TC 9639 Thermal Cycler
User Manual
Document Version 1.4
99 Washington Street
Melrose, MA 02176
Phone 781-665-1400
Toll Free 1-800-517-8431
Visit us at www.TestEquipmentDepot.com
2
1. Instrument Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5
2. Menu Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6 1. Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7
1.1 Site Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7
1.2 Unpack Thermal Cycler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7
1.3 Power On and Power Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7
1.4 Open and Close Lid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
8
2. Home Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
9
1. Manage Folder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
10
1.1 Program Library Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
10
1.2 Add Folder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11
1.3 Rename Folder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11
1.4 Delete Folder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11
2. Manage Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
12
2.1 View Program Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
12
2.2 Rename Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
12
2.3 Copy Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
13
2.4 Delete Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
13
2.5 View Last Run Programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
13 1. Create New Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
14
1. Edit Program Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
14
1.2 Set Temperature Control Mode and Lid Temperature . . . . . . . . . . . . . . . . . .
15
1.3 Add Step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
16
Constant Temperature Step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
16
1.4 Set Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
18
Contents
Benchmark Thermal Cycler User Manual
3
1.5 Edit Step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
18 1.6 Delete Step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
18 1.7 Save Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
18
2. Edit Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
19
3. Program Wizard Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
20
1. Load Samples into the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
21
2. Select Program to Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
21
3. View Run State and Control Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
22 3.1 View Run State . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
22
Run Screen . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
23
View Run Timer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
24
View Bar Chart of Sample Block Temperature . . . . . . . . . . . . . . . . . . . . . . .
24
View Temperature Record Curve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
24
View Run Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
24 3.2 Control Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
25
Pause Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
25
Skip Run Step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
25
Stop Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
25
Run Program Again . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
25
1. System Setting Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
25
2. About . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
26
3. Incubation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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4. Gradient Calculator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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5. View Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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6. Tm Calculator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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7. Check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
27
8. Configure Shortcut . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
28
9. Admin Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
29 9.1 Access Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
29 9.2 Thermal Cycler Name/IP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
30 9.3 Set Date/Time . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
31 9.4 Run-time Accuracy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
31 9.5 User Message . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Benchmark Thermal Cycler User Manual
About This Manual
4
Purpose of This
Manual
This manual provides instructions on how to set up and use the Benchmark Thermal
Cycler.
Benchmark reserves the right to modify this manual at any time without prior notice.
This manual uses the following conventions:
• Bold text indicates user operation.
For example:
Touch Ok to accept changes and return to last screen.
• Note: Provides instructions that draw your attention or may be helpful.
For example:
• IMPORTANT! Provides information that must be read carefully. Failure to follow
the information will possibly result in damage to the instrument or the user.
For example:
Suggested
Operation
Support
Information
For the service and support information, contact Benchmark Scientific by phone at
908-769-5555, or email, info@BenchmarkScientific.com.
Note:
When the instrument is set aside for a long time, disconnect the power cable from
the socket.
IMPORTANT!
To prevent electric shock, turn off the unit and disconnect the power supply
prior to cleaning.
IMPORTANT!
Turn the lid knob counterclockwise to loosen the lid before opening to
prevent damage to the lid.
For optimum screen performance and
visibility, the angle shown at the left is
suggested for operation.
Best Operating Angle
Please read the manual carefully before using the Thermal Cycler!
Benchmark Thermal Cycler User Manual
5
A [ INSTRUMENT OVERVIEW ]
Component
Function
Lid
Heats the top surface of reaction vessels to prevent sample evaporation and condensation.
Lid Knob
Regulates the height and force of lid.
Lid Handle
Opens and closes the lid.
USB Port
Connects to a USB flash drive.
Touchscreen
Views and controls the instrument.
Air Vents
Allows air to circulate into and out of the instrument.
Power Switch
Powers on (1) and powers off (0) the instrument.
Power Inlet
Connects the instrument to power socket via supplied power cable.
Ethernet Port
Connects up to 255 Thermal Cyclers to a computer.
RS232 Port
Connects the instrument to a computer.
Ethernet Port
Power Inlet
Power Switch
USB Slave
Air Vent
USB Port
Lid Handle
Lid
Lid Knob
Air Vent
Touchscreen
1. Instrument Components
Figure 1 Front View of Thermal Cycler
Figure 2 Rear View of Thermal Cycler
Table 1 Functions of Thermal Cycler Components
A Instrument Overview
Benchmark Thermal Cycler User Manual
A Instrument Overview
6
Button
Function
Returns to the Home screen.
Closes current screen and returns to previous screen.
Moves between pages (i. e., Page Up and Page Down).
Scrolls left or right to view graph or curve.
Accepts present parameters setting and closes the screen.
Close the screen without changing any parameters.
Runs a selected program or incubation mode.
To...
Touch...
Enter a number
A number button.
Enter a letter
A letter button.
Touch / to change between lowercase letters and
uppercase letters.
Join several words
Underscore character
Delete the last character in an
input field
Erase all characters
IMPORTANT!
To prevent damage, do not use sharp objects (such as a pencil) on the touch screen.
2. Menu Overview
Table 2 and Figure 3 describe buttons and virtual keyboard common to many of the screens.
Table 2 Buttons in the screens
Figure 3 Virtual keyboard
Text is entered with the virtual keyboard:
Benchmark Thermal Cycler User Manual
7
B [ GETTING STRATED ]
The Thermal Cycler is intended for indoor use. Ensure that the installation site
meets conditions below.
Power supply
The Thermal Cycler has a universal, 85V-265V power supply and is supplied
with a 3 prong plug. Be sure that the instrument is connected to a reliable
power outlet that is rated to handle the load of the thermal cycler.
Environmental
Conditions
Table 1 Temperature and humidity conditions:
Condition
Acceptable range
Ambient temperature
10 to 30°C (50 to 86°F)
Relative humidity
20 to 80%, noncondensing
Place the Thermal Cycler on a level table or bench. Avoid placing the instrument
adjacent to heaters, cooling instruments, sinks or in direct sunlight. Keep away
from any equipment that vibrates, such as a refrigerator or centrifuge. The
recommended distance between the instrument and the back wall is 20 cm (7.9
in). Two thermal cyclers can be placed side by side.
1. Remove the packaging materials and keep in case of shipping damage to the
unit.
2. Inspect the instrument for shipping damage.
3. Included in the box should be:
• Thermal cycler with block
• Appropriate power cord
• User Manual (this manual)
• Warranty registration card (to be completed and returned)
4. Move to the desired installation site.
1. Connect the power cord to the power inlet in the rear of the instrument.
2. Connect the 3-prong plug of the power cord to the wall socket. Make sure the
power cord is connected to both power inlet and socket firmly.
To power on: Turn the power switch to position ‘1’.
To power off: Turn the power switch to position ‘0’.
Note: When the instrument is not used for extended periods of time,
disconnect the power cord from the wall socket.
IMPORTANT! If the Thermal Cycler is damaged or some items are
missing or damaged, contact Benchmark Scientific.
1. Installation
1.1 Site Requirements
B Getting Started
1.2 Unpacking
1.3 Power On and Power Off
Benchmark Thermal Cycler User Manual
B Getting Started
8
The lid of the Thermal Cycler can be adjusted to come into contact with and
apply pressure to the tops of the reaction vessels. Heating of the lid protects
samples from condensation.
To open the lid:
1. Turn the lid knob counterclockwise (see the ‘Loosen’ arrow symbol on the top
surface of the lid knob) to raise the pressure plate.
2. Grasp the lid handle so that the handle clamp is pulled toward the lid handle.
3. Lift up the lid handle until the lid opens vertically. You can then place
reaction vessels in the sample block or remove samples from the block.
To close the lid:
1. Place reaction vessels into the wells of the sample block.
2. Hold the lid handle and handle clamp, and then let the lid touch the chassis
until you hear ‘click …’ sound. The lid will be locked in place.
3. Turn the lid knob clockwise (see the ‘Tighten’ arrow symbol on the top
surface of the lid knob) to reduce the lid height until resistance is felt. Then
continue to turn the lid knob clockwise until you hear ‘click …’ sound. The
lid is now pressing on the reaction vessels.
Lid Handle
Handle Clamp
Chassis
IMPORTANT!
Temperature of the lid can be very high (105°C/221°F or higher). Never
touch the inner surface of the lid when the temperature is above 43°C.
Lid Knob
1.4 Open and Close Lid
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2. Home Screen
When the instrument powers on, the boot screen is displayed for several seconds.
The Home screen is then displayed (see below).
Items in the Home screen:
a. Information Bar: lid temperature, block temperature (when the instrument is
idle or when running program which set temperature control mode as Block) or
sample temperature (when running program which set temperature control
mode as Sim-tube) and estimated remaining run-time.
b. Shows date, day and time.
Home Screen
Buttons
Button
Function
When login is enabled, touch this button to
logout the current user.
Opens Run screen.
LastRun Programs
Go to list of the last 10 run programs.
Program Library
Go to list of folders, which contain all saved
programs.
Program Wizard
Creates new program quickly.
System Setting
Sets instrument parameters and shows other
tools.
Empty Shortcut
Configures shortcut for functions or
programs.
Program Shortcut
Shows a selected program shortcut.
a
b
B Getting Started
Benchmark Thermal Cycler User Manual
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C [ MANAGE FOLDER & PROGRAM ]
In the Home screen, touch Program Library.
The Program Library screen opens.
The table lists all available folders. Folder names include the number of
programs in parentheses. Touch the header of the first or second column of the
table to sort all folders. Touch (Page Up) and (Page Down) to move
between pages.
The Preset folder contains ten preinstalled programs:
• 3Step_2000, 3Step_1000, 3Step_500: for amplifying less than 2kb, 1kb,
500bp nucleic acid templates using three-step PCR.
• 2Step_PCR: two-step PCR.
• Touchdown1 and Touchdown2: Touchdown PCR.
• Long_PCR: for amplifying of extra-long nucleic acid chain.
• RT_PCR: for synthesizing DNA from RNA by reverse transcriptase.
• Ligation_16C: for connecting segmental DNA with vector DNA at 16°C.
• Enzyme_37C: for ordinary enzyme reaction at 37°C.
The Public folder is a system folder and used as the default f for saving programs.
When plugging a flash drive into the USB port, a USB icon appears.
Touch this icon to open the USB folder. The USB folder contains programs that
are stored in the USB flash drive. Programs can be copied to and from the USB
flash drive.
Note: Programs in the Preset folder cannot be renamed or deleted. To modify
a program in the Preset folder, edit the program and then save to another
folder (see chapter D). Or copy the program to another folder (see “2.3 Copy
Program”), and then modify it.
Note: When login is enabled, all users have access to the Public folder.
1. Manage Folder
1.1 Program Library Screen
C Manage Folders, Programs
Benchmark Thermal Cycler User Manual
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Program Library
Screen Buttons
Button
Function
View
Shows programs of selected folder.
New
Creates a new folder.
Rename
Renames a selected folder.
Delete
Deletes a selected folder.
1.2 Add Folder
To add a folder:
1. In the Program Library screen, touch New.
2. In the New Folder screen, enter a folder name.
3. Touch Ok to accept changes and close the screen.
To rename a folder:
1. In the Program Library screen, select a folder and then touch Rename.
2. In the Rename Folder screen, Clear the old folder name, enter a new name,
and then touch Ok to accept changes.
To delete a folder:
1. In the Program Library screen, select a folder and then touch Delete. A
pop-up window appears.
2. Touch Yes in the displayed pop-up window to delete the folder.
Note:
The Preset folder, Public folder and USB folder cannot be renamed.
Note:
The Preset folder, Public folder and USB folder cannot be deleted.
IMPORTANT!
When you delete a folder, all programs saved in the folder will be deleted at
the same time.
Note: The folder name is not case sensitive.
C Manage Folders, Programs
1.3 Rename Folder
1.4 Delete Folder
Benchmark Thermal Cycler User Manual
C Manage Folder, Programs
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1. In the Home screen, touch Program Library.
2. In the Program Library screen, select a folder and then double click it or
touch View to open the View Program screen opens. Touch the header of the
first or second column of the table to sort all programs.
View Program
Screen Buttons
Button
Function
View/Edit
Views and/or edits program steps (see
chapter D for details).
New
Creates a new program (see chapter D for
details).
Rename
Renames a selected program.
Copy
Copies program between folders.
Delete
Deletes a selected program.
Run
Runs a selected program (see chapter E for
details).
To rename a program:
1. In the View Program screen, select a program and then touch Rename.
2. In the Rename Program screen, Clear the old program name, enter a new
name, and then touch Ok to accept changes.
Note:
The program name is not case sensitive.
Programs in the Preset folder cannot be renamed.
2. Manage Programs
2.1 View Program Screen
2.2 Rename Program
Benchmark Thermal Cycler User Manual
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2.3 Copy Program
To copy a program:
1. In the View Program screen, select a program and then touch Copy to open
the Copy Program screen.
2. In the Copy Program screen, select a Target Folder in the drop-down list box,
and then touch Copy to copy the program.
If you want to:
a. Rename the program before copy - Touch Clear to clear the old Program
Name, and then enter a new name.
b. Create a new target folder to copy the program to - Touch New Folder to
open the New Folder screen, enter a folder name, and then touch Ok to return
the Copy Program screen.
c. Touch Export to copy the program to a USB flash drive.
To delete a program:
1. In the View Program screen, select a program and then touch Delete. A
pop-up window appears.
2. Touch Yes in the displayed pop-up window to delete the program.
In the Home screen, touch Last Run Programs.
The Last Run Programs screen opens.
The Last Run Programs screen has the same appearance as the View Program
screen, but shows the recently run ten programs for quick viewing and repeat
runs. Touch Clear to clear the program list.
Note: Programs in the Preset folder cannot be deleted.
Note:
The Rename and Copy buttons are not available in the Last Run Programs
screen.
2.4 Delete Program
C Manage Folders, Programs
2.5 View Last Run Program
Benchmark Thermal Cycler User Manual
14
D [ PROGRAMMING ]
1. In the Program Library, select a folder and then double click it or touch
View to open the View Program screen.
2. In the View Program screen, touch New to open the Edit Program screen.
The Edit Program screen is used to create, view and edit programs. After adding
several steps, the screen looks like below:
Items in the Edit Program screen:
a: Step number.
b: Temperature for a constant temperature step.
c: Step holding time (hour: min: sec).
d: The start step number and amounts of additional repeats for cycles.
b a c
d
Note: To open the Edit Program screen more quickly, you can put the New
Program shortcut in the Home screen (see “Configure Shortcut” for details).
1. Create New Program
1.1 Edit Program Screen
D Programming
Benchmark Thermal Cycler User Manual
D Programming
15
Edit Program
Screen Buttons
Setting steps of a program are carried out via the buttons:
Button
Function
Head
Sets temperature control mode and lid
temperature.
Temp
Adds a constant temperature step.
Goto
Return to a former step and repeat
Edit
Edits a step.
Delete
Deletes a step.
Save
Saves the created program.
Save as
Saves another copy of the opened program.
Run
Runs the program.
1. In the Edit Program screen, touch Head.
The Head screen opens.
2. Select temperature control mode and lid temperature control mode and then
touch Ok to accept changes.
Note:
The Sim-tube mode controls the process of heating the sample block to
include the sample volume in the equation (ie a larger sample volume
requires a longer time to reach temperature). Block mode does not consider
sample volume and simply heats the block to the set temperature.
1.2 Set Temperature Control Mode and Lid Temperature
Benchmark Thermal Cycler User Manual
D Programming
16
Sim-tube is the preferred control method, especially when reaction steps are 30
seconds less. It is important to input sample volumes for the most accurate
dwell times. For lid temperature control, it is recommend to select a
temperature five to ten degrees Celsius above the highest temperature of the
program steps (e.g., the pre-denaturation step) to protect sample from
evaporation and condensation.
A PCR program comprises several steps. Each new step will be inserted after the
selected step while the initial step will be inserted without selecting a step.
The maximum amount of steps for a program is 30.
Constant
Temperature
Step
1. In the Edit Program screen, touch anywhere in the column for a step to select
it. When the step is selected, the background becomes blue .
2. Touch Temp and the Temp Step screen opens.
3. Edit Temperature and Time.
• If you touch Pause, the program will automatically pause as soon as the
desired step temperature is reached and the instrument will beep once.
Touching Resume will continue the program running. Pause can be used to
add reagents (ie hot start) or when adding or removing tubes during a step.
• Touching Forever will cuase the program to hold indefinately after reaching
this step until it is stopped manually. Steps cannot be added after a forever
step.
Note:
The lid heating will automatically turn off when block temperature is below
30°C. The lid will heat to the specified temperature before the actual
program starts running. Setting a lid temperature below ambient will cause
the program to stall.
Note:
The allowable temperature range is from 0.0°C to 99.9°C, with 0.1°C interval.
The allowable time range is from 00:00:00 to 09:06:06 hour: min: sec.
1.3 Add Step
Benchmark Thermal Cycler User Manual
D Programming
17
4. You can also set options for a step.
• Increment Temp– adds temperature increments to step with each cycle.
To set the Increment Temp function:
Touch to shift between “+” and “–” (to increase or decrease temperature
for each cycle), and then enter the number of degrees of temperature in the
textbox. The allowable temperature range is 0.1°C ~ 10.0°C.
• Increment Time – Adds time increments to the holding time within the step
for each cycle
To set the Increment Time function:
Touch to shift between “+” and “–” (to increase or decrease time for each
cycle), and then enter the seconds in the textbox. The allowable time range is 1
sec ~ 120 sec.
• Slow Ramp – Adjust the heating or cooling ramp rate.
To set the Slow Ramp function:
Enter the value of ramp rate in the textbox. Input range is 0.1 ~ 6.0°C /sec.
5. Touch Ok to accept changes and close the screen.
1. In the Edit Program screen, select a step that you want to set as the last step of
a cycle.
2. Touch Goto and the Cycle Step screen opens.
Note:
The actual maximum ramp rate of heating and cooling varies with block
module type. Refer to the instrument specifications for the maximum value.
If a value larger than the block’s maximum rate is entered, the block’s
maximum rate will be used. If you do not want to slow the running, leave
this option empty.
Note:
Parameters cannot be set that would cause a step to fall outside of the
operating range of the instrument (ie below 0°C or above 99.9°C).
Note:
Parameters cannot be set that would allow the dwell time to fall below zero.
1.4 Set Cycle
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3. From the Step drop-down list box, select the start step number of the cycle.
The steps between the last step and the start step will run repeatedly for the
specified cycle numbers.
4. Touch Cycles to add additional cycle numbers.
5. Touch Ok to accept changes and close the screen.
1. In the Edit Program screen, select a desired step.
2. Touch Edit to edit the step parameters.
3. Touch Ok to accept changes and close the screen.
1. In the Edit Program screen, touch a step to select it.
2. Touch Delete. A pop-up window appears.
3. Touch Yes in the displayed pop-up window to delete the step.
1. In the Edit Program screen, touch Save or Save As to display the Save As
Program Screen.
2. The current date and time are used as a default name. A new name can be
entered. The name is case insensitive and can be up to 30 characters.
3. From the Folder drop-down list box, select a folder to save the program to.
• To create a new folder to save the program, touch New Folder, and enter a
Note:
Allowable entered cycle numbers range: 1-100.
The actual cycle numbers will be ‘N+1’ where N stands for the entered cycle
numbers. To perform a PCR reaction with 30 cycles, then you should enter a
number of 29.
Note:
Default program name: 10 04 18 _ 13 49
last two digits of year month day hour minute
1.5 Edit Step
1.6 Delete Step
1.7 Save Program
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folder name of up to 30 characters.
4. Touch Run to both save and run the program.
Or touch Save to save but not run the program.
Or touch Export to save the program to a USB flash drive.
2. Edit Program
To edit a program:
1. In the Home screen, touch Program Library.
2. In the Program Library screen, select a folder and then double click it or touch
View.
3. In the View Program screen, select a program to be edited and then and then
double click it or touch View/Edit.
4. In the Edit Program screen, you can edit the program and then save and/or run
it following the instructions described above.
The Program Wizard function provides a quick method to create a standard
three-step or two-step PCR program and perform running.
1. In the Home screen, touch Program Wizard.
The Program Wizard screen opens. There are two screens, touch Next and
Last to shift between them.
3. Program Wizard Function
D Programming
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2. In the first screen, edit Temperature Control mode and Lid Temperature
Control mode. You can leave these parameters as default because the default
parameters can meet most PCR reactions.
3. In the second screen, touch and edit parameters of each step. Keep parameters
of a step empty to exclude the specified step. You can touch Graph to view
the graphical representation of the program.
4. Touch Save to save program or touch Run and then select whether save the
program before running according the displayed message in the pop-up
window.
Note:
• Allowable temperature range: 0.0°C to 99.9°C.
• Allowable time range: 00:00 to 99:59 min: sec.
• Allowable number of cycles: 0-101.
• The actual cycle numbers will be equal to the entered cycle numbers. So if
you would perform a PCR reaction with 30 cycles, then you should enter a
number of 30.
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E [ RUN PROGRAM ]
1. Place PCR tubes or a microplate in the sample wells of the sample block.
3. Close the lid and turn the lid knob clockwise (see the ‘Tighten’ arrow symbol
on the top surface of the lid knob) until you hear ‘click ...’ sound.
From the Home screen:
1. To select a last run program:
Touch Last Run Programs, select a program and then touch Run.
To select a program saved in a folder:
Touch Program Library, select the desired folder and then touch View to
open the View Program screen. Select a program from the list and touch Run.
After you touch Run, the Set Run Options screen opens.
2. In the Set Run Options screen, edit Temperature Control and Lid Temperature
Control.
3. Touch StartRun to begin the run. The Run screen opens.
Note:
•The caps of the tubes or film on the microplate must be sealed tightly to
prevent sample evaporation. Tubes or microplates should have heat resistance
of up to about 120°C. For best results, use thin walled tubes designed for
PCR.
•The sample wells of the sample block should keep clean.
•The height of tubes should be the same so that the lid can keep stable and
gives even pressure on each tube.
IMPORTANT!
Do not touch the surface of the sample block or lid surface because they may
be very hot (105°C/221°F or higher)!
1. Load Samples
F System Setting
2. Select Program to Run
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Run Screen
You can view the status of run using the Run screen below.
The items displayed on the Run screen:
a: In the top bar are the colored status light (the colored status light stays green
during running, changes to orange after touching the Pause button, changes to
red when an error arises and changes to white after stopping a run) and the
run status:
‘Lid’: lid temperature;
‘Block’ or ‘Sample’: block temperature (when the instrument is idle or
when temperature control mode is Block) or sample temperature (when
temperature control mode is Sim-tube);
‘Cycle’: current cycle numbers / total cycle numbers;
‘11:41:53’: Current Time.
b: Program/ Folder name (and Creator of program when login is enabled).
c: Options:
Pause: preset pause;
X °C/Cyc: Increment or decrement temperature;
X S/Cyc: Increment or decrement time;
X °C/S: Ramp rate.
d: The recent run message.
a
b
d
c
Note:
If you create a new program to run but did not save it, the program will be
given a default name ‘Admin’ and will be saved in a temporary folder
‘Temp’. After run, the temporary program will not be recorded in the list of
the Last Run Programs screen.
3. View Run State and Control Run
3.1 View Run State
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Buttons on the Run screen:
Button
Function
Pause/ Resume
Pauses and Resumes run.
Skip
Skips run step.
Stop
Stops run.
Gradient
Views bar chart of sample block
temperature.
Curve
Views real-time temperature record curve.
View Timer
Views run time.
Run Again
Runs program again.
Edit
Opens Edit Program screen to edit the
program.
Report
Views run report.
View Run Timer
1. In the Run screen, touch View Timer to view run time:
• Time Elapsed shows the time (hour:min) since the run has started.
• Time Remaining shows the estimated remaining time (hour:min) .
2. Touch to return to the Run screen.
View Bar Chart
of Sample Block
Temperature
1. In the Run screen, touch Gradient to view the temperature of each column of
sample block in real-time.
Note:
The actual remaining time may slightly differ from that shown.
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Step Time: the countdown holding time of the current step after the step
temperature reached the setting value.
2. Touch to return to the Run screen.
View
Temperature
Record Curve
1. In the Run screen, touch Curve to view the temperature record curve.
2. Touch to return to the Run screen.
View Run
Report
1. In the Run screen, touch Report to open the Run Report screen.
The report contains records of run start time, run stop time, and manual
operations during running.
Touch Export to export the report in BMP format to a USB flash drive.
2. Touch to return to the Run screen.
Pause Run
In the Run screen, touch Pause and the system will beep twice.
Skip Run Step
In the Run screen, touch Skip to skip the current running step and run the next
step.
Stop Run
In the Run screen, touch Stop and then touch Yes in the displayed pop-up
window.
Run Program
Again
In the Run screen, if the running program stopped, touch Run Again to run it
again.
Note:
The temperature will continue increase or decrease until it reaches the setting
temperature of a step.
After paused, the Pause button changes to Resume button, and you must
touch Resume to continue the program.
3.2 Control Run
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1. System
Setting
Screen
In the Home screen, touch System Setting.
The System Setting screen opens.
System Setting
Screen Buttons
Button
Function
About
Shows product information
Incubation
Performs a constant temperature incubation
experiment.
Gradient Calculator
Non-functioning
View Report
Views stored run reports.
Tm Calculator
Calculates Tm value of a primer pair.
Check
This function is reserved for service.
Configure Shortcut
Configures functions or programs shortcuts.
Admin Options
Sets instrument parameters.
Login Password
When a user other than “admin” is logged in,
the Admin Options icon will change to Login
Password icon. The user can edit their login
password using this function.
2. About
To view product information about the Thermal Cycler:
1. In the Home screen, touch System Setting.
2. In the System Setting screen, touch About and the About screen appears.
3. When you finish, touch Ok to return to the System Setting screen.
F [ SYSTEM SETTING ]
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3. Incubation
The Incubation function is used to perform a constant temperature incubation
experiment such as DNA ligation or RNA digestion.
1. In the Home screen, touch System Setting.
2. In the System Setting screen, touch Incubation.
3. In the Incubation screen, enter the required incubation temperature. If you
select Lid On, the lid will heat to reach 10°C above the incubation
temperature by default.
4. Touch Start Run to run the Incubation program and the Run screen opens.
5. In the Run screen, you can view block temperature (by touching Gradient),
view temperature record curve (by touching Curve) and run time (by
touching View Timer). You can stop running by touching Stop.
4. Gradient
Calculator
This button does not function.
5. View
Report
1. In the Home screen, touch System Setting.
2. In the System Setting screen, touch View Report to open the screen:
3. Select a report and double click it or touch Show to open the Run Report
screen.
4. After you finished, touch to return to the View Report screen.
5. In the View Report screen, you can touch Clear to clear all reports.
6. After you finish, touch to return to the System Setting screen.
6. Tm
Calculator
The Tm Calculator is used to calculate the Tm (melting temperature) and Ta
(annealing temperature) for a primer pair.
1. In the Home screen, touch System Setting.
2. In the System Setting screen, touch Tm Calculator to open the screen.
Note: The Pause, Skip, RunAgain, Edit, Report buttons are not available in
the Run screen under Incubation mode.
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3. Enter the salt concentration and the primer concentration.
4. Enter each primer sequence and then touch Calculate to view the Tm value of
each primer, the average Tm value and the Ta value.
5. After you finish, touch to return to the System Setting screen.
7. Check
This function is reserved for service.
8. Configure
Shortcut
Shortcuts appear on the Home screen and can access various functions or
programs. When login is enabled, each user can configure different shortcuts.
To configure shortcuts:
1. In the Home screen, touch:
• Any button labeled with ‘Shortcut’
or
• System Setting, then Configure Shortcut.
The Configure Shortcut screen opens.
Note:
In order to develop a successful PCR reaction, it may be necessary to select a
different Ta value from the value on the screen.
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2. In the Configure Shortcut screen, touch a check box next to a function on the
right of the screen to select a function as a shortcut.
3. If you want to select a program as a shortcut, touch Select Program.
4. In the Select Programs for Shortcut screen, select a folder from the Folder
drop-down list box and programs of the selected folder will appear. Touch the
header of the first or second column of the table to sort all programs. Touch a
program to select it and then touch Ok to return to the Configure Shortcut
screen. The program will appear in the left side list box.
5. When you finish, touch Ok to return to the Home screen.
The selected function or program will appear in the Home screen.
9. Admin
Options
The Admin Options is used to control access mode, set thermal cycler name/IP
address, set date/time, set run-time accuracy, and manage user accounts. When
login is enabled, only admin can see the Admin Options button .
To use Admin Options functions:
In the Home screen, touch System Setting, then Admin Options.
The Admin Options screen opens.
Note:
You can select no more than six functions and/or programs as Shortcuts.
To deselect a shortcut on the Home screen, you need to touch System
Setting again, and then touch Configure Shortcut. In the Configure Shortcut
screen, unselect the check box for deleting a function shortcut, or select the
program from the program list and then touch Delete Program for deleting a
program shortcut.
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9.1 Access
Control
The Access Control is used to protect personal programs and folders and limit
ordinary users to modify instrument parameters.
To enable the Access Control:
When login is enabled, log in as “admin”.
1. In the Home screen, touch System Setting.
2. In the System Setting screen, touch Admin Options.
3. In the Admin Options screen, touch Access Control.
The Access Control screen opens:
4. To enable the Access Control function, touch Require Login.
a. To allow anyone to create a new account in the Login screen, touch Allow
Create New Account by Anyone.
b. To allow an anonymous user to login, touch Enable Guest Account.
c. To allow login without password, touch Allow Login without Password.
5. Touch Ok, and restart the instrument by turning off the power switch.
After enabling the Access Control, you must login as a user on the Login
screen (see below) before you can use the instrument.
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6. After you finished experiment, touch in the Home screen to logout.
9.2 Thermal
Cycler Name/IP
To enable network control function, you need to set the IP address and a unique
Thermal Cycler Name for each instrument.
When login is enabled, log in as “admin”.
1. In the Home screen, touch System Setting.
2. In the System Setting screen, touch Admin Options.
3. In the Admin Options screen, touch Thermal Cycler Name/IP.
4. In the Thermal Cycler Name/IP screen, set a unique Thermal Cycler Name
and IP address. The name can be up to 30 characters.
5. When you finish, touch Ok to return to the Admin Options screen.
9.3 Set
Date/Time
To set Date/Time (When login is enabled, log in as “admin”):
1. In the Home screen, touch System Setting.
2. In the System Setting screen, touch Admin Options.
3. In the Admin Options screen, touch Date/Time.
4. In the Date/Time screen, enter today’s date and current time.
5. Touch Ok to accept changes and return to the Admin Options screen.
9.4 Run-time
Accuracy
The Run-time Accuracy function is used to adjust coefficient of estimated
remaining run time when the original estimated time is not accurate.
9.5 User
Message
The User Message function is used to manage user accounts.
To manage user accounts (When login is enabled, log in as “admin”):
1. In the Home screen, touch System Setting.
2. In the System Setting screen, touch Admin Options.
3. In the Admin Options screen, touch User Message.
4. The User Message screen lists all accounts currently available.
Touch the table column header to sort all users.
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• “admin”: controls all Admin Options screen functions. The default password
for admin is admin.
• “Guest”: can create, rename, copy, modify, save, delete and run programs
that stored in Public Folder, Guest Folder and USB Folder.
• All other users: can create, rename and delete non system folders; create,
rename, copy, modify, save, delete and run programs; set his or her shortcuts;
modify his or her login password (in the System Setting screen after login).
In the User Message screen:
a. To create a new user account, touch Create to open the Create User screen.
Enter user name and password (case sensitive) of no more than 30 characters.
b. To edit user password, select a user and then double click it or touch Edit to
open the Edit Password screen. Enter new password and touch Ok.
c. To delete a user account, select a user and then touch Delete. Touch Yes in the
displayed pop-up window to delete the user.
Benchmark Thermal Cycler User Manual
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