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BIO RAD PTC-0240, Operation Manual

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5-1

Creating Programs

5

Front Panel Setup  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-3

Display Screen  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-3

Navigation Keys   . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-3

Numeric Keypad  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-4

Programming Conventions  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-4

The Elements of a Program  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-4

Types of Programs  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-6

Graphical Programs  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-6

Advanced Programs  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-7

Designing a New Program  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-7

Let’s Start with an Example  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-8

The Goto Option  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-8

Considerations During Program Creation  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-9

Choosing a Temperature Control Mode  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-9

Calculated Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-9

Block Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-10

Modifying Block-Control Programs for Calculated Control  . . . . . . . . . . .5-10

Modifying a Program Designed for a Different Machine . . . . . . . . . . . . . .5-10

Choosing a Lid Control Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-11

Choosing a Temperature Ramping Rate   . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-11

Choosing a Temperature Hold Time  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-11

Choosing a Thermal Gradient  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-12

Beyond the Example Protocol: Other Considerations  . . . . . . . . . . . . . . . . . . . . .5-13

Summary of Contents for PTC-0240

Page 1: ...DNA Engine Tetrad 2 Peltier Thermal Cycler Operations Manual Version 2 0 PTC 0240 DNA Engine Tetrad 2 Cycler...

Page 2: ...DNA Engine Tetrad 2 Peltier Thermal Cycler PTC 0240 DNA Engine Tetrad 2 Cycler Operations manual Supports software version 4 0...

Page 3: ...mmediately attached Bio Rad sample block module s constitutes a thermal cycler whose purchase con veys a limited non transferable immunity from suit for the purchaser s own internal research and devel...

Page 4: ...ions 2 1 Chapter 3 Installation 3 1 Chapter 4 Operation 4 1 Chapter 5 Creating Programs 5 1 Chapter 6 Managing and Editing Programs 6 1 Chapter 7 Running Programs 7 1 Chapter 8 Using the Utilities 8 1...

Page 5: ...Tetrad 2 cycler any Alpha unit or any accessory to the cycler Doing so will void your war ranties and can put you at risk for electrical shock Return the DNA Engine Tetrad 2 cycler to the factory US...

Page 6: ...DIO ELECTRIQUE EDICTE PAR LE MINISTERE DES COMMUNICATIONS DU CANADA FCC Warning Warning Changes or modifications to this unit not expressly approved by the party responsible for compliance could void...

Page 7: ...lics will be used to indicate windowed items that are not drop down menu items or buttons such as Calculated Block and Tracking Typically these will be parameter selection items Select is meant to be...

Page 8: ...1 1 Introduction 1 Meet the DNA Engine Tetrad 2 Cycler 1 2 Using This Manual 1 2 Important Safety Information 1 3...

Page 9: ...s Intuitive DNA Engine Tetrad 2 system software with user friendly interface for programming editing file management and much more Choice of calculated temperature control for highest speed and accura...

Page 10: ...to operate the instrument Warning The DNA Engine Tetrad 2 cycler can generate enough heat to inflict serious burns and can deliver strong electrical shocks if not used according to the instructions in...

Page 11: ......

Page 12: ...ront View 2 2 DNA Engine Tetrad 2 Cycler Control Panel 2 2 DNA Engine Tetrad 2 Cycler Back View 2 3 DNA Engine Tetrad 2 Cycler Bottom View 2 3 Compatible Alpha Units 2 4 DNA Engine Tetrad 2 Specificat...

Page 13: ...1 800 4BIORAD 1 800 424 6723 www bio rad com DNA Engine Tetrad 2 Cycler Front View Figure 2 1 DNA Engine Tetrad 2 Cycler Control Panel Figure 2 2 Numeric keypad Display screen Air intake vents Alpha u...

Page 14: ...m 2 3 DNA Engine Tetrad 2 Cycler Back View Figure 2 3 DNA Engine Tetrad 2 Cycler Bottom View Figure 2 4 DNA Engine Tetrad 2 cycler rear USB A port for mouse USB B port for remote command Air exhaust v...

Page 15: ...gle Holds one 384 well microplate Flat Block Holds customer designed adapter through four screw down points Dual Block Models 30 30 Dual Holds 2 x 30 x 0 5 ml tubes 30 48 Dual Holds 1 x 30 x 0 5 ml tu...

Page 16: ...wer 1600 W maximum Fuses Two 6 3 A 250 V 5 x 20 mm Displays One 1 4 size VGA screen 320 x 240 16 colors Ports One 9 pin RS 232 serial port One ethernet port Program Capacity 1 000 typical Weight 21 6...

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Page 18: ...Up the DNA Engine Tetrad 2 Cycler 3 2 External Mouse Device 3 3 Environmental Requirements 3 3 Power Supply Requirements 3 4 Air Supply Requirements 3 4 Ensuring an Adequate Air Supply 3 4 Ensuring T...

Page 19: ...ses One power cord One external mouse device DNA Engine Tetrad 2 Peltier Thermal Cycler Operations Manual this document Unpacking Instructions for the DNA Engine Tetrad 2 Thermal Cycler If any of thes...

Page 20: ...ff Wait for 10 seconds to ensure that all fans have stopped rotating 2 Grasping the sides of the DNA Engine Tetrad 2 cycler tilt the instrument back so that the underside of the lip is visible 3 Inser...

Page 21: ...sing performance problems software error messages particularly HS Overheating and Slow Block Cycling and even automatic shut downs Special attention should be paid to airflow and air temperature in ro...

Page 22: ...s open lights on Run a typical protocol for 30 minutes to warm up the DNA Engine Tetrad 2 cycler then measure the air temperature at the back air intake vents If more than one machine is involved meas...

Page 23: ...ctively The coating eventually wears off so the block should be re coated as needed probably about once every 10 to 20 runs Your experience will be the best guide in establishing the frequency for re...

Page 24: ...4 6 Selecting the Correct Sample Vessel 4 6 0 5 ml Tubes 4 7 Thin Walled vs Thick Walled Tubes 4 7 0 2 ml Tubes 4 7 Microplates 4 7 Sealing Sample Vessels 4 8 Sealing with Oil or Wax 4 8 Sealing with...

Page 25: ...plement a boot up protocol lasting about 1 minute 30 sec onds During the boot sequence the user is presented with several options including 1 Selftest Choose number 1 on the keypad to instruct the DNA...

Page 26: ...n is a 1 4 size VGA screen for displaying thermal cycler condi tions and programs Operation Keys Navigation keys left and right arrows next back Use to move around within the display screen Numeric ke...

Page 27: ...ing Moto Alpha units Installing an Alpha Unit Caution Do not insert or remove an Alpha unit with the DNA Engine Tetrad 2 cycler turned on electrical arcing can result Read the safety warning at the be...

Page 28: ...trad 2 cycler see the Caution above 2 Pull upward on the handle When the lock releases you will hear a click and the Alpha unit will slide a little outward from the center of the cycler The electrical...

Page 29: ...e over the thumbwheel as the lid closes over the sample block A click signifies that the Hot Bonnet lid s latch has engaged Selecting the Correct Sample Vessel The DNA Engine Tetrad 2 cycler s wide va...

Page 30: ...es up to 2 3 C second so the faster heat transfer provided by thin walled tubes allows protocols to be significantly shortened 0 2 ml Tubes All types of thin walled 0 2 ml tubes may be used Bio Rad of...

Page 31: ...i 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 A pipette tip can then be used to pier...

Page 32: ...2296 and ALP 2238 Each pad may be used for approximately 25 runs Adjusting the Hot Bonnet Lid s Pressure The pressure exerted by the Hot Bonnet lid must be manually adjusted to fit the sample vessels...

Page 33: ...heel has been turned mark it at the quarter turn positions or every sixth bump on the thumbwheel there are 24 total bumps Loading Sample Vessels into the Block When using a small number of tubes load...

Page 34: ...event escape of these compounds See Appendix 4 B of this chapter for important information regarding safe use of these compounds in polypropylene tubes and polypropylene and poly carbonate microplates...

Page 35: ...rted s e t a l p o r c i m l l e w 4 8 3 s e i r e s P S M d e t r i k s l l e h S d r a H s e t a l p o r c i m l l e w 6 9 s e i r e s P S H d e t r i k s l a e s o r c i M s e t a l p o r c i m l l...

Page 36: ...olycarbonate is somewhat permeable both to water and the 35S breakdown product This problem is exacerbated when polycarbonate plates are held at high temperatures for long periods of time or when the...

Page 37: ...a fume hood and be aware that vessels may be contaminated on the outside after thermal cycling Please be certain that you are using the appropriate detection methods and cleaning procedures for this...

Page 38: ...Example 5 8 The Goto Option 5 8 Considerations During Program Creation 5 9 Choosing a Temperature Control Mode 5 9 Calculated Control 5 9 Block Control 5 10 Modifying Block Control Programs for Calcu...

Page 39: ...l Programming Window 5 20 Selecting a Step 5 20 Editing Step Parameters 5 20 Deleting a Step 5 21 Adding a Step 5 21 Entering a Temperature Step 5 21 Entering a Gradient Step 5 24 Entering a Goto Step...

Page 40: ...ler s control panel see figure 2 2 allow the operator to enter navigate and manipulate programs These programs are nec essary to control the various dynamic capabilities of the DNA Engine Tetrad 2 cyc...

Page 41: ...nel such as ENTER 1 and LEFT will be used to indicate windowed menu items or buttons such as PROGRAMS RUN and UTILITIES Italics will be used to indicate windowed items that are not drop down menu item...

Page 42: ...1 C from left to right across the block The maximum programmable temperature is 105 C the minimum programmable temperature is 30 C GoTo step Directs the program to cycle back to an earlier step a spec...

Page 43: ...ep when the target temperature is reached Types of Programs There are two types of Tetrad 2 programs basic and advanced Basic programming fea tures a graphical interface and a graphical representation...

Page 44: ...ical programs can be opened and edited in advanced mode only a subset of advanced programs can be opened and edited in basic mode Advanced programs that meet the criteria outlined above for graphical...

Page 45: ...ting raw program you write may look something like this Raw program 1 92 C for 30 seconds 2 60 C for 3 minutes 3 92 C for 30 seconds 4 60 C for 3 minutes 5 92 C for 30 seconds 6 60 C for 3 minutes con...

Page 46: ...o possible ways each of which has different implications for the speed and accuracy of sample heating These include Calculated Control and Block Control Calculated Control When using calculated contro...

Page 47: ...Under block control the temperature of samples will lag behind the temperature of the block The length of the time lag depends on the vessel type and sample volume but typically is between 10 and 30...

Page 48: ...s Off No power is applied to the heated lid In this mode condensation will occur at a rate consistent with the incubation temperature and the type of tube or plate sealant being used This option is re...

Page 49: ...mable temperature gradient feature allows for optimization of an incubation temperature in a single experiment by analyzing a number of different temperatures simultaneously The thermal gradient deliv...

Page 50: ...w temperature ramp can also be included to ensure proper product annealing In addition some protocols can include a sustained incubation at sub ambient tem peratures to preserve the integrity of the p...

Page 51: ...dicated At the screen bottom the program control buttons Run Instant Stop Pause Skip and Graphs allow the operator global or line by line control of the program currently loaded into memory These will...

Page 52: ...am entering a program in graphical mode essentially involves editing the graphically displayed TEMPLATE program The TEMPLATE program will be the last graphical program that was saved In this section w...

Page 53: ...he control or lid mode select the box in front of that field In either case the Mode Selection window appears Using the Mode Selection Window For the purposes of this example we have decided to use Ca...

Page 54: ...n programs and Cancel the current programming session Using the File Save As Window The Save and Save As buttons are probably the most important buttons in the graphical programming window since a pro...

Page 55: ...Select OK You will be returned to the File Save As window The display will have changed slightly with our newly created folder appearing in the Folder list We will want to save our program in this ne...

Page 56: ...then high light the folder of interest Click the Edit Password button If the folder has an existing password you will be prompted to enter the Old and New passwords Confirm the spelling of the new pas...

Page 57: ...line s or arrow depicting that step will turn red Select a step by positioning the cursor in the step s column and clicking once A flashing insertion point will appear in the temperature field of that...

Page 58: ...ee the sections immediately following for complete instructions on adding specific types of steps and entering step parameters Now let s begin entering the steps for our example program Entering a Tem...

Page 59: ...t pointer in the temperature field of step 1 and select by clicking once A flashing insertion point will appear in the temperature field See the Selecting a Step and Editing Step Parameters sections o...

Page 60: ...ever Step two of our program is also a temperature step but with an incubation temperature of 92 0 C and a duration of 30 seconds If step two in the displayed protocol is a temperature step follow the...

Page 61: ...for a gradient is 24 C and the minimum is 1 C Fractional degrees are not accepted Recall that in our example protocol the gradient step should specify a range of 45 C to 65 C and a duration of 3 minu...

Page 62: ...peat steps 2 and 3 an additional 29 times A graphical program can only contain one goto step This goto step cannot be the first or only step in the protocol If there is a goto step blue arrow in the d...

Page 63: ...selecting the Forever box after specifying the incubation temperature The duration of the step will be displayed as a blue infinity symbol If there are any additional steps displayed in the graphical...

Page 64: ...Lid Control Mode for the program Refer to the Considerations During Program Creation section earlier in this chapter for information on temperature and lid control modes We have decided for the purpos...

Page 65: ...gramming mode follow the instructions in the Using the File Save As Window section above to create a new folder named FOLDER2 and a new program named ADV 1 After selecting OK you will be returned to...

Page 66: ...the bottom of the window Once the step is selected any new steps that are added will be inserted after the Lid Control Mode step Tip Before entering a new step always select the insertion point first...

Page 67: ...temperature step in the cycling portion of our program incubates at 92 C for 30 seconds We would also like the cycler to beep after reaching this temperature Position the cursor over the appropriate...

Page 68: ...ields for specifying the Lower Temperature and the Higher Temperature of the gradient range as well as the gradient hold Time The maximum gradient range is 24 C and the minimum range is 1 C Below the...

Page 69: ...es displayed are quite accu rate for each well in that column 0 4 C of actual column temperature Select Close Select OK The program listing should now appear as follows Since the program step listing...

Page 70: ...ed to increase the incubation time by 5 seconds per cycle In the Temperature Step window you would implement the following Enter 60 C in the Temperature field Enter 1 in the Time Min field Select Exte...

Page 71: ...ng process as this is our initial denaturation step and should not be repeated more than once Position the cursor in the Additional Number of Cycles field and select Enter 29 in the field Select OK Th...

Page 72: ...s For further instruction on running the Moto Alpha unit see The Moto Alpha Unit which appears at the end of this chapter The Slow Ramp Option Earlier we described the Extend Time option for a tempera...

Page 73: ...mple and Time enter 30 seconds as an example Select Increment Temp Select Set Parameters for the Increment Temp option The Increment Temperature window appears Select Decrease Position the cursor over...

Page 74: ...r 00 01 00 Beep on Target 2 Incubate at 92 C for 00 00 30 Beep on Target 3 Gradient from 45 C to 65 C for 00 03 00 4 Cycle to step 2 for 29 more times 5 Incubate at 10 C forever End The program is now...

Page 75: ...f reaction vessel Once set the same pressure is maintained until the lid is readjusted for a different type of vessel Lid pressure is set either through the front panel of the cycler or through the re...

Page 76: ...4 Editing a Program 6 4 Editing a Graphical Program 6 5 Editing an Advanced Program 6 6 Highlighting and Selecting Program Steps 6 6 Deleting a Step 6 6 Inserting a Step 6 7 Editing a Step 6 7 File Ut...

Page 77: ...e DNA Engine Tetrad 2 cycler and stored in the MAIN folder These programs are listed in Appendix C Any of the protocols saved on the DNA Engine Tetrad 2 cycler whether created by the user or preprogra...

Page 78: ...l graphical programs can be opened and edited in advanced mode only a subset of advanced programs can be opened and edited in basic mode Advanced programs that meet the criteria outlined for graphical...

Page 79: ...a graphical program the program can no longer be opened or edited in basic mode We will open our example graphical program GRAPH 1 in basic mode The proce dure is similar to that described above for...

Page 80: ...Entering a Program Using Graphical Mode in Chapter 5 specifically The Graphical Programming Window section for more information To replace step 3 the gradient step with a temperature incubation at 60...

Page 81: ...as those for step creation Selection can also be done via the left mouse button In order to insert or edit steps the user of the DNA Engine Tetrad 2 cycler should become familiar with these conventio...

Page 82: ...5 Your program should appear as follows Temperature Control Mode Calculated Lid Control Mode Constant at 100 C 1 Incubate at 94 C for 00 01 00 Beep on Target 2 Incubate at 92 C for 00 00 30 Beep on T...

Page 83: ...ng saving copying deleting and moving You can also delete a folder These functions with the exception of saving can be accessed from the Programs drop down menu on the Status window menu bar Saving an...

Page 84: ...a number of programs you may want to create separate folders to organize them Perhaps you will use separate folders for different users or experimental series To copy a program Highlight the From Fold...

Page 85: ...program window is very similar to the open program window We provide a convenient program listing at the bottom of the window so that you can determine whether you truly wish to delete the program Hig...

Page 86: ...lder The copy in the From Folder is deleted You will not be prompted with a verification step for this move so exercise some caution Deleting a Folder No command set would be complete without a folder...

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Page 88: ...stant Incubation Feature 7 2 Running Programs 7 4 The Run Program Window 7 5 During the Run 7 6 Run Status 7 6 Terminating a Run 7 8 Pausing Resuming a Run 7 8 Skipping a Step 7 8 Inaccessible Feature...

Page 89: ...ange from 5 0 C to 105 C 4 C to 100 C with the Slide Chambers Alpha unit This feature can be used for performing ligations digestions etc or with slides per forming overnight humidified hybridizations...

Page 90: ...ing the heated lid Select the desired block s Select OK The block s will now incubate at the desired temperature The Status window will display the status of the selected block Use the block selection...

Page 91: ...ult name TEMPLATE by performing a save as Graphical programs with the default name TEMPLATE can not be run The Run Program window will appear allowing you to specify the block on which the pro tocol s...

Page 92: ...lect Calculated Mode Parameters window that is appropriate for the type of program and Alpha unit that you are using Parameters entered here will allow precise temperature calculations by the DNA Engi...

Page 93: ...ndicated Users can scroll through the temperature display graph Left and right arrow buttons allow the leading edge dashed vertical green line to be advanced or subtracted as long as the minimal time...

Page 94: ...l that convenient and rapid toggling between the Status and Graphs windows can be achieved by selecting the button in the lower right of the Status and Graphs windows respectively To simultaneously vi...

Page 95: ...step in a running program select Skip at the bottom of the Status window A confirmation screen will ask you to confirm the skip select Yes to skip to the next step in the protocol displayed in the St...

Page 96: ...ning multiple protocols considerations should be made as to the compatibility of the program with the available Alpha units Please review Chapter 4 Operation for a more complete treatment of Alpha uni...

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Page 98: ...2 Control 8 3 Remote 8 3 Config 8 4 User Name 8 4 Set Date Time 8 4 Bay Configuration 8 5 Bay Identification 8 5 Comm Config 8 5 Service 8 5 Network 8 6 Update Soft Network Config 8 6 Gradient Calc 8...

Page 99: ...d 2 cycler providing access to user name control remote command mode and the date and time settings The Utilities submenu is selectable from the Status window Utilities has five options with submenus...

Page 100: ...on a Mac The cycler is now ready to be run in remote mode Select the Auto Remote check box to direct the DNA Engine Tetrad 2 cycler to auto matically enter remote mode upon subsequent power up This f...

Page 101: ...name before executing a program In this manner any potential user can deter mine the owner of a block the person running a program as the name will be displayed when the block is selected in the Statu...

Page 102: ...ED located next to it Select a particular bay and specify the Number of Times to Flash LED This utility is useful trying to identify which of the cycling bays is considered Bay 3 or Bay 4 when running...

Page 103: ...Update Soft and Network Config utilities To view the available software upgrades and or perform an upgrade begin by estab lishing internet access via an Ethernet 10BaseT connection Connect the ethern...

Page 104: ...the DNA Engine Tetrad 2 using a serial cable and a Windows based PC This kit is available free of charge from Bio Rad Request item number SWU 0200 Gradient Calc The Gradient Calculator allows you to v...

Page 105: ...e instrument will indicate that it is Ready to accept files 3 During the boot up sequence of the sending instrument select the Send Files option by entering 2 on the numeric keypad 4 To execute the fi...

Page 106: ...tenance 9 Cleaning the DNA Engine Tetrad 2 Cycler 9 2 Cleaning the Chassis and Block 9 2 Cleaning the Air Ventss 9 2 Cleaning Radioactive or Biohazardous Materials Out of the Block 9 3 Changing the Fu...

Page 107: ...rical shorting If you use oil in the block a practice not recommended by Bio Rad see Using Oil to Thermally Couple Sample Vessels to the Block in Chapter 4 clean the wells whenever the oil has become...

Page 108: ...al fusing which means that live power may still be available inside the unit even when a fuse has blown or been removed Never open the DNA Engine Tetrad 2 base You could receive a serious electrical s...

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Page 110: ...2 System Problems 10 2 Error Messages 10 3 Problems in Power Up 10 8 Problems with System Performance 10 9 Problems with an Alpha Unit 10 10 Problems Related to Protocols 10 10 Problems due to Enviro...

Page 111: ...ell as Alpha units Exact nature of the problem Frequency of the problem i e is the problem repeatable Steps already taken to troubleshoot the problem i e controls performed System Problems The Status...

Page 112: ...be checked auto matically during and after the run and you will be notified if any per sistent problem is found No action is required at this time 19 BSF LI An irregularity was detected in the block s...

Page 113: ...2 HSO PT The heat sink reached a tempera ture higher than normal and the prgram was automatically stopped Adequate airflow is nec essary to prevent the heat sink from overheating Please observet he fo...

Page 114: ...Please delete unused programs or call 800 4BIORAD in the US or Canada or your local distrib utor outside the US or Canada 18 PSF A possible fault was detected in the in sample probe The thermal contro...

Page 115: ...egularity was detected in a power supply temperature sensor The sensor will be checked and you will be notified if any problem is found No action required at this time 2 HSO PT The heat sink reached a...

Page 116: ...quired Temperature mode has been automatically switched to Calculated control for this run only 25 GF The thermal gradient has not been achieved as quickly as expected This may indicate a possible pro...

Page 117: ...e a problem should be consistent and repeatable Figure 10 1 Power up Troubleshooting Flowchart Turn power on Was 1 hit to enter Selftest Is the fan on Unit defective return for service Unit ready Plug...

Page 118: ...be a consistent repeatable problem Figure 10 2 System Performance Troubleshooting Flowchart Unit ready Select 1st block Select last block Are temperatures indicated on the display Are temperatures ind...

Page 119: ...re intended as a starting point for further investigation Should the DNA Engine Tetrad 2 system check out OK we recommend positive controls for troubleshooting purposes Following is a general descript...

Page 120: ...emperatures of primers using available computer programs or empirical testing Wrong temperature control method used Use List utility to check tempera ture control method for protocol change if needed...

Page 121: ...aximize desired product and minimize primer dimers Reaction working but unexpected extra prod ucts or smear is seen Nonspecific hybridization occurring during setup Program a hot start into the protoc...

Page 122: ...on Frequent shutdowns due to overheating Frequent Slow Block Cycling HS Overheat and HS Overheating error messages Machine is not receiving enough air Make sure air intake vents are not obstructed by...

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Page 124: ...improper packaging of returned goods 2 Repair or modifications done by anyone other than Bio Rad Laboratories 3 Use with tubes plates or sealing materials not specified by Bio Rad Laboratories for us...

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Page 126: ...nly and the terms of the SOFT WARE PRODUCT license below apply BY OPERATING THE CYCLER OR INSTALLING COPYING OR OTHERWISE USING THE SOFTWARE PRODUCT OR ANY UPDATE THERETO YOU AGREE TO BE BOUND BY THE...

Page 127: ...ird party end user in connection with the sale of the CYCLER to such third party end user provided that i the SOFTWARE PRODUCT and THIRD PARTY SOFTWARE are transferred in their entirety to the third p...

Page 128: ...the extent allowed by applicable law implied warranties on the SOFTWARE PRODUCT if any are limited to the same ninety 90 days 3 2 Customer Remedies BIO s entire liability and your exclusive remedy sha...

Page 129: ...LIMITED TO THE PURCHASE PRICE PAID BY LICENSEE FOR THE CYCLER AND SOFTWARE PRODUCT 4 2 The CYCLER SOFTWARE PRODUCT and THIRD PARTY SOFTWARE are not intended for HIGH RISK ACTIVITIES as defined below I...

Page 130: ...fending clause will be modified so as to be enforceable and as modified shall be fully enforced and the remainder of the AGREEMENT will continue in full force and effect 7 3 Intellectual Property Righ...

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Page 132: ...0 5 C cycle 4 72 30 5 GOTO 2 29X 6 95 30 7 45 30 8 72 30 9 GOTO 6 29X 10 72 7 00 11 4 12 END 2 step Fast PCR protocol using iTaq polymerase iTAQ FST Step Temp Time 1 98 30 2 92 01 3 70 10 4 GOTO 2 34X...

Page 133: ...00 6 4 7 95 30 8 65 30 9 GOTO 7 39X 10 72 7 00 11 4 12 END C 2 Tech Support 1 800 4BIORAD 1 800 424 6723 www bio rad com 3 step nested primer protocol NEST PR3 Step Temp Time 1 95 4 00 2 95 30 3 55 30...

Page 134: ...editing 6 6 6 8 See also Editing a program extend time option 5 33 goto step entering 5 34 gradient step entering 5 31 5 32 increment temp option 5 36 5 37 inserting a step 6 7 lid control step enteri...

Page 135: ...e block models 2 4 slide block 2 4 B Bleach using in block 9 2 Block control 5 10 Block selection incompatibility 7 8 Block status lights 4 4 C Calculated control 5 9 Chill out liquid wax 4 8 Cleaning...

Page 136: ...Deleting a step graphical program 5 21 6 5 Deleting programs 6 10 Display screen location of 2 2 E Editing a program advanced 6 6 6 8 deleting a step 6 6 editing a step 6 7 inserting a step 6 7 selec...

Page 137: ...moving programs 6 11 saving edited programs 6 8 Folder creating new 5 18 deleting 6 11 naming 5 18 Forever incubation advanced program 5 37 graphical program 5 26 Front panel 5 2 See also Control pane...

Page 138: ...a step 5 20 6 5 forever incubation entering 5 26 goto step entering 5 25 gradient step entering 5 24 opening 6 4 selecting a step 5 20 specifications 5 6 5 7 temperature step entering 5 21 5 24 Graphs...

Page 139: ...10 M Maintenance 9 2 Microplates removing 3 6 selecting 4 7 Microplate sealing mat 4 9 4 12 Microseal A film 4 8 4 12 Microseal B adhesive seals 4 9 4 12 Microseal F foil 4 9 4 12 Microseal P pads 4 9...

Page 140: ...32 8 3 Power cord plugging in 3 2 Power supply requirements 3 4 acceptable power cords 3 4 Program adjusting for sample vessel type 4 6 4 7 advanced 5 27 5 37 extend time option 5 33 goto step enterin...

Page 141: ...ample 5 8 other considerations 5 13 editing 6 4 6 8 See also Editing a program advanced 6 6 6 8 graphical 6 5 elements end step 5 5 go to step 5 5 gradient step 5 5 lid control mode 5 4 temperature co...

Page 142: ...19 6 8 types 5 6 5 7 advanced 5 7 graphical 5 6 Programming conventions 5 4 R Radioactive contamination choosing microplates and tubes 4 13 cleaning 4 14 problem with 35S nucleotides 4 13 solutions t...

Page 143: ...ct 4 10 loading into block 4 10 sealing reason for 4 8 selection chart 4 12 with Hot Bonnet lid and caps film 4 8 with oil or wax 4 8 selection 4 6 0 2 ml tubes 4 7 0 5 ml tubes 4 7 microplates 4 7 se...

Page 144: ...hods block control 5 10 calculated control 5 9 modifying a program from a different machine 5 10 modifying block control programs 5 10 Temperature hold time 5 11 Temperature increment See Increment te...

Page 145: ...in power up 10 8 problems w environment setup or maintenance 10 13 problems w system performance 10 9 problems with alpha unit 10 10 protocol problems 10 10 system problems 10 2 U Uniformity See Therm...

Page 146: ...ion relates is in conformity to the following standards or normative documents IEC61010 1 EN61326 CLASS A following the provisions of the 73 23 EEC 89 336 EEC 93 68 EEC Directive This product is impor...

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Page 148: ...3 4 5018111 6450092 93 Israel 03 951 4127 Italy 39 02 216091 Japan 03 5811 6270 Korea 82 2 3473 4460 Latin America 305 894 5950 Mexico 55 52 00 05 20 The Netherlands 0318 540666 New Zealand 64 9 415...

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