0.2 °C
•Variable ramping: 0.1 to 3.0 °C/s
•Increment/Decrement time: 0:00:01 to 0:59:59
•Increment/Decrement temperature: 0.1 to 3 °C
•Lid heating temperature range: 40 to 110 °C
•2 x USB, 1 x Ethernet interfaces (MS Windows®or Linux)
Note: USB interfaces only support standard USB sticks, cord mouse and keyboards!
•Dimensions (B x H x D) : 22 x 30 x 33 cm (XTender: 22 x 20 x 33 cm)
•Weight incl. block: 8.9 kg (XTender:8.3 kg)
•Pollution rate: 2
•Environmental temperature range: +10 °C to +35 °C
•Max. relative humidity: 70 %
•Maximum height above sea level: 2000 m
•Noise level: < 37 dB (A)
Gradient feature (optional)
•Maximal gradient range over 8 columns, respectively: 30 °C (± 15 °C)
•Temperature range Gradient: 30 to 100 °C
•Gradient accuracy: ± 0.2 °C
User interface/functions
•Touch sensitive (capacitive) TFT-Display (800 x 480) (not included in the XTender)
•Direct help function
•Internal flash memory for 500.000 typical PCR programs in free configurable
folders/subfolders. Unlimited number of programs via network PC or USB stick
•Free PC software for the generation of PCR programs on the computer
•Unlimited number of steps per program
•Password protected user accounts with variable access rights
•GLP reports for complete recording of all runs
•QuickStart function of the last used program
•Automatic restart after power failure, Power-Fail-Denaturation, Instant Incubation
•Remote control and monitoring of instruments via PC-software
•MP3 sounds free of choice
•Master-/Slave-control
Block capacity
•96 well Universal block with lid heating and automatic height adaption for 96 x 0.2 ml tubes
and 96 well PCR plates (non-skirted and half-skirted)
Power supply
100 - 240 V AC, 50/60 Hz, max. 860 VA
For indoor use, only!

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CONNECTIONS
1x USB interface
1x USB interface
Ethernet interface
AC Power inlet
Status LED
Main power switch

9vwr.com I Instruction manual VWR®PCR Cycler XT96
Before first use, ensure that the voltage requirements of the PCR Cycler exactly match your local AC
power supply. Connect the PCR Cycler to the AC power supply only by the AC power cord delivered
with your PCR Cycler XT. Only connect the PCR Cycler XT to electric power systems with an earth
conductor. The AC power inlet is located at the rear of the Cycler. To disconnect the cycler
from the AC power supply, remove the AC power cord from the AC power inlet. The
accessibility of the AC power inlet must be not hindered or obscured in any way.
If a service is required, contact your local distributor or the manufacturer (see "TECHNICAL SERVICE
AND ORDER INFORMATION", page 36).
The serial number of the PCR Cycler is located underneath the instrument. Unauthorised work on the
device voids the warranty.
The surface of the device should be decontaminated with a lint-free cloth soaked with 70% ethanol
before sending. Please fill in and sign the decontamination certificate and send it to the
manufacturer together with the device.
For safety reasons the device must be switched off and the mains plug pulled before cleaning is
performed!
INSTALLATION OF THE PCR CYCLER XTENDER96
The VWR thermal cycler XTender96 is a fully equipped PCR Thermal cycler without a Touch screen, the
ideal device controlled by a PC or from another XT96 Thermal cycler.
To connect multiple XTender96 Thermal Cyclers, you need:
- An Ethernet cable for each XTender96 Thermal Cycler
- A network or an external network router (DHCP server is required)
Please ask your network administrator for the required settings.
Set up the Connections
1. Connect the Ethernet cable to the back of the thermal cycler and connect the other end of the
cable to the network.
2. Repeat step 1 for each thermal cycler.
3. Power on the XTender96 thermal cycler.
4. Plug the “Network Configuration USB-Stick” into an USB port of the XTender96 thermal cycler.
Note: For each XTender96 thermal cycler, a new “XT96ConfigFile” file must be created.
5. The XTender96 Thermal Cycler will recognize the USB stick and set up the network configuration
automatically. After finalization, the instrument will switch of.
6. Remove the “Network Configuration USB-Stick” from the USB port of the XTender96.
7. Power on the XTender96 thermal cycler
8. Follow the instructions in “Remote Control” on page 33 and 34 of the manual to enable a
remote control from a XT96 Thermal cycler or from a PC.

10 vwr.com I Instruction manual VWR®PCR Cycler XT96
Generate a “Network Configuration USB-Stick”
1. Power on a XT96 Thermal Cycler (Master unit)
or start the XT96 PC Software on your PC.
2. Use the “System” dialogue in the Software and
click on “Thermal Block” and “Configure USB
Stick”
3. Insert an USB Stick into the Cycler or PC.
4. Configure the network settings for the
XTender96 thermal cycler, as shown in the
picture.
5. Make sure each instrument name is unique and press OK.
6. A “XT96ConfigFile” file will be generated and stored on the USB stick.
7. Use this “Network Configuration USB Stick” to set up the Network configurations on your
XTender96 Thermal Cycler.
Note: Every XTender96 Thermal Cycler needs a separate “XT96ConfigFile” file where the
instrument name is unique.
OPERATING THE PCR CYCLER XT96
General operation
The operation of the thermal cycler can be run by the internal touch screen, by using the touch sensitive
surface of the display or by using a mouse connected to an available USB port. Furthermore, the
thermal cycler can also be controlled by computer integrated to a network. The supplied application
software offers the same functions as the internal thermal cycler software, except for some system
settings.
If the user has to enter numbers or text the corresponding field has to be touched on the touch screen
or clicked with the mouse. An appropriate keyboard will appear on the screen according to the
expected entry.

11 vwr.com I Instruction manual VWR®PCR Cycler XT96
All functions of the thermal cycler will be served by operating elements explained in the following
chapters. An operating element is activated by touching the screen or clicking the mouse.
Operating elements which are not available in an actual operating mode are displayed in a grey
colour. Not all operating buttons are available in each operating mode.
Turn on the cycler using the power switch on the back panel of the Cycler. When the PCR Cycler XT96
starts, it runs a self-test to verify proper functions and then displayed the RUN screen.
To open the lid, press the butten on the lid gently.
Place the reaction vessels into the 96 well block. To ensure uniform heating and cooling of samples,
reaction tubes must be in complete contact with the block. Block must be clean.
Press the lid downwards till the lid locks, the height of the heating lid will be adjusted automatically.
If the touch screen of the Thermal cycler will not be used for at least 2 minutes, a group view will be
shown. Displayed information is: Thermal cycler connected to this device, status of each cycler and
time remaining. Press to close this screen.
Did you know?
Shorter PCR protocols and moderate temperatures (8°C – 10°C) in the “Store-Step” will reduce the
power consumption of your PCR Thermal cycler dramatically. For saving energy and prevent excessive
condensation.
Tube and Strip:
To enable a homogeny pressure of the heating lid, distribute single tubes and strips over the whole
block. When using only one or a few tubes – load at least one empty tube in each corner of the block.
Fig : Ideal positioning Tubes and Strips

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Status LED:
Status
LED Light
Self-Test
White light – flashes
Standby
White light – turns on
PCR Run
Colour change
Store-Step
Blue light – glowing
Incubation Mode
Red light – glowing
Remote Control connected
Green light – flashes
Warning
Orange light – flashes
Error
Red light – flashes
Main Menu
The main menu consists of seven dialogues, which can be selected via tabs at the right side of the
screen. Each dialogue contains a help button for direct help function. The functions of the individual
dialogues are explained below.
Change User
This dialogue is used for selecting a User.
The user account management, user groups or single users can be configured in
the System dialogue (see page 11).
Incubate
This dialogue is used for selecting and executing the incubation mode. It can be
activated to manually program temperatures of the thermal plate and heated lid.
This is useful for fast and easy incubations similar to a digital dry bath. Further
instructions for the Incubation Mode are given on page 13.
Run
This dialogue is used for selecting, executing
and monitoring existing PCR
protocols. A detailed description of the 'Run' dialogue is given on page 14.
Programs
This dialogue is used for creating, editing and organizing PCR protocols (see page
20).

13 vwr.com I Instruction manual VWR®PCR Cycler XT96
GLPs
This dialogue is used for displaying and organizing GLP reports created by the
thermal cycler (see page 26).
Explorer
This dialogue is used for creating, editing and organizing files and folders created
by the thermal cycler (see page 28).
Diagnostics
This dialogue is used for monitoring the actual temperature profile of the
thermoplate. Also,
the temperature of the heated lid and the temperature of the
cycler interior are displayed (see page 30).
System
This dialogue is used for changing the general settings of the device and for the
user management functions (see page 31)
. The 'System' dialogue is also used for
checking serial and version numbers of hardware and software, respectively.
Help Button
Use this button to activate (deactivate) the direct help mode. The help function is
active, when the button appears pressed. If the mouse pointer is visible a question
mark appears alongside. By touching a function button or other dialogue element
the corresponding help window will appear. Closing the opened window or
pressing the help button again, will deactivate the direct help mode and the
system returns to normal operation.
Change User
Change User
Use this button to select a user from a list. Group rights of this user are shown on
the right side of the screen.
To change the settings or implement new users, please go to the User Management
dialogue in the System dialogue (page 29)
The factory-set password for the Administrator is admin.

14 vwr.com I Instruction manual VWR®PCR Cycler XT96
Incubation Mode
Run incubation
Use this button to set the device into the incubation mode. The temperature for the
thermal plate and lid can be set manually.
Setting the block and lid temperature and timer
Set temperatures of block and lid and time by entering the values of choice in the
corresponding editor fields. By entering values < 35 °C / 104 ºF the lid heating will
be turned off.

15 vwr.com I Instruction manual VWR®PCR Cycler XT96
Start / Stop
Use this button to start and quit the incubation mode. Heating of the thermal plate
and lid are then activated / deactivated.
Timer
The clock shows the time passed by in the incubation mode.
Block
Current temperature of the thermal plate.
Lid
Current temperature of the lid heat.
Run dialogue
The Run dialogue is used for running and monitoring existing PCR protocols. Two versions are available,
the “Simple Mode” with reduced information or the “Expert-Mode” with access to all main functions.
Run dialogue: Overview – “Simple Mode”
The following functions are found in the 'Run' dialogue:
Expert Mode /
Simple Mode
Stop Button
Start Button
Time remaining
Program name
Select Program
Cycler selection
User
Protocol Wizard
Progressbar

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Select Program
Using this button,
a stored or recently used PCR protocol can be selected and
loaded. Also, the Protocol Wizard can be used to create new Protocols.
Run dialogue: Overview – “Expert Mode”
The following functions are found in the 'Run' dialogue:
Protocol window
Cycler selection
User
List view /
diagram view
Expert Mode /
Simple Mode
Start
Info Button
Select protocol
Program name
Recently used Protocols
use pin to lock a protocol in the list
Open Explorer
Stop

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Run dialogue: Operating elements – “Simple Mode”
Select program
Using this button, a stored or recently used PCR protocol can be selected and loaded.
Also, the Protocol Wizard can be used to create new Protocols.
Info button
Use this button to display details of a PCR protocol (name, program options, author,
settings and comments).
Start / Pause
Use this button to start a PCR protocol or pause a PCR protocol that is in progress.
Stop
Use this button to stop a PCR protocol that is in progress.
Select Program dialogue – Recent Protocols / Protocol Wizard
Stored programs or recently used
PCR protocol can be selected and
loaded. Also,
the Protocol Wizard
can be used to create new
Protocols.
If a recently used program is
selected,
the chosen program will
be loaded in the run dialogue by
clicking .

18 vwr.com I Instruction manual VWR®PCR Cycler XT96
Protocol Wizard
The Wizard is a
useful tool for a fast
and automatic creation of PCR
programs
like 3-Step, 2-
Step and
Gradient Programs.
A
three-step program consists of a
separated
s
tep for denaturation,
a
nnealing (priming) and elongation.
In a two
-
step program, the
annealing
and
elongation steps are
combined
in a single step.
How to use the 3-Step Wizard:
1. Enter the number of cycles
2.
Enter the denaturation temp
(recommendation 95°C) and time (s)
3.
Enter the primer annealing
temperature.
Note: In general, the annealing
temperature is about 5°C below the
calculated average primer pair
melting temperature (Tm)
4.
Enter the
elongation Temp (72°C
recommended) and time.
Note:
Elongation time (s) = product
length [bases] /
1000 [bases] * 60 s
Press OK
to create a 3-step-PCR
Protocol
with the selected settings.
Press
to save or to
save and start the new protocol.
Run dialogue: Operating elements – “Expert Mode”
Select program
Using this button,
a stored or recently used PCR protocol can be selected and loaded.
Also, the Protocol Wizard can be used to create new Protocols.
Info button
Use this button to display details of a PCR protocol (name, program options, author,
settings and comments).

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Start / Pause
Use this button to start a PCR protocol or pause a PCR protocol that is in progress.
Stop
Use this button to stop a PCR protocol that is in progress.
List view
Push this button to view the selected program in list view.
Diagram view
Push this button to view the selected program in diagram view.
If the path for the printer is already entered, simply click for printing.
Using the button
, a test printing will be performed to check the correct
settings.
Starting a program
If a program is opened, the
contents of the program can be
seen in the program window. The
loaded program is started by
using the 'Start' button.
A program is running
General: 'Pause' and 'Stop'
button
After starting the chosen program,
you can use these buttons to either
pause or to stop the program.

20 vwr.com I Instruction manual VWR®PCR Cycler XT96
'Pause' button
If the 'Pause'
button is pressed during the
operating sequence, the program is paused and
the 'Start'
button appears which can be used to
continue the program.
During the break the status 'Paused' is shown.
'Stop' button
If this button is
pressed after starting a program,
the adjoining security query appears.
By confirming the security query with 'Yes', the
program will be stopped.
Status Display
In this window the following information on the status is shown during a run:
Cycle:
The number of
finished cycles is
shown
Lid:
Temperature of
the heated lid
Time remain.:
Remaining time
of PCR program
Block:
Average temperature
of the thermal block
Total Progress:
T
otal Progress of
PCR program in %