C1000 Touch™ Thermal Cycler Instruction Manual Catalog #184-1100 #185-1138 #185-1148 #185-1196 #185-1197
C1000 TouchTM Thermal Cycler Manual Copyright ©2011 Bio-Rad Laboratories, Inc. Reproduction in any form, either print or electronic, is prohibited without written permission of Bio-Rad Laboratories, Inc. Gmail is a trademark of Google, Inc. LICENSE NOTICE TO PURCHASER This base unit, Serial No.
C1000 TouchTM Thermal Cycler Manual Bio-Rad Laboratories Resources Bio-Rad provides many resources for scientists. The Bio-Rad website contains useful information for running PCR and real-time PCR experiments: • www.bio-rad.com This site includes links to technical notes, manuals, product information, and technical support. This site also provides many technical resources on a wide variety of methods and applications related to PCR, real-time PCR, and gene expression.
C1000 TouchTM Thermal Cycler Manual Table 2. Writing conventions. (Continued) Convention Meaning WARNING! Explains crucial information about a topic that may lead to injury to the user, instrument damage, or data loss. Touch X Touch X using your finger. For example, touch the NEW button means use your finger to touch the NEW button on the screen. Touch X > Y From menu X, touch Y. For example, touch MAIN > RUN means touch the RUN button in the MAIN menu.
C1000 TouchTM Thermal Cycler Manual Instrument Safety Warnings The following warning labels display on the instrument, and refer directly to the safe use of this C1000 Touch thermal cycler (Table 4). Table 4. Instrument safety warning labels. Icon Meaning Warning about risk of harm to body or equipment. Operating the C1000 Touch instrument before reading this manual can constitute a personal injury hazard. Only qualified laboratory personnel should operate this instrument.
C1000 TouchTM Thermal Cycler Manual • IEC 61010-1:2001 Safety Requirements for Electrical Equipment for Measurement, Control, and Laboratory Use, Part 1: General Requirements • IEC 61010-2-010:2003 Safety Requirements for Electrical Equipment for Measurement, Control, and Laboratory use, Part 2-010: Particular Requirements for Laboratory Equipment for the Heating of Materials • IEC 61010-2-081:2001+A1:2003 Safety Requirements for Electrical Equipment for Measurement, Control, and Laboratory use, Part 2-081
C1000 TouchTM Thermal Cycler Manual device” under 47 CFR 15.103(c), in regard to the cited FCC regulations in effect at the time of manufacture • Note regarding Canadian EMC compliance: Le present appareil numerique n’emet pas de bruits radioelectrique depassant les limites applicables aux appareils numeriques de class A prescrites dans le reglement sur le brouillage radioelectrique edicte par le Ministere des Communications du Canada • Cables.
C1000 TouchTM Thermal Cycler Manual Table of Contents Bio-Rad Laboratories Resources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ii Warranty . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ii Writing Conventions Used in This Manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ii Safety and Regulatory Compliance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
C1000 TouchTM Thermal Cycler Manual Chapter 7. Maintenance and Troubleshooting . . . . . . . . . . . . . . . . . . . . . 43 Cleaning and Maintaining the C1000 Touch Thermal Cycler . . . . . . . . . . . . . . . . . 43 Maintaining Sufficient Airflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45 Replacing Fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 Appendix A: References . . . . . . . . . . . . . . . . .
C1000 TouchTM Thermal Cycler Manual 1 Introduction to the C1000 TouchTM Thermal Cycler Read this chapter for information on setting up the C1000 Touch thermal cycler.
C1000 TouchTM Thermal Cycler Manual The back panel of the C1000 Touch thermal cycler includes data ports (Figure 2). • USB B port — connects the C1000 Touch thermal cycler to a computer • USB A ports — connects up to three S1000 thermal cyclers to the C1000 Touch thermal cycler.
C1000 TouchTM Thermal Cycler Manual • Lid lever — opens and closes the lid • Lid force knob — sets lid force and seals the reaction • Status LED — turns on to indicate that the block is in use Figure 3 shows the components of a 96-well fast reaction module. Lid force knob Lid Lid lever Status LED Cooling fins Figure 3. Components of a reaction module.
C1000 TouchTM Thermal Cycler Manual To insert a 1000-series reaction module into the reaction module bay of the thermal cycler base, follow these instructions: 1. With the locking bar in the down position and the lid lever of the reaction module pointing to the front, lift the reaction module into the reaction module bay (Figure 4). Leave 1–2 cm of space in front of the module. Lid lever (front) Leave space here Locking bar (down position when unlocked) Figure 4.
C1000 TouchTM Thermal Cycler Manual Operating the Reaction Module Lid The inner lid of the reaction module applies heat and force to the reaction vessel lids (caps or tape) to produce consistent and successful reactions. Heating the inner lid prevents condensation, while applying force seals the reaction to prevent evaporation. WARNING! After a run, the heated inner lid can remain hot. Use caution when opening and closing the lid. To open the lid, use the following steps: 1.
C1000 TouchTM Thermal Cycler Manual turning the lid force knob counterclockwise one full turn. Reapply the correct lid force by following the instructions in step 3. Lid force knob (turn clockwise to secure the lid) Figure 7. Adjust the lid force by turning the lid force knob. Loading Sample Vessels into the Reaction Block To ensure uniform heating and cooling of samples, vessels must be in complete contact with the reaction block.
C1000 TouchTM Thermal Cycler Manual To initiate the functions on the home screen, touch the associated button.
C1000 TouchTM Thermal Cycler Manual Setting Up Email Notification A run complete confirmation and run report can be emailed directly to any computer with Internet access. To configure the outgoing email from the C1000 Touch thermal cycler, use the following instructions: 1. Touch the Log In button on the home screen to log in to the thermal cycler as the Administrator. NOTE: The logged in user name appears to the left of the log out button when you return to the home screen. 2.
C1000 TouchTM Thermal Cycler Manual 8. Touch the Send Email button. A test email will be sent to the test email address. 9. Touch the Cancel button to return to the server settings screen. 10.Touch the Back button to return to the tools menu. Setting up a custom server 1. Touch the New Server button (Figure 11). Figure 11. New Server button. 2. Touch the Mail Server Address button and enter an address using the pop-up alphanumeric keypad. 3.
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C1000 TouchTM Thermal Cycler Manual 2 Creating, Editing, Naming, and Saving Protocols Read this chapter for information on creating and editing protocols. • Creating a new protocol or editing an existing protocol (page 11) • Sample volume and lid temperature (page 17) • Naming a protocol (page 19) • Saving a protocol (page 19) Creating a New Protocol or Editing an Existing Protocol To create a new protocol: 1. Touch the New Protocol button on the home screen to open the new protocol screen.
C1000 TouchTM Thermal Cycler Manual To edit an existing protocol: 1. Touch the Saved Files button on the home screen to open the saved files screen. 2. Select a file to edit (Figure 13). Figure 13. Selected file to edit. 3. Touch the Edit button to open the edit protocol screen. The protocol will display in a graphical format. 4. Select a desired step by touching anywhere in the step. 5. Change a time or temperature by touching the desired button and entering a value using the pop-up numeric keypad. 6.
C1000 TouchTM Thermal Cycler Manual Protocol Parameters Table 7 lists the parameters for temperature and gradient steps with the limits of the parameters. Table 7. Protocol steps and parameters of the C1000 Touch thermal cycler. Step Name Parameters and Ranges Description Temperature Temperature in °C: The target Instructs the thermal cycler to ramp to temperature between 0.0 and the target temperature and hold that 100.
C1000 TouchTM Thermal Cycler Manual Changing Target Temperature and Hold Time To change the target temperature and hold time in a temperature step, follow these instructions: 1. Touch the desired time or temperature button of the step to edit. 2. Use the pop-up numeric keypad to enter a new value for the target temperature or hold time. Inserting a Protocol Step Insert a protocol step if a new temperature, GOTO, or gradient step is needed.
C1000 TouchTM Thermal Cycler Manual 2. In the Step Options window, touch the Gradient checkbox. A check mark will appear in the gradient checkbox and the gradient range will appear (Figure 14). Figure 14. The Step Options window displays the gradient. 3. Touch any gradient temperature to change the value by using the pop-up numeric keypad. NOTE: A gradient range must be between 1 and 24°C.
C1000 TouchTM Thermal Cycler Manual Touch the OK button to confirm. Changing the Ramp Rate To emulate a thermal cycler that runs at a slower ramp rate than the C1000 Touch thermal cycler, change the ramp rate of the appropriate protocol step. To modify the ramp rate: 1. Select a step in the protocol and touch the Options button. 2. Touch the Ramp Rate button. 3. Enter a value using the pop-up numeric keypad. 4. Touch the OK button to confirm. 5.
C1000 TouchTM Thermal Cycler Manual Adding or Removing a Beep A beep is a sound that the thermal cycler emits when it reaches the target temperature of a protocol step. To add or remove a beep: 1. Select a step in the protocol and touch the Options button. 2. Touch the Beep checkbox. A check mark will appear in the Beep checkbox. 3. Touch the OK button to confirm. 4. To remove the beep, select a step in the protocol and then touch the Options button. The Step Options window opens.
C1000 TouchTM Thermal Cycler Manual • Lid temperature — determines the temperature of the heated lid.
C1000 TouchTM Thermal Cycler Manual 2. Enter a value using the pop-up numeric keypad. 3. Touch the OK button to confirm. Naming a Protocol A new protocol requires a name, which can be changed later if desired. When editing an existing protocol, the user has the option of renaming the protocol. Renaming the protocol does not remove the original protocol. To name a protocol from the new protocol or protocol editor screen: 1. Touch the Name button. 2. Enter a name using the pop-up alphanumeric keypad. 3.
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C1000 TouchTM Thermal Cycler Manual 3 Running Protocols Read this chapter for instructions on running protocols.
C1000 TouchTM Thermal Cycler Manual In Figure 18, the protocol will start running on both blocks at the same time. Figure 18. Multiple blocks running the same protocol at the same time. 5. Confirm or change the run parameters before starting the run. TIP: The value entered in the Sample Volume field determines the temperature control mode. If a sample value greater than 0 (zero) is entered, the instrument uses Calculated Mode to calculate the target temperature.
C1000 TouchTM Thermal Cycler Manual Figure 20. Add additional settings to your protocol including running in DNA Engine Ramp mode and sending an email notification upon run completion. 7. Touch the OK button to confirm. 8. Start the run by touching the OK button on the run confirm window. Monitoring a Run During a run, the status buttons on the home screen (buttons contains an icon of the instrument and time remaining) provide a quick way to monitor all blocks.
C1000 TouchTM Thermal Cycler Manual Touch View Status to return to the status screen. Figure 21. The status screen. Figure 22. Screen shows status by time remaining. Pausing and Resuming a Run A running protocol may be temporarily paused from the protocol status screen. During a pause, the thermal cycler continues heating or cooling to the target temperature, while the lid temperature is maintained.
C1000 TouchTM Thermal Cycler Manual 2. To resume the protocol, touch the Resume button. Skipping Steps in a Protocol Skip a step if it is necessary to shorten a protocol while it is still running. By repeatedly skipping steps, it is possible to bypass several cycles of a GOTO loop and shorten a protocol. 1. To skip the current protocol step in the status screen, touch the Skip button. 2. Touch the Skip button multiple times to skip more than one step.
C1000 TouchTM Thermal Cycler Manual The Incubate screen opens (Figure 23). Figure 23. The Incubate screen. NOTE: The default block temperature, hold time, and lid temperature will be the same as the most recently run incubation. NOTE: When incubation is occurring at temperatures below 30oC, the lid will maintain a temperature of 31°C to prevent excessive condensation. 2.
C1000 TouchTM Thermal Cycler Manual 4 Protocol AutoWriter Read this chapter for information on using the Protocol AutoWriter. • Creating a protocol with the Protocol AutoWriter (page 27) • Overview of the Protocol AutoWriter (page 29) • The Ta calculator (page 30) Creating a Protocol with the Protocol AutoWriter Follow these steps to use the Protocol AutoWriter for creating a new protocol: 1. Touch the Protocol AutoWriter button on the home screen. 2. Select the enzyme to be used for the reaction.
C1000 TouchTM Thermal Cycler Manual 4. Touch the Annealing Temperature button and enter the Ta in °C. 5. Touch the radio button corresponding to the desired reaction speed. The annealing temperature and estimated total run time will change as the speed is changed. The annealing temperature used in the program will be 4°C below the primer average Tm for the standard speed and 2°C below the primer Tm average for fast speed. The unadjusted primer Tm average will be used for the ultrafast speed. 6.
C1000 TouchTM Thermal Cycler Manual NOTE: If the primer Tm values are greater than 4°C apart, the Protocol AutoWriter uses the lower primer Tm value + 2°C as a basis for calculating the Ta value, which can be further modified by the enzyme and reaction speed selections. NOTE: The Ta calculator generates an annealing temperature for standard speed with iTaq DNA polymerase. When using a different enzyme, the speed settings automatically adjust the Ta. 5.
C1000 TouchTM Thermal Cycler Manual The Protocol AutoWriter uses information about the reaction to automatically write a protocol. This feature enables the user to enter the following information about the PCR experiment: • Primers — enter the reaction Ta for the primers being used.
C1000 TouchTM Thermal Cycler Manual In the nearest neighbor method, the melting temperature calculations are based on the thermodynamic relationship between entropy (order or a measure of the randomness of the oligonucleotide), enthalpy (heat released or absorbed by the oligonucleotide), free energy, and temperature, where: /\H = /\G + T* /\S where /\H = Enthalpy value, Cal/Mole*K T = temperature, Kelvin.
C1000 TouchTM Thermal Cycler Manual The oligonucleotide sequence should be at least 14 bases long to give reasonable Tm values. Less than 14 bases uses the base pair counting method (Figure 26). INTERACTION AA TT AT TA AC TG AG TC TA AT TT AA TC AG TG AC CA GT CT GA CC GG CG GC GA CT GT CA GC CG GG CC Delta (H) 9.1 8.6 6.5 7.8 6 9.1 5.6 5.8 5.8 7.8 11 11.9 5.6 6.5 11.1 11 Delta (S) 24 23.9 17.3 20.8 16.9 24 13.5 12.9 12.9 20.8 26.6 27.8 13.5 17.3 26.7 26.6 Figure 26. Breslauer interaction constants.
C1000 TouchTM Thermal Cycler Manual 5 Managing Files and Folders Read this chapter for information on managing protocol files and folders. • The saved files screen (page 33) • Managing files and folders (page 34) The Saved Files Screen Many functions begin with choosing a protocol from the saved files screen.
C1000 TouchTM Thermal Cycler Manual • Recent location — contains a list of all previously run protocols • Real-time data location — contains the last 100 real-time PCR data files • User locations — contains folders created by users for personal protocol storage.
C1000 TouchTM Thermal Cycler Manual In Figure 28, the new folder will be created in the C1000 Touch thermal cycler location (named SC005016). Figure 28. Select the location where the folder will be created. 3. Touch the New Folder button and enter a folder name using the pop-up alphanumeric keypad. Then touch the OK button to confirm. Copying a Folder To copy a folder to another location: 1. Touch the Saved Files button on the home screen. 2. Select the folder to be copied. 3.
C1000 TouchTM Thermal Cycler Manual Deleting a Folder To delete a folder and all of its contents: 1. Touch the Saved Files button on the home screen. 2. Select the folder to be deleted. 3. Touch the Folder Options button. 4. Touch the Delete button. 5. Touch the Yes button to confirm. Renaming a Folder To rename a folder: 1. Touch the Saved Files button on the home screen. 2. Select the folder to be renamed. 3. Touch the Folder Options button. 4. Touch the Rename button. 5.
C1000 TouchTM Thermal Cycler Manual Figure 30. Select the new location and folder. NOTE: If desired, touch the New Folder button to create a new folder to copy the file into. 7. Touch the Save button and confirm that the file was successfully copied. Deleting a File To delete a file: 1. Touch the Saved Files button on the home screen. 2. Select the protocol to be deleted. 3. Touch the File Options button. 4. Touch the Delete button. 5. Touch Yes to confirm. Renaming a File To rename a file: 1.
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C1000 TouchTM Thermal Cycler Manual 6 Advanced Functions Read this chapter for information on advanced functions on the C1000 TouchTM thermal cycler.
C1000 TouchTM Thermal Cycler Manual Use the following steps to log in to or log off the C1000 Touch thermal cycler: 1. Touch the Log In button on the home screen and select a user. 2. Enter the password using the pop-up alphanumeric keypad, and then touch the OK button. NOTE: A password can contain a combination of letters and numbers. NOTE: The alphanumeric keypad will not be displayed if the user account does not have a password. 3.
C1000 TouchTM Thermal Cycler Manual Once a user is logged in as the administrator, the User and Admin menus are visible. The administrator has access to all User and Admin functions. Figure 32 shows some of the Admin menu functions. Figure 32. The Admin menu. NOTE: Only a logged in Administrator may access the Admin menu. The functions in the Admin menu offer the following options: • System Settings — for setting the user access levels to Open or Login required.
C1000 TouchTM Thermal Cycler Manual • Ethernet port — for connecting the thermal cycler to a network Controlling S1000 Thermal Cyclers with the C1000 Touch Thermal Cycler Up to three S1000 thermal cyclers can run under the control of a C1000 Touch thermal cycler. Each S1000 thermal cycler can be connected to the C1000 Touch thermal cycler through the USB A ports of the C1000 Touch thermal cycler.
C1000 TouchTM Thermal Cycler Manual 7 Maintenance and Troubleshooting Read this chapter for information on maintaining the C1000 TouchTM thermal cycler and troubleshooting problems. • Cleaning and maintaining the C1000 Touch thermal cycler (page 43) • Maintaining sufficient airflow (page 45) Cleaning and Maintaining the C1000 Touch Thermal Cycler The C1000 Touch thermal cycler requires little maintenance for proper operation and precise thermal control.
C1000 TouchTM Thermal Cycler Manual WARNING! Do not use abrasive detergents or rough material; they can scratch the control panel. • Clean the reaction module bay. Clean with a damp soft cloth to remove debris and spilled liquids. Cleaning the bay allows precise heating and cooling of the reaction block WARNING! Never use cleaning solutions that are corrosive to aluminium. Avoid scratching the surface of the bay; surface scratches can interfere with precise thermal control.
C1000 TouchTM Thermal Cycler Manual • Clean the outer lid surface of the reaction module. Use a damp cloth or tissue to clean spills off the outside case. If needed, use a mild soap solution and rinse the surface with a damp cloth. Cleaning the cover prevents corrosion Maintaining Sufficient Airflow The C1000 Touch thermal cycler requires sufficient airflow to heat and cool precisely to the correct target temperature.
C1000 TouchTM Thermal Cycler Manual Replacing Fuses Fuses on the C1000 Touch thermal cycler are designed to blow in case of severe power surges or other causes of electrical short. This process protects both the user and the instrument from excessive electric charge. Fuses on the C1000 Touch thermal cycler rarely need to be replaced. However, some institutions prefer to replace fuses on a regular basis to maintain uninterrupted operation.
C1000 TouchTM Thermal Cycler Manual Appendix A: References 1. Breslauer KJ, et al. (1986). Predicting DNA duplex stability from the base sequence, Proc Nat Acad Sci 83, 3746–3750. 2. Sugimoto N, et al. (1996). Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes, Nucleic Acids Res 24, 4501–4505.
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C1000 TouchTM Thermal Cycler Manual Protocol AutoWriter software, when Ta is not known, 28 A adding beep, 17 extended time, 16 temperature gradient, 14 temperature increment, 16 advanced functions, 39 air flow testing for, 45 air intake vents, 1 air vents, 1 attached folders, 34 B beep, 13, 17 Bio-Rad Laboratories contact information, ii resources, ii technical support, ii web site, ii Breslauer, 31, 32, 47 interaction constants, 32 27 D deleting folder, 36 protocol, 37 E editing a protocol, 14 adding
C1000 TouchTM Thermal Cycler Manual reducing overall run time, 30 steps in a protocol, 29 Ta calculator, 30 when the Ta is unknown, 28 H hold time changing, 14 I R increment adding, 16 definition, 13 incubating samples, 25 ending the incubation, ramp rate, 13 changing, 16 definition, 13 removing, 16 reaction block loading samples into, 6 reaction vessels, 2 reaction module bay, 1 reaction modules cleaning, 44 cooling fins, 2 lid, 2 lid force knob, 3 lid lever, 3 loading sample vessels, 6 loading samp
C1000 TouchTM Thermal Cycler Manual S S1000 thermal cycler connecting to C1000 cycler, 42 operating with a C1000 cycler, 42 safety compliance, iv warning labels, iii sample volume changing, 18 role in PCR outcome, 17 saving protocol, 19 service testing, 2 skipping steps in a protocol, 25 specifications for safe use, iv regulatory compliance, iv Sugimoto, 31, 47 SYSTEM folder, 34 functions, 41 warning messages, 46 warranty, ii web site, ii writing conventions in the manual, ii T Ta calculator overview, 3
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