Peqlab peqSTAR 2X User manual

Instruction Manual
Thermal cycler
peqSTAR 2X Double block thermal cycler
peqSTAR 96X, 84X and in situ X thermal cycler
v1212E
Creating the future together
.

Instruction Manual peqSTAR X thermal cyclers
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CONTENT
page
1 System Overview 1
2 Safety instructions 1
License Notice 2
4 Installation 2
4.1 Content of delivery 2
4.2 Installing the thermal cycler 2
4. Operation of the thermal cycler 2
4.4 Connections of the thermal cyclers
5 General Operation
6 Main menu 4
6.1 Run 4
6.2 Programs 4
6. Diagnostics 4
6.4 GLPs 4
6.5 System 4
6.6 Help Button 4
7 Run dialogue 5
7.1 Run dialogue: Overview 5
7.2 Run dialogue: Operating elements 5
7.2.1 Incubation mode 5
7.2.2 Start 5
7.2. Stop 5
7.2.4 Pause 5
7.2.5 Info button 6
7.2.6 Lid lock / unlock 6
7.2.7 Select program 6
7. Select Program dialogue 6
7.4 Info Button 6
7.4.1 Steps 6
7.4.2 Program Options 7
7.4. Print 7
7.5 Lid lock / unlock 7
7.6 Starting a program 7
7.7 A program is running 8
7.7.1 General: 'Pause' and 'Stop' button 8
7.7.2 'Pause' button 8
7.7. 'Stop' button 8
7.7.4 Status Display 8
7.7.5 Program window 9
7.7.6 Save GLP Report 9
7.7.7 Not create GLP Report 9
7.7.8 Switch off the GLP report query 9
8 Incubation mode 10
8.1 Run incubation 10
8.2 Setting the block and lid temperature 10
8.2.1 Stop 10
8.2.2 Lid lock / unlock 10
8.2. Timer 10
8.2.4 Block 10
8.2.5 Lid 10
9 Programs 11
9.1 Program selection 11
9.1.1 Open a program 11
9.1.2 Copy 11

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9.1. New program 12
9.1.4 New folder 12
9.1.5 Delete 12
9.1.6 'Info' button 12
9.2 Operating elements of the 'Programs' dialogue 1
9.2.1 Entering a command 1
9.2.2 List view 1
9.2. Diagram view 1
9.2.4 New program 14
9.2.5 Open a program 17
9.2.6 Info-Button 17
9.2.7 Deleting a command from the program 17
9.2.8 Saving a program 17
9.2.9 Save & Run 17
9.2.10 Editing a command 17
9. Available commands (program steps) 18
9. .1 Unlock 18
9. .2 Lock 18
9. . Heat Lid 18
9. .4 Temperature 19
9. .5 'Elongation Time' and 'Melting Temp.' 19
9. .6 Gradient step 19
9. .7 Cycle: 21
9. .8 Start Cycle - Manual cycle beginning 21
9. .9 Close Cycle - Manual cycle ending 21
9. .10 Pause 21
9. .11 Store 21
10 Diagnostics 22
10.1 Operation of the 'Diagnostics' dialogue 22
10.2 General view 2
10.2.1 Zones 2
10.2.2 Single view 2
10.2. Automatic scrolling active 2
10.2.4 Automatic scrolling inactive 2
11 GLPs dialogue 24
11.1 Displaying a GLP report 24
11.2 Operating elements of the 'GLPs' dialogue 24
11.2.1 Select GLP 24
11.2.2 Open GLP report 24
11.2. Printer 24
11.2.4 Delete 25
11.2.5 Copy 25
11.2.6 New folder 25
12 System 26
12.1 Time / Date 26
12.2 Show/Hide mouse cursor 26
12. User Call 26
12. .1 Sound 26
12. .2 Email 27
12.4 User Management 28
12.4.1 Change User 29
12.4.2 User Management 29
12.4. Setting up a new user group 0
12.4.4 User logout 1
12.5 Network Settings 2
12.6 Hardware

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12.6.1 Overtemp test
12.7 Firmware
12.7.1 Control Unit
12.7.2 Power Unit 5
12.8 Print 5
12.9 Display 6
12.9.1 Brightness 6
12.10 Protocol 6
12.11 LAN Control 6
12.11.1 New Lan Connect 6
12.11.2 Lan Connect 7
12.11. Lan Disconnect 7
12.11.4 Zigbee Configure 7
12.11.5 Zigbee Connect 8
12.11.6 Zigbee Disconnect 9
12.12 USB Recovery 9
12.1 Service 9
1 Maintenance & repair of the Thermal cycler 40
1 .1 Cleaning, maintenance and repair of the thermal cycler 40
1 .2 Test of the overtemperature protection 40
1 . Temperature check-up 40
1 .4 Calibration 40
14 Warranty 40
15 Disposal Instruction 41
16 Technical data 41
16.1 General characteristics 41
16.2 Gradient feature (optional) 41
16. User interface/functions 41
16.4 Block capacity 42

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1SYSTEM OVERVIEW
The peqSTAR X thermal cyclers are the ideal PCR devices for all molecular biological and biochemical laboratories
working in the field of basic research or routine diagnostic. The 250 °C HTR (High Temperature Range) Peltier
technology allows quick changes in temperature up to 5 °C/sec (max). The individual monitoring and controlling
of each of the eight or 16 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 (except for the in Situ block).
The peqSTAR X thermal cyclers are equipped with a touch-sensitive, graphic colored 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 the Microsoft Windows
®
or Linux network. 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:
Notice:Notice:
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 m!
2SAFETY INSTRUCTIONS
Before the first use of the thermal cycler please read the instruction manual entirely.
Special notice should be taken of the following
Caution o dangerous voltage
Please ensure the voltage indicated on the device exactly matches your local electrical supply.
Caution o dangerous explosive material
Explosive or reactive material mustn’t be heated in the thermal cycler.
Caution - liquids
Ensure that no liquids can enter the device.
Reaction tubes must be filled outside of the thermal cycler.
Caution - hot sur aces
The thermal plate, the heated lid and the reaction tubes quickly reach temperatures above
50 °C. There is danger of burning! Keep the lid closed until the temperature reaches 0 °C or
less. Only use materials (tubes, tube caps, plates and sealing films) which are heat resistant to
120 °C.
Caution – environment
The ventilation of the device must not be covered.
Note:
Note:Note:
Note: If the thermal cycler is used in any manner not specified in these instructions, the intended protection of the
user can not be guaranteed.

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3LICENSE 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. 5,656,49 , 5,0 8,852,
5, ,675, 5,475,610 (claims 1-159 and 164-166), 6,70 ,2 6 (claims 7-10) and 7,2 8,517 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. 6,814,9 4 and its non-U.S. counterparts,
which describe and claim thermal cyclers capable or real-time detection.
4INSTALLATION
4.1 Content o delivery
1 Thermal cycler
1 Power cord
1 Instruction manual
1 CD PC-software 'peqSTAR Manager'
Please check delivery for completeness and transport damage upon arrival. 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!
4.2 Installing the thermal cycler
Check the packaging for any transport damage. Remove the packaging and place the thermal cycler onto a solid
surface. The device should not be exposed to direct sunlight. There should be enough space to make sure that the
ventilator grills on the front and back are not covered and sufficient ventilation is provided. The accessibility of the
mains switch must be assured and not 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. Room temperature
between 4 °C und 25 °C is advised.
All original packaging should be stored in case a need arises to return the instrument to the supplier.
4.3 Operation o the thermal cycler
Before starting up the thermal cycler for the first time make sure that your local power supply is matching the
voltage and frequency range of the device. Plug in the mains plug of the thermal cycler to an electricity supply with
PE connection. The outlet and the power switch are located at the back of the device. The mains switch serves as
disconnection from the mains supply. The serial number is written onto a typed label at the bottom of the device.
The device should only be used by authorized staff. To ensure this, a user management with appointing rights for
specific users is available in the device.
More details about this and a detailed instruction manual can be found in the following chapters.

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4.4 Connections o the thermal cyclers
5GENERAL OPERATION
The operation of the thermal cycler can be run by the internal touch screen, either using the touch sensitive surface
of the display or by using a mouse connected to a free USB port. Furthermore the thermal cycler can also be
controlled by computer integrated to a net work or wireless ZigBee connection (option). The supplied application
software offers the same functions as the internal software of the thermal cycler, 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.
All functions of the thermal cycler will be served by operating elements explained in the following chapters. An
operating element is activated by touching or clicking with the mouse.
Operating elements which are not available in an actual operating mode are displayed in a grey color. Not all
operating buttons are available in each operating mode.
2x USB interface
2x USB interface
Ethernet interface
Mains power inlet
Mains switch

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6MAIN MENU
The main menu consists of five dialogues, which can be selected via tabs at the right side of the screen. PeqSTAR
2X thermal cyclers offer two tabs 'L' (left) and 'R' (right) for choosing the desired block. This option is not available
for peqSTAR 96X, 84X und in situ X systems. Each dialogue contains a help button for direct help function. The
functions of the individual dialogues are explained below.
6.1 Run
This dialogue is used for selecting, executing and monitoring existing PCR protocols. A detailed
description of the 'Run' dialogue is given in chapter 7. Additionally, the incubation mode can
be activated here in order 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 in chapter 8.
6.2 Programs
This dialogue is used for creating, editing and organizing PCR protocols (see chapter 9).
6.3 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
chapter 10).
6.4 GLPs
This dialogue is used for displaying and organizing GLP reports created by the thermal cycler
(see chapter 11).
6.5 System
This dialogue is used for changing the general settings of the device and for the user
management functions (see chapter 12).
. .
. The 'System' dialogue is also used for checking serial
and version numbers of hardware and software, respectively.
6.6 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.

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7RUN DIALOGUE
The Run dialogue is used for running and monitoring existing PCR protocols.
7.1 Run dialogue: Overview
The following functions are found in the 'Run' dialogue:
7.2 Run dialogue: Operating elements
7.2.1 Incubation mode
Using this button the incubation mode can be activated. In this mode block and lid temperatures
can be adjusted manually (see chapter 8).
7.2.2 Start
Use this button to start a PCR protocol.
7.2.3 Stop
Use this button to stop a PCR protocol which is in progress.
7.2.4 Pause
Use this button to pause a PCR protocol which is in progress.
Program window
Block selection left / right
(only for peqSTAR 2X systems)
Direct help
List view /
diagram view
Lid lock /
unlock
Incubation Mode /
Stop Button
Start Button
Info Button
Select program
Program name

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7.2.5 Info button
Use this button to display details of a PCR protocol (name, program options, author, settings,
comments and program steps).
7.2.6 Lid lock / unlock
Use this button to lock or unlock the lid. Furthermore the button shows the current status of the
lid.
7.2.7 Select pro ram
Using this button a stored PCR protocol can be selected and loaded.
7.3 Select Program dialogue
Stored programs can be selected and
loaded by using this button.
If a program is selected the adjoining
window appears.
If a program is marked, the 'i' button
appears.
By 'Open' the chosen program will be
loaded in the run dialogue.
Further information on this dialogue can be found at chapter 9.1.1
7.4 In o Button
Using this button a new window will open, which shows detailed information of the chosen
program. If wanted, this information could be printed. The header contains program name and
the link to the program.
You will have the following options:
You will have the following options:You will have the following options:
You will have the following options:
7.4.1 Steps
Using this tab, the single steps of
the selected program are listed.

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7.4.2 Pro ram
Options
Using this tab, the settings of
the selected program are
shown.
7.4.3 Print
With peqSTAR X thermal
cyclers, PCR programs and
GLPs could be printed on a
network printer. Using this
dialogue, you can type in the
path for a printer in the
network.
Please refer to your local
network administrator for the
required settings.
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.
7.5 Lid lock / unlock
Use this button to lock or unlock the lid.
For systems with HPL lids(High Pressure Lid) there is the option to define the lid pressure in an
opening dialogue.
7.6 Starting a program
If a program is opened, the
content of the program can be
seen in the program window.
The loaded program is started
by using the 'Start' button.

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7.7 A program is running
7.7.1 General: 'Pause' and
'Stop' button
After starting the chosen program, you
can use these buttons to either pause or
to stop the program.
7.7.2 'Pause' button
If the 'Pause' button is pressed during the operating
sequence, the adjoining window appears. If this
request is confirmed, 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.
7.7.3 '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.
7.7.4 Status Display
In this window the following information on the status is shown during a run:
Cycle:
Cycle:Cycle:
Cycle:
The number of
finished cycles is
shown
Lid:
Lid: Lid:
Lid:
Temperature of the
heated lid
Time remain.:
Time remain.: Time remain.:
Time remain.:
Remaining time of
PCR program
Total Progress:
Total Progress: Total Progress:
Total Progress:
Total progress of
PCR program in %
Block:
Block:Block:
Block:
Average temperature of
the thermoblock

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7.7.5 Pro ram window
In the program window the blue flashing bar is
showing the actual program step.
7.7.6 Save GLP Report
If stopping the program after the security query, the
adjoining query to create a GLP report appears.
Note: The GLP report query also appears when a
program is finished.
Will the query be confirmed by 'Yes', a GLP report
will be created and shown on the display. It will be
saved under the file name <program name>_<date>_
<time>.glp if not deleted by the user. For this the
adjoining window is shown.
The GLP report can be opened and printed in the
'GLPs' dialogue (see chapter 11).
7.7.7 Not create GLP Report
There will be no GLP report created for the aborted program. At the next run the GLP report query will
appear again. You will return to the 'Run' dialogue, which shows the last chosen program, which can be
started again.
7.7.8 Switch off the GLP report query
When you press this button, there will be no GLP reports created in the future. After the abort or end of a
program no GLP report query will appear again. The setting can be reset in the system dialogue (see
chapter 12.7.1.2).

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8INCUBATION MODE
8.1 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.
8.2 Setting the block and lid temperature
Set temperatures of block and lid by entering the values of choice in the corresponding editor
fields. By entering values < 40 °C the lid heating will be turned off.
8.2.1 Stop
Use this button to quit the incubation mode. Heating of the thermal plate and lid are then
deactivated.
8.2.2 Lid lock / unlock
Use this button to lock or unlock the lid.
For systems with HPL lids(High Pressure Lid) there is the option to define the lid pressure in an
opening dialogue.
8.2.3 Timer
The clock shows the time passed by in the incubation mode.
8.2.4 Block
Actual temperature of the thermal plate.
8.2.5 Lid
Actual temperature of the lid heat.

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9PROGRAMS
The 'Programs' dialogue serves for generating and editing PCR protocols (programs). This is a list of commands,
which the thermal cycler performs in sequence after starting the program. The 'Programs' dialogue provides an
editor for this purpose.
9.1 Program selection
By touching the 'Programs' dialogue the selection dialogue shows up where a new program can be set or an
existing program can be opened to edit.
The selection dialogue can be opened at any time in the program editor by using the adjoining button .
Existing programs can be selected and opened for editing, folders can be created and new programs can be
generated, copied and deleted.
The operation of the dialogue is as follows:
The operation of the dialogue is as follows:The operation of the dialogue is as follows:
The operation of the dialogue is as follows:
9.1.1 Open a pro ram
Saved programs can be selected with this button. By touching the desired program it will be
selected of the file list and opened by using the 'Open' button. After this the thermal cycler
returns to the 'Pograms' dialogue. After the selection of a program several operating elements
are available, which are described in chapter 9.2 and 9. .
Note: The command 'Open' is only active, when only one program is marked. Via 'Open' the
chosen program will be loaded in the 'Programs' dialogue.
9.1.2 Copy
Pushing this button saved programs or
folders can be copied. Several
programs/folders can be marked via
mouse click simultaneously if the option
'Multiple Selection' is chosen. Marked
programs/folders are shown with a blue
background.

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By using the 'Copy' button the following dialogue appears:
In this dialogue the directory can be selected.
Copy the files with 'OK' or quit the operation with 'Cancel'.
9.1.3 New pro ram
A new program can be generated, after pushing this button the program’s name has to be
defined. Optionally author, user, any comment and different program options can be entered.
These data serve for information and can also be retrieved in the 'Run' dialogue.
9.1.4 New folder
Use this button to create a new subfolder after selecting an existing folder, in which the new
subfolder should be created.
9.1.5 Delete
Programs or folders can be deleted with this button.
9.1.6 'Info' button
Further details at chapter 7.4.
Destination for the copied files
(desired folder has to be selected
by clicking)
List of the selected files to copy

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9.2 Operating elements o the 'Programs' dialogue
The 'Program window'
'Program window''Program window'
'Program window' displays the list of commands (steps) the program is composed of. The 'List of available
'List of available'List of available
'List of available
commands'
commands' commands'
commands' is displaying all steps which can be entered into a program. The meaning of the single commands is
explained in chapter 9. . The function buttons
function buttonsfunction buttons
function buttons serve for editing of programs and the administration of program
files on the system and will be described in the following.
Function buttons o the 'Programs' dialogue:
9.2.1 Enterin a command
To enter a new command into a program the desired line has to be selected. From the left side of the
program window a blue arrow will point on the desired line. After selecting the program command of
the list in the left window it can be inserted into the desired place via the '+' button. Alternatively this
can be made by double click on the program command. Thereupon the corresponding parameters will
be asked. To enter a parameter the desired input field has to be touched. A keyboard will be shown
on the screen.
9.2.2 List view
Pushing this button, the selected program will be displayed in the list view, like shown in chapter 9.2.
9.2.3 Dia ram view
Pushing this button, the selected program will
be displayed in the diagram view, like shown
at the right.
Program window
Name of the PCR pro-
gram and total time List of available
commands
Direct help

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9.2.4 New pro ram
A new program can be generated, after pushing this button the program’s name has to be defined.
Optionally author, user, any comment and the program options can be entered.
9.2.4.1 New Cyclerprogram
Enter the name of the PCR program,
optionally also add name of the author and
a comment.
‘Path’ shows you the directory where the
program is stored. Over the button
you could change the path.
9.2.4.2 Program Options
Using the button the
adjoining window appears:
9.2.4.3 Power Fail Denaturation
If 'Power Fail Denaturation' is activated by
pushing the 'checkbox' the
adjoining dialogue appears:
If a power failure had happened while a program was
running the thermal cycler restarts the program at the
point it was stopped as soon as the power returns
(Autorestart after power failure).
Additionally, if the option 'Power Fail Denaturation' is
activated the thermal block will heat to the stated
temperature for the set time before continuing with the
program.
9.2.4.4 Global Program amp
Using the Checkbox a global
ramp rate in °C/s can be programmed. This global ramp
rate will be used in all temperature and gradient steps of
the PCR program, but could be changed in a single
temperature or gradient step manually by entering the
desired value at the step.

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9.2.4.5 Gradient Control
Using the Checkbox you can
decide whether in a gradient step the plateaus (Plateaus
synchronized) or the Ramps (Ramps synchronized) should
be synchronized for all rows.
9.2.4.6 Tube Control
With the Checkbox you have the
possibility to adjust temperature regulation for a
temperature step accordingly to sample volume. If
necessary, the temperature regulation will perform short-
term deliberate overshoots and undershoots depending
on the entered sample volume during PCR run.
9.2.4.7 Emulation
Using the Checkbox the thermal cycler
will perform PCR like the chosen cycler, emulating its
performance. This function could be useful if a PCR
program should be transferred to the peqSTAR from
another type and model of thermal cycler.