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BIO RAD PTC-100 Operation Manual
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BIO RAD PTC-100 Operation Manual

BIO RAD PTC-100 Operation Manual

Thermal cycler
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PTC-100
Thermal Cycler
®
Operations Manual
Version 9.0
(applicable to revision 6 instruments only)

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Summary of Contents for BIO RAD PTC-100

  • Page 1 PTC-100 Thermal Cycler ® Operations Manual Version 9.0 (applicable to revision 6 instruments only)
  • Page 2 PTC-100 ® Thermal Cycler Operations Manual Version 9.0 (applicable to revision 6 instruments only)
  • Page 3 Copyright ©2005, Bio-Rad Laboratories, Incorporated. All rights reserved. Reproduction in any form, either print or electronic, is prohibited without written permission of Bio-Rad Laboratories, Inc. Chill-out, Concord, Hard-Shell, Hot Bonnet, Microseal, Multiplate, PTC-100, and Slide Griddle are trademarks belonging to Bio-Rad Laboratories, Inc.

  • Page 4: Table Of Contents

    Declaration of Conformity ..........DoC-1 Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 5 Warning: Do not open or attempt to repair the PTC-100 cycler or any accessory to the PTC-100 cycler. Doing so will void your warranties and can put you at risk for electrical shock. Return the PTC-100 cycler to the factory (US customers) or an authorized distributor (all other cus- tomers) if repairs are needed.
  • Page 6 Safe Use Guidelines The PTC-100 cycler is designed to be safe to operate under the following conditions: • Indoor use • Altitude up to 2000 m • Ambient temperature 4°–32°C • Humidity 10-90%, noncondensing • Transient overvoltage per Installation Category II, IEC 664 •...
  • Page 7 A programming option is termed “selected” when the cursor is positioned in front of it. Use the «Select» keys (see fig. 2-3) to move the cursor. In some screens, selected items are also displayed in all-capital letters. Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 8 Meet the PTC-100 Cycler ........
  • Page 9 Thank you for purchasing a Bio-Rad PTC-100 thermal cycler. Designed by a team of molecular biologists and engineers, the PTC-100 cycler will meet your needs for a reli- able, easy-to-use, programmable thermal cycler. The latest (revision 6) PTC-100 cycler features: •...

  • Page 10: Introduction

    Safe operation of the PTC-100 cycler begins with a complete understanding of how the machine works. Please review this entire manual before attempting to operate the PTC-100 cycler. Do not allow anyone who has not reviewed this manual to operate the machine.

  • Page 11: Table Of Contents

    Layout and Specifications PTC-100 ® Cycler with Hot Bonnet ® Lid ........2-2 Models Available .

  • Page 12: Ptc-100 ® Cycler With Hot Bonnet ® Lid

    PTC-100 Operations Manual PTC-100 Cycler with Hot Bonnet Lid Models Available 60-well block: holds 60 x 0.5 ml tubes 96-well block: holds 96 x 0.2 ml tubes or one 96-well microplate Front View (Fig. 2-1) Thumbwheel Lid release button Hot Bonnet lid...

  • Page 13: Back View (Fig. 2-2)

    Power cord jack Hot Bonnet jack (with cord plugged in) Hot Bonnet cord Air intake vents Control Panel (Fig. 2-3) Power light LCD window Cancel key Left and right selection keys Proceed key Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...

  • Page 14: Accessories

    Displays: One 4 x 20 LCD alphanumeric display Memory: 99 typical programs in up to 12 individual folders Weight: 7.0kg Dimensions: PTC-100 cycler with Hot Bonnet lid, 23 x 28 x 26 cm Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 15 Packing List ............3-2 Setting Up the PTC-100 ®...
  • Page 16 If any of these components are missing or damaged, contact Bio-Rad or the author- ized distributor from whom you purchased the PTC-100 cycler to obtain a replacement. Please save the original packing materials in case you need to return the PTC-100 cycler for service. See Appendix B for warranty information.
  • Page 17 All cordsets used with the PTC-100 cycler must be rated to carry at least 10A at 125V or 250V, the latter specification depending upon the supply voltage used. Additionally, the cordset must meet all other applicable national standards—thus at a minimum, the cordset should...

  • Page 18: Troubleshooting

    Place the PTC-100 cycler where you plan to use it, and turn it on. Try to reproduce what will be typical operating conditions for the instrument in that location, particu- larly any heat-producing factors (e.g., nearby equipment running, window blinds...

  • Page 19: Operation

    Operation Turning the PTC-100 ® Cycler On ......... . 4-2 Understanding the Main Menu .
  • Page 20 L i s t E d i t F i l e s Setup The PTC-100 cycler is now ready to execute programs. Understanding the Main Menu The Main Menu is the common access point to all programming and instrument con- figuration screens: •...
  • Page 21 Power light: Glows blue when the PTC-100 cycler is powered up. Opening and Closing the Lid Opening the PTC-100 cycler with Hot Bonnet lid: Push on the button at the lid’s center and lift the lid (see fig. 4-1). Closing all PTC-100 cycler models: Push the lid down to cover the block. Make sure that lid pressure is correctly adjusted by using the thumbwheel as described in the “Adjusting the Hot Bonnet Lid’s Pressure”...
  • Page 22 10 µl. 0.2 ml Tubes All types of thin-walled 0.2 ml tubes may be used. Bio-Rad offers high-quality 0.2 ml tubes in a number of styles, including individual and strip tubes.
  • Page 23 The samples are usually pure enough for analysis without an extraction. Chill-out liquid wax (available from Bio-Rad) is an easy-to-use alternative to oil. This puri- fied paraffinic oil solidifies at 14°C and is liquid at room temperature. By programming a hold at low temperature, the wax can be solidified at the end of a run.
  • Page 24 Do not turn the thumbwheel more than three-quarters of a turn. This can make it hard or impossible to close the lid and puts excessive strain on the latch holding the lid closed. Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 25 Firmly press the tubes or microplate into the block wells. Using Oil to Improve Thermal Contact With two exceptions (see below), Bio-Rad does not recommend using oil to thermally couple sample vessels to the block, for the following reasons: •...
  • Page 26 The Slide Griddle adaptor heats up to four glass slides for in situ protocols. The Slide Griddle adaptor may be used with PTC-100 cyclers that have the 96-well block or the 60-well block. See the Slide Griddle Operations Manual and Passive Slide Griddles for Bio-Rad Thermal Cyclers for instructions on operating the Slide Griddle adaptor.
  • Page 27 System Selection Chart The following sample vessels and sealing options are recommended for use with the PTC-100 cycler and are available from Bio-Rad. To place an order, call 1-800-4BIORAD.  Reaction vessel fits block/sealing option fits reaction vessel without modification.
  • Page 28 1. Substitute the low-energy beta emitter P in cycle sequencing. P nucleotides are not subject to the same kind of chemical breakdown as S nucleotides, and they have not been associated with volatile breakdown products. 4-10 Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 29 Caution: Harsh cleaning agents (such as those above) are corrosive and must be thoroughly rinsed away within a few minutes of application. They can eat away the surface finish of the blocks. Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com 4-11...

  • Page 31: Running Protocols

    Running Protocols Running a Protocol ........... . . 5-2 Choosing a Stored Protocol to Run .
  • Page 32 Select yes to use the heated lid at the target temperature specified in the Setup Menu (see Chapter 8), or select no to apply no heat to the lid. Press «Proceed», and the protocol will begin running. Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 33 When the protocol run finishes, a long beep sounds, and a notification screen is displayed: Run: CUSTOM1 PROGRAM COMPLETE To tal time: 1:20:31 Certain error messages may also be displayed in this screen (see Chapter 10). Press «Proceed» to return to the Main Menu. Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 34 Stopping a Running Protocol Press either «Stop» or «Cancel» to stop a running protocol. A cancellation confirmation screen will be displayed: Run: CUSTO M 1 Stop CUSTO M 1 ? Yes _NO Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 35 (see below). Resuming a Protocol after a Power Outage If a power failure occurs when a protocol is running, the PTC-100 cycler will hold the protocol in memory for a minimum of 24 hours to a maximum of 7 days, depending on environmental conditions.
  • Page 36 PTC-100 Operations Manual Use the keypad to enter any incubation temperature from 0°C to 100°C, then press «Proceed». The PTC-100 cycler will incubate the sample at the specified temperature until «Cancel» or «Stop» is pressed. When the sample block reaches the incubation temperature, a timer begins running in the lower right-hand corner of the screen.

  • Page 37: Creating Programs

    Creating Programs The Elements of a Program ..........6-2 Designing a New Program .
  • Page 38 Two of the steps are mandatory, and two are optional: 1. Temperature step (mandatory): Sets a temperature for the block and the length of time the block is held at that temperature. The PTC-100 cycler brings the block to this temperature at its maximum rate of heating or cooling, unless modifying instructions are added to the program.
  • Page 39 Designing a New Program Translating a Protocol into a Program Until you are completely familiar with programming the PTC-100 cycler, you may find it helpful to first translate the protocol into PTC-100 program steps and options on paper. Write down the protocol to be programmed, one step per line. Then, write the type of program step that goes with the protocol steps at the end of each line.
  • Page 40 PTC-100 Operations Manual Entering a New Program Programming the PTC-100 cycler involves four steps: 1. Initiating the program 2. Naming the program 3. Entering the program’s steps 4. Entering the end step Each step involves entering values from the keypad or making selections from a menu.
  • Page 41 Enter: CUSTO M 1 1= 92.0 Time: _ Enter the hold time for the step (30 seconds is used in the example below). Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 42 PTC-100 Operations Manual Note: If a hold time of zero (0) is entered, the PTC-100 cycler will hold the block at the target temperature indefinitely. Press «Proceed». The hold time will move to the second line of the screen, and a...
  • Page 43 The last line of the screen allows entry of the number of the step the program should cycle back to. Enter the number of the step the program should cycle back to (1 is used in the example below). Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 44 Select one of the displayed choices, then press «Proceed»: • Yes accepts the step, stores the program, and displays the Main Menu. • No displays the Enter Menu so that additional steps can be added. Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 45 (see the “Elements of a Program” section at the beginning of this chapter for more information). • Beep modifies a temperature step or a ramp step, causing the machine to beep when a specified target temperature is reached. Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 46 To enter an extend option, select Ext from the Options Menu of a temperature step, then press «Proceed». The first ext screen will be displayed: Enter: CUSTO M 1 1= 92.0 for 0:30 S e c / c y c l e : _ 6-10 Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 47 Use the Options Menu to enter another option for the step. (Option will not be displayed if a ramp step is being modified, since beep is the only option available for ramp steps.) Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com 6-11...
  • Page 48 «Select» key moves it forward. • To change selected values or add an option: To change a value, move the cursor to it, then press «Cancel». Enter the new value, then press «Proceed». 6-12 Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 49 Keeping a Permanent Record of Programs Occasionally, in the course of repairing a defective PTC-100 cycler, it is necessary to replace the chip that stores all custom user protocols. To avoid losing your protocols in such an event, always maintain an up-to-date record of them.

  • Page 51: Editing Programs

    Editing Programs Editing a Stored Program ..........7-2 Initiating Editing .
  • Page 52 (CUSTOM1 is used in the following and all succeeding examples in this chapter), then press «Proceed». In either instance, after you press «Proceed», the first editing screen will be displayed (see next section). Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 53 Insert allows a step to be added before the displayed step. • Delete deletes the displayed step. • Option allows an option to be added to or deleted from the displayed step, if it is a temperature or a ramp step. Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 54 If deleting an Inc or Ext option, you will be prompted to enter new values for °C/cycle: _ or sec/cycle: _. Press «Cancel», then select Yes from the confirmation menu to delete the option. Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 55 «Cancel». A cancellation confirmation screen will be displayed: Edit: CUSTO M 1 Cancel Changes? Select Yes, then press «Proceed». All editing changes will be abandoned, and the Main Menu will be displayed. Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...

  • Page 57: Using The Utilities

    Using the Utilities Locating a Stored Program ..........8-2 File Utilities .
  • Page 58 • Assign passwords to folders • Copy, delete, rename, or move programs To display the Files Menu, select Files from the Main Menu, then press «Proceed». Files: _Copy Delete Move Rename Folder Secure Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 59 Using the Utilities Creating a Folder The PTC-100 cycler’s memory can hold up to 12 folders, including the <MAIN> folder. New programs are placed in the <MAIN> folder by default unless a different folder is specified. To create a folder, select Folder from the Files Menu, then press «Proceed». A naming...
  • Page 60 «Proceed». If more than one folder of programs is present in the machine, a screen allowing you to specify the folder the program will be copied to will be displayed: Copy CUSTOM1 to: _<FOLDER1> <FOLDER2> <FOLDER3> Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 61 To delete a program, select Delete from the Files Menu, then press «Proceed». Locate the program to be deleted (see “Locating a Stored Program” at the beginning of this chapter), then press «Proceed». A confirmation screen will be displayed: Delete: CUSTOM1 Delete program? _YES Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 62 Set a target temperature and a minimum temperature for the Hot Bonnet heated lid • Look up the PTC-100 cycler’s software version number To display the Setup Menu, select Setup from the Main Menu, then press «Proceed»: Setup: LI D Version Note: The Lid option will only appear if the heated lid is attached.
  • Page 63 Lid target: 1 05°C Specify a lid temperature at least 10°C higher than any temperature used in the protocol; we suggest 105°C. Press «Proceed» to apply the temperature and return to the Main Menu. Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 64 At times it is necessary to determine the version number of the software installed in the PTC-100 cycler (e.g., to report a problem to Bio-Rad). To do this, select Version from the Setup Menu, then press «Proceed». The software version number and the instru- ment’s serial number will be displayed:...

  • Page 65: Maintenance

    Maintenance Cleaning the Chassis and Block ......... . 9-2 Cleaning the Air Vents .
  • Page 66 If these vents become clogged with dust and debris, airflow to the PTC-100 cycler’s heat sink can be hampered, eventually causing overheating and shutdowns (see “Air Supply Requirements”...
  • Page 67 Maintenance Changing the Fuses The circuits in the PTC-100 cycler are protected by two fuses. When a fuse blows, the PTC-100 cycler immediately shuts down and cannot be turned back on. The machine records the event as a power loss, so if a protocol is running when a fuse blows, the machine will resume the protocol run when the fuse is replaced and power restored (see “Resuming a Protocol after a Power Outage”...
  • Page 69 Troubleshooting Error Messages ............10-2 Problems Related to Protocols .
  • Page 70 Call 1-800-4BIORAD (in the US or Canada) , or your distributor. Heat Pump Failure Heat pump sensor is not Instrument needs servicing. Call working properly. 1-800-4BIORAD (in the US or Canada) , or your distributor. 10-2 Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 71 Program Too Long The program size exceeds the Reduce the size of the program by maximum allowed. using Goto steps and Inc and Ext options (see Chapter 6). Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com 10-3...
  • Page 72 Template not of sufficient purity. Check extraction and purification protocols. Add additional purification steps if necessary. Multiple templates or host DNA in Check nucleic acid preparations sequencing reactions. by gel electrophoresis. 10-4 Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 73 Reaction vessels not making good Use only high-quality tubes/plates thermal contact with sample block. that fit block snugly. Ensure that wells are free of foreign materials that would interfere with tube/plate seating. Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com 10-5...
  • Page 74 LCD window, or text in microprocessor is malfunctioning. instrument off, then back on while window freezes or scrolls pressing the Cancel key at the same repetitively. time. If problem persists, contact Bio-Rad or your distributor. 10-6 Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 75 15Þ 0:00:00 (forever) 37Þ - 1HR 37Þ 1:00:00 4Þ 0:00:00 (forever) 37Þ -6HR 37Þ 6:00:00 4Þ 0:00:00 (forever) 65Þ 65Þ 0:00:00 (forever) DENATURE 95Þ 0:05:00 BOIL 100Þ 0:05:00 CUT&KILL 37Þ 1:00:00 70Þ 0:05:00 Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 76 Appendix B Warranties The PTC-100 thermal cycler is warranted against defects in materials and workmanship. For specific Warranty information, contact your local Bio-Rad office. If any defects should occur during the warranty period, Bio-Rad will replace the defective parts without charge.

  • Page 78: Index

    4-11, 9-2 radioactive materials 4-11, 9-2 solutions to use 4-11, 9-2 Condensation in tubes following holds 4-5 Control panel keys 4-3 layout 2-3 light 4-3 using 4-3 Copying a program 8-4 Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com In-1...

  • Page 79: Declaration Of Conformity

    Extend time option 6-2. See also Programs: options, types of Factory-installed protocols A-1 FCC warning v File Utilities 8-2–8-8 Folder assigning a password 8-3 creating 8-3 deleting 8-4 Fuses, changing 9-3 Goto step 6-2 entering 6-7–6-8 In-2 Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 80 List utility 8-6 Main folder 5-2 Menus Edit Menu 7-3 Enter Menu 6-5 Files Menu 8-2 Main Menu 4-2 Options Menu 6-9 Setup Menu 8-6 Microplates selecting 4-4 Microseal 'A' film 4-6 Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com In-3...
  • Page 81 6-11 end step 6-8 extend option 6-10 goto step 6-7 Increment option 6-10 temperature step 6-5 general process 6-4 initiating a program 6-4 naming a program 6-4 revising during 6-12 In-4 Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 82 5-5 factory-installed 5-2 manually stepping through 5-4 pausing while running 5-4 problems with 10-4 running choosing protocol to run 5-2 reading completion screen 5-3 reading runtime screen 5-3 stopping while running 5-4 Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com In-5...
  • Page 83 4-9 Sealing selection chart 4-9 Secure 8-3 Selection keys, location of 2-3 Self test 4-2 Setting up the machine 3-2 air supply requirements 3-3 environmental requirements 3-2 power supply requirements 3-3 In-6 Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com...
  • Page 84 8-4 creating folder 8-3 deleting a program 8-5 deleting folder 8-4 moving a program 8-5 renaming programs 8-5 list 8-6 setup 8-6 determining software version number 8-8 Warranty information B-1 Tech Support: 1-800-4BIORAD • 1-800-424-6723 • www.bio-rad.com In-7...
  • Page 86 IEC61010-1 EN61326: CLASS A following the provisions of the 73/23/EEC, 89/336/EEC & 93/68/EEC Directive. This product is imported into the EU by Bio-Rad Laboratories, Ltd., Bio-Rad House, Maxted Road, Hemel Hempstead (London area), Hertfordshire HP2 7DX England. 13 September, 2004...
  • Page 88 Bio-Rad Laboratories, Inc. Web site www.bio-rad.com USA 800 4BIORAD Australia 02 9914 2800 Austria 01 877 89 01 Belgium 09 385 55 11 Brazil 55 21 3237 9400 Life Science Canada 905 712 2771 China 86 21 6426 0808 Czech Republic 420 241 430 532 Denmark 44 52 10 00 Finland 09 804 22 00 France 01 47 95 69 65...