Benchmark Scientific Benchmark Scientific T5000-384 Manual
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
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1. Instrument Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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2. Menu Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6 1. Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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1.1 Site Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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1.2 Unpack Thermal Cycler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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1.3 Power On and Power Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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1.4 Open and Close Lid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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2. Home Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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1. Manage Folder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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1.1 Program Library Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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1.2 Add Folder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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1.3 Rename Folder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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1.4 Delete Folder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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2. Manage Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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2.1 View Program Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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2.2 Rename Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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2.3 Copy Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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2.4 Delete Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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2.5 View Last Run Programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
13 1. Create New Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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1. Edit Program Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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1.2 Set Temperature Control Mode and Lid Temperature . . . . . . . . . . . . . . . . . .
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1.3 Add Step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Constant Temperature Step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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1.4 Set Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Contents
Benchmark Thermal Cycler User Manual
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1.5 Edit Step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
18 1.6 Delete Step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
18 1.7 Save Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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2. Edit Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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3. Program Wizard Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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1. Load Samples into the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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2. Select Program to Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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3. View Run State and Control Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
22 3.1 View Run State . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Run Screen . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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View Run Timer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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View Bar Chart of Sample Block Temperature . . . . . . . . . . . . . . . . . . . . . . .
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View Temperature Record Curve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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View Run Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
24 3.2 Control Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Pause Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Skip Run Step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Stop Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Run Program Again . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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1. System Setting Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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2. About . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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8. Configure Shortcut . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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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
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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
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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
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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
Benchmark Thermal Cycler User Manual
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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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