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MJ Mini™ Gradient Thermal Cycler - Bio-Rad

1. A E ASA ek 64 2 3 rro Ser Gat tee edi et e pl Arnone Ol etr be ead ted d 65 Viewing the East Program RUN ivi ee mee ebur ee eee he ERE UE S 69 Changing the Default Settings of the Heated Lid 66 Performing sas sales cse E ARRA BARI RAN ORA Be 66 Gradient Calculator ner eet a debe e opel ote ew pede WO e how ete a od 67 Determining the Software Version Number sses reesti nn 68 Changing the Contrast of the LCD Display oooocoooccconcc mnn 68 60 Locating Stored Program Many of the utilities on the MJ Mini cycler accessible by selecting Files or Tools from the Main Menu require you to locate a program stored in the machine The actions necessary to do this depend on whether your programs have been stored in the lt MAIN gt folder or in custom folders If all programs have been stored in lt MAIN gt The screen will list all the programs that lt MAIN gt contains Copy _IPRFikb iPRF8kb iPRF15kb TAQ FST lt MAIN gt LONG 2 LONG 3 NEST PR2 NEST Select the desired program from this list If programs have been stored in custom folders The screen will list all the folders residing in the machine on the left side of the screen As you scroll through the list of folders by using the Select keys a list of programs that reside in each folder is displayed on t
2. 1 95 4 00 2 95 30 3 65 30 4 GOTO 2 40X 5 72 7 00 5 4 oo 6 95 30 7 65 30 8 GOTO 6 40X 9 72 7 00 10 4 oo are END NEST PR3 Step Temp Time 1 95 4 00 2 95 30 3 55 30 4 72 30 5 GOTO 2 40X 6 72 7 00 7 4 8 95 30 9 55 30 10 72 30 11 GOTO 8 40X 12 72 7 00 13 4 14 END 2 step long PCR protocol using iTaq polymerase LONG 2 Step Temp Time 1 95 4 00 2 95 30 3 65 3 00 Ext 15s cycle 4 GOTO 2 35X 5 72 7 00 6 4 7 3 step long PCR protocol using iTaq polymerase LONG 3 Step Temp Time 1 95 4 00 2 95 30 3 55 30 4 72 3 00 Ext 15s cycle 5 GOTO 2 35X 6 72 7 00 7 4 oo 8 END In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com BIO RAD 79 80 BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Index A Air supply requirements ensuring adequate air supply 15 ensuring air is cool enough 15 troubleshooting problems with 15 Beep option See Programs options types ofBleach using in block 70 C Chill out liquid wax 20 Cleaning air vents 70 and biohazardous materials 70 and radioactive materials 24 70 chassis and block 70 removing oil from block 70 solutions to use 70 Condensation in tubes following holds 20 Control panel 10 keys 18 lights 19 using 18 D Documentation conventions graphic 6 terminology 6
3. The MJ Mini thermal cycler and associated accessories are covered by a standard Bio Rad warranty Contact your local Bio Rad Laboratories office for the details of the warranty In the 5 call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com BIO RAD Documentation Conventions Typographic Conventions Example Meaning lt lt PROCEED gt gt The names of keyboard keys are encased in double angle brackets Italics Select Edit from the Main Menu This instrument system is labeled For Research Use Only Graphic Conventions The programming screens displayed in the LCD window can display up to seven lines of text at one time Example New Lid 100 C ABCD Vol 20uL 1 92 0 FOR 0 30 2 LOWER TEMP Terminology A programming option is termed selected when the option is highlighted In this manual the selected terms are outlined see the example above BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Introduction MJ Mini Thermal CyclerS ia nri nenea kamna eee Important Safety Information lisse tees MJ Mini Thermal Cyclers The MJ Mini thermal cycler features Premium cycling in a medium capacity cycler the MJ Mini thermal cycler can hold 48 x 0 2 ml tubes 12 x 0 5 ml tubes or one 48 well microplate Ability to program and maintain a 16 C temperature gradient
4. the example below since the MAIN folder is highlighted the list of programs that reside in the MAIN folder appears on the right Run PROGRAMS lt MAIN gt iPRF1kb lt FOLDER1 gt iPRF8kb lt FOLDER2 gt iPRF15kb LONG 2 LONG 3 Select the folder that contains the protocol you wish to run then press the right Select key to toggle over to the list of protocols located in that folder Use the Select keys to scroll through the listed protocols and select the desired protocol then press Proceed BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Running Protocols In either instance after you press Proceed a screen similar to the one below will be displayed Run iPRF1kb Sample Vol 20yl RUN VIEW The top line of the screen will identify the selected protocol IiPRF1kb in the example The other lines on the screen will request information needed to set up the temperature control method explained below Enter the reaction volume and press Proceed The cursor moves over to the Run option However before you run the protocol you may select to VIEW the protocol steps by selecting View and pressing Proceed View Lid 100 C iPRF1kb Vol 20ul 1 95 0 2 00 2 92 0 0 01 3 70 0 0 10 The steps are listed along with the default heated lid temperature and selected reaction volume In this case you need to use the Select key
5. Cancel to move back one space and erase the previous character entered Likewise you may use the left and right Select keys move the cursor across the field to alter any of the characters in the name Simply move the cursor over the character you need to change and reenter a character When the name is complete press Proceed once to accept the last character and again to accept the whole name If the name is already in use for a program a screen saying Name In Use will be displayed If this happens press Proceed then enter a different name Choosing a Temperature Control Mode Choosing a Heated Lid Temperature When the program name has been entered you will be prompted to enter a heated lid temperature Enter a value for the heated lid and press Proceed A default temperature may appear in the field if you wish to use this temperature press Proceed Note See page 52 at the end of this chapter for information on selecting a heated temperature Choosing a Thermal Cycling Volume After selecting a lid temperature you must specify the thermal cycling reaction volume Enter a value for reaction volume and press Proceed By entering a sample volume in this field acceptable range 1 100 ul whole integers only the cycler will enter Calculated Temperature Control mode The cycler will take into account the sample volume in utilizing small temperature overshoots to rapidly bring the sample to its target temp
6. MJ Mini Gradient Thermal Cycler Instruction Manual Catalog PTC 1148 MJ Mini Gradient Thermal Cycler Instruction Manual Catalog 1148 LEGAL NOTICES Copyright 2009 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 NOTICE TO PURCHASER This base unit Serial No in combination with its immediately attached Bio Rad sample block module s constitutes a thermal cycler whose purchase conveys a limited non transferable immunity from suit for the purchaser s own internal research and development and for use in human in vitro diagnostics and all other applied fields under one or more of U S Patents 5 656 493 5 333 675 5 475 610 claims 1 44 158 160 163 and 167 only and 6 703 236 claims 1 7 only or corresponding claims in their non U S counterparts owned by Applera Corporation No right is conveyed expressly by implication or by estoppel under any other patent claim such as claims to apparatus reagents kits or methods such as 5 nuclease methods Further information on purchasing licenses may be obtained by contacting the Director of Licensing Applied Biosystems 850 Lincoln Centre Drive Foster City California 94404 USA These products are covered by one or more of the following U S patents or their foreign counterparts owned by Eppendorf AG U S Patent No
7. 2 Incubation periods are timed according to how long the samples not the block reside at the target temperature 3 The machine automatically compensates for vessel type and reaction volume Block Control Block Control provides less accurate control of sample temperatures than Calculated Control provides Under Block Control the temperature of samples always lags 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 seconds Block Control is chiefly used to run protocols developed for other thermal cyclers that use Block Control Modifying Block Control Programs for Calculated Control Block control programs can be changed to calculated control by subtracting at least 15 20 seconds from each temperature step Some empirical testing may be required to adjust modified programs for optimum performance Modifying a Program Designed for a Different Machine The ramp option can be used to adapt programs designed for thermal cyclers with slower maximum heating and cooling rates than the MJ Mini thermal cycler In addition a given protocol will occasionally work better with a slower rate of temperature change adjusting the ramp rate can be used to optimize the program for such a protocol Entering a New Program Programming the MJ Mini cycler moves through five steps Initiating the program Naming the program Choosing a heated lid temperatur
8. A protocol cannot be paused before the target temperature for a given step has been reached If Pause is pressed before this point the block continues heating or cooling until the target is reached and then the protocol is paused BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Running Protocols Stopping a Running Protocol Press Cancel to stop a running protocol A cancellation confirmation screen will be displayed Running iPRF1kb Step 1 90 0 0 25 Temp 90 0 0 10 Cycle 2 of 39 Cancel iPRF1kb Yes No Select Yes then press Proceed to cancel the protocol The total run time for the protocol will be displayed PROGRAM CANCELLED Total Time 3 21 Press Proceed to return to the Main Menu Note If the cycler is currently ramping to a temperature the thermal cycler will continue ramping until it reaches its target temperature at which point you will be able to cancel the program Note Turning off the machine does not stop a running protocol The MJ Mini cycler will assume the protocol was stopped by a power outage and will resume running the protocol when the machine is turned back on see below In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com BIO RAD 31 32 Resuming a Protocol After a Power Outage If a power failure occurs when a protocol is running the MJ Mini cycler will hold th
9. CYCLE 1 2 Select one of the displayed choices then press Proceed Yes accepts the Inc value and displays the Enter Menu again Use the Enter Menu to enter the next step in the program No allows reentry of the Inc value Option displays the Options Menu again Use the Options Menu to enter another option for the step Entering an Extend Option 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 New Lid 100 C ABCD Vol 20 1 92 0 FOR 0 30 2 50 0 FOR 0 30 SEC CYCLE Similar to the increment option the temperature step being modified appears on the bottom line of this screen The plus sign means that the screen is set up to enter progressive lengthening of hold time Press the key to switch to a minus sign allowing entry of a progressive shortening of hold time Press to change back to a plus sign Enter the numerical value of the increase or decrease in hold time In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com RAD 47 48 Note You may only use whole numbers here 1 1 used in the example below New Lid 100 C ABCD Vol 20 1 92 0 FOR 0 30 2 50 0 FOR 0 30 SEC CYCLE Press Proceed The Ext value just entered will be incorporated into the protocol and a confirmation menu will be displayed on the
10. PLEASE RETURN TO BIO RAD Alpha unit has exceeded its maximum temperature or sensor has a malfunction Contact Bio Rad Laboratories FOR SERVICE and is not measuring temperature accurately so the protocol was terminated FAILURE OF HS PS SENSOR Both heat sink and power supply Contact Bio Rad Laboratories PLEASE RETURN TO BIO RAD sensors have failed protocol was FOR SERVICE terminated FAILURE OF PREHEATING LID PLEASE RETURN TO BIO RAD FOR SERVICE Lid sensor has failed during lid preheat protocol was terminated Contact Bio Rad Laboratories FAILURE OF REAR FRONT BLK SENSOR PLEASE RETURN TO BIO RAD FOR SERVICE Failure means that the sensor was deemed short open or had changed more than 3 C in a 50 ms period and that this condition was present for more than 2 seconds Contact Bio Rad Laboratories FAILURE OF HEATSINK SENSOR PLEASE RETURN TO BIO RAD Failure means that the sensor was deemed short open or had changed Contact Bio Rad Laboratories ms period and that this condition was present for more than 2 seconds FOR SERVICE more than 3 C in 50 ms period and that this condition was present for more than 2 seconds FAILURE OF AMP SENSOR Amp sensor failed Failure means that Contact Bio Rad Laboratories PLEASE RETURN TO BIO RAD the sensor was deemed short open or FOR SERVICE had changed more than 3 C in a 50 FAILURE OF PS SENSOR PLEASE RETURN TO BIO RAD FOR Machine is
11. Stores all custom user protocols To avoid losing your protocols in such an event always maintain an up to date record of them In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com BIO RAD 51 52 Selecting Heated Lid Option The Heated Lid The heated lid of the Alpha unit reduces condensation of water vapor on the upper surface of reaction vessels and eliminates the need for mineral oil or paraffin as a vapor barrier Normally when a reaction is heated vapor forms and condenses on the cooler upper surfaces of the vessel Such condensation can adversely affect a reaction because as water is lost the reaction solution becomes more concentrated The heated lids maintains a higher temperature in the upper part of reaction vessels which keeps water vapor from condensing Constant Mode Programming the heated lid on the MJ Mini thermal cycler occurs in Constant Mode In Constant Mode one lid temperature value is set and the lid maintains that temperature constantly unless the block temperature goes below ambient temperature in which case the lid shuts off Constant Mode can be used in special cases such as when you want the lid temperature to be set below the highest temperature in the cycling protocol see below The default temperature setting in Constant Mode is 100 C Choosing a Lid Temperature One might expect that using a high lid temperature is always desirable to ensure that
12. When the sample block reaches the incubation temperature and when the heated lid achieves the set temperature a timer begins running on the screen To stop and start the timer press Pause Tip The Pause feature is useful if you need to temporarily remove samples that must be incubated for a precise period of time Pausing the timer while samples are not in the block allows you to track the exact duration of their incubation In the 5 call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com BIO RAD 33 94 BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Creating Programs The Elements or a Prograrri lia len ne E ee 36 Designing a New Program du e A Re A A ad 36 Entering a NEw Program aa aa qwe en hand 38 Modifying a Program Step with the Options eee 46 Revising During Programming iia AAA A AAA AAA cds 50 Deleting ai Progralm pst TR AE is peat ees cO 51 Keeping a Permanent Record of Programs 51 Selectirig a Heated Lid Option s uu sti te AA ee DER CA Ro be EA 52 35 36 The Elements of a Program MJ Mini cycler programs consist of a series of steps encoding a protocol These steps are run using one of two possible temperature control methods calculated control or block control Programs may con
13. C 92 0 Press Proceed The target temperature will move to the third line of the screen and the bottom line BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Creating Programs allows a hold time to be entered for the temperature step Enter the hold time for the step 30 seconds is used in the example below Lid 100 C Vol 20uL Note If a hold time of zero 0 is entered the MJ Mini thermal cycler will hold the block at the target temperature indefinitely Press Proceed The hold time will move to the third line of the screen and a confirmation menu will be displayed on the last line New Lid 100 C ABCD Vol 20uL 1 92 0 FOR 0 30 ES No Option Select one of the displayed choices then press Proceed Yes accepts the step and displays the Enter Menu again Use the Enter Menu to enter the next step in the program No allows reentry of the target temperature and hold time for the step Option displays the Options Menu see Modifying a Program Step with the Options p 46 Tip Avoid programming many short holds of only a few seconds each This can overheat the block causing the Heat Sink Overheated or Power Supply Overheated error messages to be displayed and triggering automatic shutdowns if the block exceeds its maximum allowable temperature Entering a Gradient Step When you reach the step at which a gradien
14. Creating Programs Select Yes to enter the step into memory and proceed to the next step select No to reject or edit the current step To preview select Option then Preview Preview gives the calculated temperature for each row ROW A 66 0 000000 64 9 000000 C 62 8 000000 0 59 9 000000 E 56 3 000000 F 53 4 000000 G 51 2 000000 50 0 000000 Editing a Gradient Step To edit a gradient step select Edit from the Main Menu The program will be displayed as follows New Lid 100 C ABCD Vol 20 1 92 0 FOR 0 30 2 50766 0 30 Use the Select keys to scroll to the step you want to edit and press Proceed At this point you will be given the option to INS Insert a step before the selected step DEL delete the highlighted step EDIT the cursor will move over the various fields you have entered for temperature and step duration both of which can be reentered and OPTION more on these options later In order to edit the gradient step highlight Step 2 and select Proceed Next select EDIT The cursor keys can be used to move between the lower temperature limit the higher temperature limit and the time hold Key in the new values then press Proceed Using the Gradient Calculator Following the analysis of a completed PCR protocol you want to discern the exact temperature at which a particularly successful reaction was run To recreate the gradient select the Tools com
15. Lid 100 C BASIC Vol 20yl 9 10 0 C FOREVER 10 END END INS End saves the changes and displays the Main Menu This ends the editing session Insert allows another step to be added just before the End step Cancelling Editing Changes To cancel all editing changes made to a program use the Select keys to move the cursor to any step number then press Cancel A confirmation screen will be displayed which will ask you whether or not you wish to save the changes you ve made Edit Lid 100 C BASIC Vol 20ul 9 10 0 C FOREVER 10 END Save changes YES No To cancel your edits select No then press Proceed All editing changes will be abandoned and the Main Menu will be displayed BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 C Utilities Locating a Stored Program ss sie A EV db S DOR ed 60 HIS UMSS oat Edu sade ole E ROREM UD Peta Ee eiu 60 Creating a Folder ora dte UE eges en Ga wd ecu Pe A 61 Assigning a Password to a Folder see wisin nie DEEE enn 61 Del tirig a Eolder ex e E RC an 62 Renaming a Folder s as eda ee ERN ESAE eR adea RE hir 63 Gopylng a Prograrti uuu oe eu Su ete eo e RID ede rt E ok YW 63 Moving A Program sa neg e t em cR Nt IR eL BINE OR we ER 64 D eletirig a Pregram 2s a ee OBS LV 64
16. Proceed The folder will be renamed and the Main Menu will be displayed Copying a Program The copy utility copies a program and gives the copy a new name Copies can be placed in the original folder or a new one To copy a program select Copy from the Files Menu then press Proceed Locate the program to be copied see Locating a Stored Program p 60 then press Proceed If more than one folder of programs is present in the machine a screen allowing you to specify the folder to which the program will be copied is displayed Copy CUSTOM to MAIN lt FOLDER1 gt lt FOLDER2 gt Select a destination folder to copy the program then press Proceed A naming screen will be displayed Copy CUSTOM1 to New Name Name the copied program see Naming the Program chapter 6 then press Proceed The program will be copied to the specified folder under the new name and the Main Menu will be displayed In the 5 call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com BIO RAD 63 64 Moving a Program To move a program select Move from the Files Menu then press Proceed Locate the program to be moved see Locating a Stored Program p 60 then press Proceed A screen listing all folders will be displayed Select the folder the program should be moved to then press Proceed The program will be moved to the new folder and the Main M
17. Protocol Running a protocol on the MJ Mini thermal cycler involves two steps 1 Choosing a stored protocol to run 2 Setting up the temperature control method Either a custom designed protocol or one of the factory installed resident protocols may be run See appendix A for descriptions of the resident protocols which may be edited to fit your needs see chapter 7 for instructions on editing stored programs All the factory installed protocols are stored in a single folder called the lt MAIN gt folder at the time of shipping Choosing a Stored Protocol to Run With the Main Menu displayed select Run then press Proceed One of two types of screen will be displayed depending on whether custom protocols have been stored in the lt MAIN gt folder or in custom folders If all protocols have been stored in the lt MAIN gt folder A screen listing the protocols will be displayed Custom protocols are listed first followed by the factory installed programs Run PROGRAMS lt MAIN gt iPRF1kb iPRF8kb iPRF15kb LONG 2 LONG 3 Use the Select keys to scroll through the listed protocols Scroll past the last or first listed protocol to see the next screen down or up Select the desired protocol then press Proceed f custom protocols have been stored in one or more custom folders A list of folders will appear on the left of the screen and a list of programs residing in these folders will appear on the right
18. S call toll free at 1 800 4BIORAD 1 800 424 6723 3 Installation Packing EOS a A SD MEM Reb REOR EE ed Setting Up the My Mini IFIStrUltmernt ker ee ee ee ere ag cken Environmental Requirements ee hrs Power Supply Requirements e etie ER bu ae E b Air Supply Requirements x esr RR CAL ae D dC edd 14 Packing Checklist After unpacking the MJ Mini thermal cycler check to see that you have received the following One MJ Mini thermal cycler Two spare fuses One power cord MJ Mini Gradient Thermal Cycler Instruction Manual this document If any of these components is missing or damaged contact Bio Rad Laboratories to obtain a replacement Please save the original packing materials in case you need to return the instrument for service Setting Up the MJ Mini Instrument The MJ Mini cycler requires minimal assembly plugging in the power cord Insert the power cord plug into its jack at the back of the machine See fig 3 for location of jack then plug the cord into an electrical outlet Environmental Requirements Ensure that the area where the thermal cycler is installed meets the following conditions for reasons of safety and performance Nonexplosive environment Normal air pressure altitude below 2000 m Ambient temperature 5 31 C Relative humidity up to 80 Unobstructed access
19. a hardware change These upgrades require return of the cycler to Bio Rad or an authorized distributor Changing the Contrast of the LCD Display You may change the contrast of the LCD display In order to do so select Contrast from the Tools Menu then press Proceed When you are presented with the Contrast Control screen you may use the right Select key to increase the LCD screen contrast and the left Select key to decrease contrast Once the display has been optimized press Proceed to accept the changes or Cancel to reject these changes Pressing either Proceed or Cancel will bring you back to the Main Menu BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Maintenance Cleaning the MJ Mini Thermal sA ai oa oa a a a E OE mm 70 Cl aning the Chassie and Block rar Yar A Act 70 Cleaning the Vents oeni a en A sn AA Aa 70 Cleaning Radioactive or Biohazardous Materials Out of the Block 70 Changing the FUSES sess ute pute Raton ura R AUR Lara 71 69 70 Cleaning the MJ Mini Thermal Cycler Cleaning the Chassis and Block Clean the outside of the thermal cycler with a damp soft cloth or tissue whenever something has been spilled on it or the chassis is dusty A mild soap solution may be used if needed Clean block wells with swabs moistened with water 95 ethanol or 1 100 d
20. back to 1 is used in this example and press Proceed A line allowing an additional number of cycles to be entered will be displayed New Lid 100 C ABCD Vol 20 1 92 0 FOR 0 30 2 50766 0 30 3 GOTO 1 ADDTNL CYCLES 44 BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Creating Programs Enter the additional number of times the program should cycle back to the step 3 is used in the example below Press Proceed The number of additional cycles will be included in the protocol and a confirmation menu will be displayed on the last line New Lid 100 C ABCD Vol 20uL 1 92 0 FOR 0 30 2 50766 0 30 3 GOTO 1 3 TIMES OK YES No Select one of the displayed choices then press Proceed Yes accepts the step and options for the next step in the protocol TEMP GRAD GOTO END No allows reentry of the step number and number of additional cycles Entering the End Step To enter the End step select End from the Enter Menu The single End screen will be displayed New Lid 100 C ABCD Vol 20 1 92 0 FOR 0 30 2 50766 0 30 3 GOTO 1 4 END OK YES No This screen automatically enters End on the next line of the screen next to a step number and displays a confirmation menu for the step on the last line of the screen Select one of the displayed choices then press Proceed Yes accepts the s
21. common access point to all programming and machine configuration screens RUN Executes a program NEW Allows new programs to be entered EDIT Allows modification of stored programs VIEW Accesses utilities that display a program s steps FILES Accesses file management utilities TOOLS Accesses machine configuration screens Using the Control Panel The control panel see fig 2 includes operation keys status indicator lights for heating and cooling an LCD window for displaying programming and machine status text and a numeric keypad for entering values into programs Operation Keys Select keys left right up down arrows Move the cursor one space or option in the LCD window Proceed Enter Accepts a selected menu or screen option during a protocol run advances the program to its next step Cancel Terminates a running protocol during program creation or editing cancels the last entry Pause Pauses a protocol during execution Instant Initiates a program that sets up the MJ Mini as a simple incubator BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Operation Screen Switches between protocol status screens the Main Menu and a time remaining display in the LCD window during a protocol run addition this button toggles between the Main Menu and the About screen for the instrument and allows the users to alternately v
22. front to back along the block for protocol optimization in a single run Integrated Hot Bonnet heated lid for oil free thermal cycling The heated lid pressure may be manually adjusted to permit the seating of different vessels Intuitive software with an easy to read interface for rapid input of programs which may contain advanced protocol steps such as auto time extension auto temperature increment and variable ramp rates Choice of calculated sample temperature control for highest speed and accuracy or block control for compatibility with protocols designed for a variety of instrument types Space saving design for easy setup and transportation Instant Incubate feature for continuous temperature incubations Customizable factory installed protocols Important Safety Information Safe operation of the MJ Mini thermal cycler begins with a complete understanding of how the machine works Please read this entire manual before attempting to operate the system Do not allow anyone who has not read this manual to operate this machine strong electrical shocks if not used according to the instructions in this manual Please read the safety warnings and guidelines at the front of this manual and exercise all precautions outlined in them Warning The Mini cycler can generate enough heat to inflict serious burns can deliver Warning Do not block the MJ Mini cycler s air vents see Figure 4 for locations Obs
23. is exacerbated when polycarbonate plates are held at high temperatures for long periods of time or when the plates are sealed for oil free thermal cycling Polypropylene Reaction Vessels Polypropylene tubes and microplates are manufactured with very thin walls to enhance thermal transfer The thin walls are somewhat fragile and can craze or develop small cracks when subject to mechanical stress Undamaged thin polypropylene tubes may also be somewhat permeable to the 355 breakdown product Either way there have been reports of 35 passing through the walls of 0 2 ml polypropylene tubes of several different brands during thermal cycling Contamination problems are rarer with 0 5 ml polypropylene tubes but instances have been reported No data are yet available on radioactive contamination with polypropylene microplates The Solution 1 Substitute the low energy beta emitter P in cycle sequencing nucleotides are not subject to the same kind of chemical breakdown as S nucleotides and they have not been associated with volatile breakdown products 2 355 must be used three things will help control contamination an oil overlay inside the tubes min eral oil in the thermal cycler outside the tubes and use of thick walled 0 5 ml tubes Always run 3S thermal cycling reactions in 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 d
24. just made will be cancelled so that another value may be entered or another menu option chosen Press Proceed after changing a value so that the program will accept it To Change Values for Earlier Steps in the Program While creating a program you may move the cursor between fields by using the Select keys This will allow you to edit temperature or time hold values in previously entered steps Position the cursor on any step number and press Cancel The previously entered value will be deleted and you may enter a new value for that field Press Proceed to continue programming In order to change the type of step that you want in the protocol e g changing a Gradient step to a standard Temperature step you must first delete the step you wish to replace and then subsequently insert the new step in its place as demonstrated below Move the cursor to the number of the step you wish to remove then press Proceed You will be presented with the Edit Menu options New Lid 100 C ABCD Vol 20uL 1 92 0 FOR 0 30 2 50766 0 30 3 GOTO 1 25 TIMES 4 END INS DEL EDIT OPTION At this point you may choose to delete the gradient step and replace it with a temperature step Use the Select keys to scroll through the options and with DEL selected press Proceed The step will be deleted and subsequent steps renumbered Press the Select keys to scroll through the program again and reinsert a Temp
25. not getting enough air or air being taken in is warmer than 31 C Contact Bio Rad Laboratories SERVICE HEATSINK HAS OVERHEATED Machine is running a protocol consisting Make sure machine gets enough air and PLEASE RETURN BIO RAD of many cycles of only a few seconds that temperature of air being taken in is FOR SERVICE each 31 C or cooler Correct air supply problems and run protocol again If error message persists contact Bio Rad or your local distributor HEATSINK HAS OVERHEATED PLEASE RETURN TO BIO RAD FOR SERVICE Machine is running a protocol consisting of many cycles of only a few seconds each Contact Bio Rad Laboratories to discuss protocol HEATSINK HAS OVERHEATED PLEASE RETURN TO BIO RAD FOR SERVICE Sensor malfunction has allowed base to heat block over its maximum allowable temperature triggering automatic protocol shutdown Unit needs servicing contact Bio Rad Laboratories to discuss protocol HEATSINK IS OVERHEATING CHECK AIR FLO See causes for HEATSINK HAS OVERHEATED See actions for HEATSINK HAS OVERHEATED 74 Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Troubleshooting Error Message Probable Cause Action MEMORY IS CORRUPT Rarely seen message indicating that memory has been corrupted Unit needs servicing contact Bio Rad or your local distributor ME
26. temperature final incubation there is no need to maintain a heated lid since evaporation is no longer an issue On this same screen you may set the default sample volume of the reactions that you wish to run in the thermal cycler You do not need to change this value each time you run a protocol with a different sample volume whenever you create a new program or decide to run a program that is stored on the thermal cycler you will be asked to input your sample volume The volume set in the Default Setting screen will appear To change any of the values on this screen use the Select keys to move the cursor over the appropriate field and enter a new value Pressing Proceed will accept the value and move the cursor to the next field Repeatedly pressing Proceed will move the cursor over all three fields and will return you to the Main Menu If you have incorrectly entered a value you may hit the Cancel key to clear the field and start again If you have already pressed Proceed and moved past the field where you incorrectly entered a value exit the Default Settings menu by entering Proceed several times until the Main Menu is displayed and then select the Tools utility and reenter the Default Settings menu Performing a Self Test The self test utility drives the instrument through a rapid battery of tests to ensure that the heat block and other components of the instrument are functional In order to perform a self t
27. the last run that was performed on the Mini thermal cycler select Tools from the Main Menu then press Proceed TOOLS LAST RUN DEFAULT SETTINGS SELF TEST GRADIENT CALCULATOR VERSION CONTRAST A list of all Tool Utilities is displayed Highlight Last Run and press Proceed A screen will be displayed with information relevant to the last run LAST RUN INCUBATE HOTLID 100 30 VOLUME ELAPSED ERRORS SOFTWARE v 1 1A Included are the program name the settings for the heated lid in the example above 100 is the programmed lid temperature in C and 30 is the block temperature at which the heated lid turns off see below the sample volume the duration of the protocol and whether any errors were encountered addition the last line of the screen displays the instrument software version To return to the Main Menu press Proceed In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com BIO RAD 65 66 Changing the Default Settings of the Heated Lid From the Tools Menu select Default Settings and press Proceed You will be presented with the following screen DEFAULT SETTINGS Lid Target 100 C Turn off Below 30 C Sample Vol 20uL You can change the temperature of the heated lid as well as the minimum block temperature below which the heated lid will automatically turn off Following a run when the block is cooling to a low
28. the samples to the programmed temperatures Block control The thermal cycler adjusts the block s temperature to maintain the block at programmed temperatures independent of sample temperature Calculated Control Calculated Control is the method of choice for most types of programs yielding the most consistent most reliable and fastest programs When using calculated control the thermal cycler maintains a running estimate of sample temperatures based on the block s thermal profile the rate of heat transfer through the sample tube or slide and the sample volume or mass Since this estimate is based on known quantities and the laws of thermodynamics sample temperatures are controlled much more accurately than with Block Control Hold times can be shortened significantly when protocols are run under Calculated Control In addition to the simple convenience of spending less time running reactions shorter protocols also help preserve enzyme activity and minimize false priming Cycling denaturations run under Calculated Control are usually optimal at 5 seconds Annealing extension steps can also be shortened but the periods for these will be reaction specific In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com BIO RAD 37 38 Calculated Control provides for shorter protocols in three ways 1 Brief and precise block temperature overshoots are used to bring samples to temperature rapidly
29. to air that is 31 C or cooler see below Protection from excessive heat and accidental spills Do not place the MJ Mini thermal cycler near heat sources such as radiators and protect it from the danger of having water or other fluids splashed on it which can cause shorting in its electrical circuits Power Supply Requirements The Mini thermal cycler requires 100 240 V 50 60 Hz and grounded outlet This cycler can use current in the specified range without adjustment so there is no voltage setting switch Power cords for outlets other than the US 120 V outlet may be purchased from computer stores since they are also used for most desktop computers and printers and meet international standard IEC 320 The power cord must be rated to carry at least 10 A at 125 V or 250 V depending on the voltage available in your nation The quality of the power cord can be further ensured by making certain it is inscribed with the trademark of UL CSA TUV VDE or another national testing agency Note Do not cut the supplied 120 V power cord and attach a different connector Use a one piece molded connector of the type specified above BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Installation Air Supply Requirements The MJ Mini thermal cycler requires a constant supply of air Air is taken in from vents at the front of the instrument is exhausted from vents at the back s
30. typographic 6 E Electromagnetic interference 5 Environmental requirements 14 F aluminized foil 21 F FCC warning 5 Fuses changing 71 G Gradient entering a gradient step 41 gradient calculator 48 66 H Hot Bonnet adjusting lid pressure 21 selecting a heated lid option 52 Increment option See Programs options types of Instant incubation 32 L Layout back view 11 bottom view 11 control panel 10 front view 10 Menus Edit Menu 54 Files Menu 60 Main Menu 18 Options Menu 46 Tools Menu 65 Microseal film 21 B adhesive seals 21 F aluminized foil 21 81 O Oil use of in block See Sample vessels Operation turning machine on 18 P Packing checklist 14 Passwords See Utilities files assigning password to folder Power cord location of jack 11 plugging in 14 Power supply requirements 14 acceptable power cords 14 Programming choosing a temperature control method 36 deleting a program 51 entering step beep option 49 end step 45 extend option 47 GoTo step 44 gradient step 41 Increment option 46 temperature step 40 initiating a program 39 modifying block control programs for calculated control 38 modifying programs designed for other machines 38 naming a program 39 revising during 50 Programs designing 36 38 choosing temperature control method See Temperature control methods translating protocol into programs 36 using GoTo steps to shorten programs 37 editing 54
31. MORY IS NEARLY FULL Protocol memory is nearly full Deleted unused protocols and folders from memory Reduce size of stored programs by using GoTo and the Inc and Ext options NO MEMORY AVAILABLE All available protocol memory storage has been filled Deleted unused protocols and folders from memory Reduce size of stored programs by using GoTo and the Inc and Ext options POWER SUPPLY OVERHEATED PLEASE RETURN TO BIO RAD FOR SERVICE Machine is not getting enough air or air being taken in is warmer than 31 C Make sure machine gets enough air and that temperature of air being taken in is 31 C or cooler Correct air supply problems and run protocol again If error message persists contact Bio Rad Laboratories POWER SUPPLY OVERHEATED PLEASE RETURN TO BIO RAD FOR SERVICE Machine is running a protocol consisting of many cycles of only a few seconds each Heatsink does not have time to dissipate heat generated by rapid cycling Eventually its maximum allowable temperature is exceeded and the protocol was terminated Contact Bio Rad Laboratories to discuss protocol POWER SUPPLY OVERHEATED PLEASE RETURN TO BIO RAD FOR SERVICE Sensor malfunction has allowed base to heat block over its maximum allowable temperature triggering automatic protocol shutdown Unit needs servicing contact Bio Rad Laboratories to discuss protocol POWER SUPPLY OVERHEATING CHECK AIR FLOW See causes for POWER SU
32. OOLS Running iPRF1kb Reading the Protocol Completion Screen When the protocol finishes a long beep sounds and the Main Menu appears From this Main Menu you may select the Screen button to review the parameters of the protocol that just finished running LAST RUN iPRF1kb HOTLID 99 30 VOLUME ELAPSED ERRORS SOFTWARE Certain error messages may also be displayed in this screen see chapter 10 Press Proceed to return to the Main Menu In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com BIO RAD 29 30 Manually Stepping Through a Protocol During a protocol run pressing Proceed allows you to advance the protocol to the next programmed step even if the machine is currently ramping the block s temperature see chapter 6 for information on ramping A confirmation screen will be displayed Running iPRF1kb Step 1 90 0 0 25 Temp 90 0 0 10 Cycle 2 of 39 Goto next step Yes No Select Yes then press Proceed The protocol will advance to its next step Pausing a Running Protocol Press Pause to temporarily stop a running program The clock will be replaced with the word Pause on the runtime protocol screen Running iPRF1kb 90 0 0 25 90 0 PAUSE 2 of 39 The samples are held at the displayed temperature until either the Pause or the Proceed key is pressed which causes the protocol run to resume
33. PPLY OVERHEATED Unit needs servicing contact Bio Rad to discuss protocol See actions for POWER SUPPLY OVERHEATED SELFTEST FAILURE PLEASE RETURN TO BIO RAD FOR SERVICE Selftest has failed Contact Bio Rad Laboratories SLOW BLOCK CYCLING PLEASE Block has not reached target Make sure machine gets enough air and RETURN ALPHA UNIT SOON temperature within expected time Unit that temperature of air being taken in is will begin beeping and will continue to 31 C or cooler Correct air supply problems beep until target temperature is reached and run protocol again If error message protocol is manually progressed to its persists contact Bio Rad Laboratories next step or protocol is halted Problem often results from machine not getting enough air or taking in air that is warmer than 31 SLOW GRADIENT PLEASE Block failed to achieve gradient in the Unit needs servicing contact Bio Rad RETURN ALPHA UNIT SOON expected time Laboratories In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com 75 76 BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Appendix Preinstalled Protocols 78 2 step Fast PCR protocol using iTaq polymerase TAQ FST Step Temp Time 1 98 0 30 2 92 0 01 3 70 0 10 4 GOTO 2 35X 5 72 0 15 6 END 2 step PCR protocol usin
34. S lt MAIN gt IPRFikb lt FOLDER1 gt PRF8kb lt FOLDER2 gt PRF15kb BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Editing Programs Select the folder containing the program you wish to edit then use the right Select key to move the cursor to the right hand menu in order to scroll through the list of programs located within that folder Select the program to be edited IPRF1kb 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 Tip To retain the original version of a program copy the program see Copying a Program chapter 8 and then edit the copy Editing the Program The first editing screen displays the lid temperature sample volume and program step Edit Lid 100 C iPRF1kb Vol 20uL 1 95 0 FOR 0 30 2 95 0 FOR 0 01 3 72 0 FOR 0 10 4 GOTO 2 35X 5 72 0 FOR 0 15 Use the Select keys to scroll up and down through the program The cursor will progressively move to the step number and the individual values for each step To change an individual value in a step position the cursor on it and type the new value then press Proceed The new value will be displayed on the screen To cancel a change press Cancel followed by Proceed The original value will be res
35. S DE CLASS A PRESCRITES DANS LE REGLEMENT SUR LE BROUILLAGE RADIOELECTRIQUE 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 the user s authority to operate the equipment Note This equipment has been tested and found to comply with the limits for a Class A digital device pursuant to Part 15 of the FCC Rules These limits are designed to provide reasonable protection against harmful interference when the equipment is operated in a commercial environment This equipment generates uses and can radiate radiofrequency energy and if not installed and used in accordance with the instruction manual may cause harmful interference to radio communications Operation of this equipment in a residential area is likely to cause harmful interference in which case the user will be required to correct the interference at his own expense Shielded cables must be used with this unit to ensure compliance with the Class A FCC limits Regarding Compliance Although this design of instrument has been tested and found to comply with Part 15 Subpart of the FCC Rules for a Class A digital device please note that this compliance is voluntary for the instrument qualifies as an Exempted device under 47 CFR 15 10 c in regard to the cited FCC regulations in effect at the time of manufacture Warranty
36. SEC OK YES No Select one of the displayed choices then press Proceed Yes accepts the step and displays the Enter Menu again Use the Enter Menu to enter the next step in the program No allows reentry of the ramp rate and finish temperature Entering a Beep Option To enter a beep select Beep from the Options Menu for a temperature step then press Proceed The word Beep will be displayed under the temperature step and a confirmation menu will be displayed on the last line Select one of the displayed choices then press Proceed New Lid 100 C ABCD Vol 20 1 92 0 FOR 0 30 2 50 0 FOR 0 30 BEEP OK YES No Option Yes accepts the Beep option and displays the Enter Menu again Use the Enter Menu to enter the next step in the program No cancels the Beep option Option displays the Options Menu again if a temperature step is being modified Use the Options Menu to enter another option for the step In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com BIO RAD 49 50 Revising During Programming To change values in a program that you are entering follow the procedures described below This editing method should be used to change just a few values at a time To make many changes or to delete or add entire steps use the Edit mode see chapter 7 To Change the Last Value Entered or Menu Option Chosen Press Cancel The choice
37. Sealing with the Hot Bonnet Lid The Hot Bonnet heated inner lid maintains the air in the upper part of sample vessels at a higher temperature than the reaction mixture This prevents condensation of evaporated water vapor onto the vessel walls and lid so that solution concentrations are unchanged by thermal cycling The Hot Bonnet lid also exerts pressure on the tops of vessels loaded into the block helping to maintain a vapor tight seal and to firmly seat tubes or the plate in the block Caps film adhesive seals or mats must be used along with the Hot Bonnet lid to prevent evaporative losses Note When tubes are cooled to below ambient temperatures a ring of condensation may form in tubes above the liquid level but below the top of the sample block This is not a cause for concern since it occurs only at the final cool down step when thermal cycling is complete Microseal A film offers a quick alternative to sealing microplates or arrays of tube strips This film is specially designed to seal tightly during cycling yet release smoothly to minimize the risk of aerosol formation and cross contamination of samples Microseal A film designed to cover a 96 well plate is easily cut for use with fewer than 96 samples Microseal adhesive seals feature an aggressive adhesive effective from 20 C to 110 C which allows secure sample storage or transport before and after cycling The clear polyester backing allows easy inspe
38. ad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Operation Turning the MJ Min Cycler Ones es ee reete Understanding the Menu zs st rein A ph i ea eed eee ted Using Me Control Panel x xt ers toss eive pe eo ab Aes adieu an ead Opening and Closing a Sample Block e ns Selecting the Correct Sample Vessel rs S aling Sample VesselS ia dag ems EUR RD RUBRA Fea XR ine Loading Sample Vessels into the Block nnn Tube Microplate and Sealing System Selection Chart Safety Warning Regarding Use of S Nucleotides 18 Turning the MJ Mini Cycler Move the power switch to o the position The fan will turn on and the Cooling Heating lights on the keyboard will flash The MJ Mini cycler will enter a self test of the heat pumps Note Ifthe sample block or the heat sink is not at ambient temperature typically because the sample block was recently in use the machine will skip the self test If the self test does not detect any problems the Main Menu is displayed Alternatively depressing the Screen button will bring you to the main screen RUN VIEW NEW FILES EDIT TOOLS Block is idle The MJ Mini cycler is now ready to execute programs Understanding the Main Menu The Main Menu is the
39. adding an option 56 cancelling editing changes 58 deleting a step 56 editing a step 56 editing in graphical mode 57 inserting new step 56 saving edited program 58 options types of 36 program steps types of 36 renaming See Utilities file Protocols and power failure 32 factory installed 26 78 manually stepping through 30 pausing while running 30 running choosing protocol to run 26 reading completion screen 29 reading runtime screen 28 setting up temperature control method 27 stopping while running 31 5 Safety general instructions 8 guidelines for safe use 4 warnings 4 Sample block closing 19 maximum rate of heating and cooling 12 opening 19 Sample vessels ensuring good thermal contact 22 loading into block 22 sealing reason for 20 with Hot Bonnet and Caps Film 21 with oil or wax 20 selection 19 0 2ml tubes 20 0 5ml tubes 20 microplates 20 selection chart 23 use of oil to improve thermal contact with block 22 Self test 18 66 Setting machine up 14 Specifications 12 gradient specifications 12 I Temperature control methods block control 37 calculated control 37 Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Index U Utilities file assigning password to folder 61 copying a program 63 creating a folder 61 deleting a program 64 deleting a folder 62 moving a program 64 renaming a program 64 tools changing the contrast of the LCD display 68 ch
40. anging the default settings of the heated lid 66 determining the software version 68 gradient calculator 66 performing a self test 66 viewing the last program run 65 Warranties 5 In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com BIO RAD 83 Life Science Group Bulletin 10968 Rev US EG Bio Rad Laboratories Inc Web site www bio rad com USA 800 4BIORAD Australia 61 02 9914 2800 Austria 01 877 89 01 Belgium 09 385 55 11 Brazil 55 21 3237 9400 Canada 905 364 3435 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 Germany 089 318 840 Greece 30 210 777 4396 Hong Kong 852 2789 3300 Hungary 36 1 455 8800 India 91 124 4029300 Israel 03 963 6050 Italy 39 02 216091 Japan 03 6361 7000 Korea 82 2 3473 4460 Mexico 52 555 488 7670 The Netherlands 0318 540666 New Zealand 0508 805 500 Norway 23 38 41 30 Poland 48 22 331 99 99 Portugal 351 21 472 7700 Russia 7 495 721 14 04 Singapore 65 6415 3188 South Africa 27 861 246 723 Spain 34 91 590 5200 Sweden 08 555 12700 Switzerland 061 717 95 55 Taiwan 886 2 2578 7189 United Kingdom 020 8328 2000 09 0459 0809 Sig 0308
41. ay be marked with a colored marking pen or piece of tape Note As an aid in gauging how much the thumbwheel 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 at least one empty tube in each corner of the block to ensure that the Hot Bonnet lid exerts even pressure on the sample tubes see Adjusting the Hot Bonnet Lid s Pressure above To ensure uniform heating and cooling of samples sample vessels must be in complete contact with the block Adequate contact is ensured by always doing the following Ensure that the block is clean before loading samples see chapter 9 for cleaning instructions Firmly press individual tubes or the microplate into the block wells Using Oil to Thermally Couple Sample Vessels to the Block With two exceptions See below Bio Rad does not recommend using oil to thermally couple sample vessels to the block for the following reasons Calculated control protocols do not run accurately when oil is used Oil traps dirt which interferes with thermal contact between vessels and the block Calculated control protocols do not run accurately when oil is used Oil traps dirt which interferes with thermal contact between vessels and the block Caution If you use oil in the block use only mineral oil Never use silicone oil It can dama
42. come clogged with dust and debris airflow to the sample block s heat sink is hampered causing performance problems related to overheating The air intake vents are particularly likely to collect dust since their holes are much smaller than those of the air exhaust vents Tip To prevent problems with overheating institute a regular program of checking for dust buildup Cleaning Radioactive or Biohazardous Materials Out of the Block When cleaning machines that have been running radioactive or biohazardous reactions consult your institution s radiation safety officer or biosafety officer regarding cleaning methods monitoring and disposing of contaminated materials BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Maintenance Changing the Fuses The circuits in the MJ Mini cycler are protected by two fuses 6 3 A fast acting 5 x 20 mm When a fuse blows the thermal 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 run when the fuse is replaced and power restored See Resuming a Protocol After a Power Outage chapter 5 Warning The MJ Mini cycler incorporates neutral 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 thermal cycler base You could receive a
43. ction of sample wells Microseal B clear adhesive seals are ideal for thermal cycling in all polypropylene and polystyrene microplates Microseal B adhesive seals can be easily cut for use with fewer than 96 samples Microseal F aluminized foil acts as a barrier against evaporation from 20 C to 105 C In addition to cold storage applications it can also be used for thermal cycling sample volumes gt 25 ul The foil is thin enough to pierce with a pipet tip for recovery of sample from individual wells Microseal F foil is easily cut for use with fewer than 96 samples Adjusting the Hot Bonnet Lid s Pressure The pressure exerted by the Hot Bonnet lid must be manually adjusted to fit the sample vessels being used Once set the Hot Bonnet lid can be opened and closed repeatedly without readjustment as long as neither the tube or microplate type nor the sealing method is changed Any change in vessel type or sealing method requires readjustment of the Hot Bonnet lid Follow these steps to adjust the pressure exerted by the inner lid 1 Make sure the block s wells are clean Even tiny amounts of extraneous material can decrease ther mal conductance and interfere with the proper seating of a microplate or tubes 2 Open the Hot Bonnet lid Turn the thumbwheel all the way counterclockwise to completely raise the inner lid 3 Load either a microplate or at least eight individual tubes into the sample block The inner l
44. e and sample volume Entering the program s steps Entering the End step Note Entering a new program occurs Textual Mode Graphical Mode Edits to previous saved program can take place in Graphical Mode See Chapter 7 for more information on editing in Graphical Mode Each step involves entering values from the keyboard or making selections from a menu Programs may be edited as they are being entered Programs are automatically saved when the End step is entered They are stored in the lt MAIN gt folder unless folders have been created for them BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Creating Programs Initiating the Program To initiate a new program select NEW from the Main Menu then press Proceed A naming screen will be displayed Lid 100 C Vol 20ul Naming the Program Name the program an eight character word consisting of any combination of letters and numbers Press the up Select key to scroll forward and the down Select key to scroll backward through the alphabet When the character needed is displayed next to Name press Proceed The character will be accepted and the cursor will move one space to the right Numbers and periods may also be inserted by pressing the corresponding keys on the keypad After any of these buttons are pressed the cursor automatically moves to the right You may use
45. e protocol in memory for a minimum of 24 hours to a maximum of 7 days depending on environmental conditions When power is restored the protocol will begin running from the point at which it was interrupted and a notice about the power interruption will be displayed The notice will identify the step and the cycle at which the power failure occurred as well as the block s temperature at the time power was restored Running A C POWER FAILED CYCLE 1 STEP 1 RECOVERED AT 46 8 PRESS PROCEED TO CONTINUE Press Proceed to remove this screen The protocol s diagrammatic screen will immediately be displayed Using the Instant Incubation Feature The MJ Mini cycler may be converted to a constant temperature incubator by pressing Instant A screen allowing use of the heated lid will be displayed INCUBATE Use heated lid Yes NO Use the Select keys to enable or disable the heated lid then press Proceed A screen allowing entry of the incubation temperature will be displayed Incubate to 75 0 Use the keypad to enter any incubation temperature from 0 C to 99 9 C then press Proceed The thermal cycler will incubate the sample at the specified temperature until Cancel is pressed BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Running Protocols Incubating to 75 0 STEP 1 75 0 FOREVER TEMP 75 0 Preheating Lid
46. e the bottom row represents the front row of the block ROW A 570 000000 B 56 5 000000 55 6 000000 D 543 000000 52 8 000000 51 5 000000 50 5 000000 50 0 000000 noting at which temperature successful reactions were run at users are able to convert gradient programs to non gradient programs by using the temperatures in subsequent runs In the 5 call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com BIO RAD 67 68 Determining the Software Version Number At times it is necessary to determine which version of software is installed on your Mini cycler e g to report a problem to Bio Rad technical support To do this select Version from the Tools Menu then press Proceed The current version number will be displayed VERSION 1 1Ci CTRL Ci EXEC Ci EDIT Ci COMM Ci FILE ERRS Ci PORT Ci GRPH Ci The top line reports the software version number 1 1Ci in the example The other four lines refer to the eight pages that the software has been broken into and their associated versions Ci in the example Bio Rad periodically updates the software to incorporate new features Most upgrades are available free of charge for units under warranty and may be installed into a MJ Mini cycler electronically from a desktop computer Contact your Bio Rad sales representative or an authorized distributor for details Occasionally upgrades may require
47. e to edit a program in graphical mode however the editing that can be performed is limited to changing value fields such as incubation temperatures hold times number of GoTo loops In graphical mode you are unable to insert or delete steps nor can you add options to temperature steps However for changing values in a program s steps graphical editing is a rapid way to accomplish this As mentioned on p 55 saving a stored program under a new name allows you to build a new protocol off an existing one without losing the original To edit a program graphically select Edit from the Main Menu You will be presented with a Text Mode display of the protocol steps Edit Lid 100 C IPRFikb Vol 20uL 1 95 0 FOR 0 30 2 95 0 FOR 0 01 3 72 0 FOR 0 10 4 GOTO 2 35 5 72 0 FOR 0 15 Use the Select keys to scroll past the header fields of the lid temperature and the sample volume fields Once the cursor is placed over a step in the protocol you may use the Screen button to display the program graphically 95 0 0 30 Protocols are listed in an abbreviated manner with each step listed on the left Use the Select keys to scroll up and down through the steps As the cursor moves over the various temperature steps the duration of each step is listed at the top of the second column When a Golo step is highlighted the second column displays the step number that the cycler will return to as well as the number of t
48. ed to certain program steps to modify their effects 1 Increment Modifies a temperature step to allow a progressive increase or decrease of temperature 0 1 10 0 C per cycle each time the step is executed in a cycle This is useful in touchdown pro grams when the annealing temperature of an oligonucleotide is not known 2 Extend Modifies a temperature step to allow progressive lengthening or shortening of a temperature Step hold by 1 60 sec cycle each time a step is executed in a cycle This is useful for accommodat ing an enzyme with diminishing activity 3 Beep Modifies a temperature step to make the machine beep when the target temperature is reached Designing a New Program Translating a Protocol into a Program Until you are completely familiar with programming the MJ Mini cycler you may find it helpful to first translate the protocol into 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 If a protocol step involves an option as well as a program step write both names down on the same line Finally write the End step at the bottom of the list programs will not run without this step Number the lines 1 through N where N is the final End line BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Creating Programs Us
49. ee fig 4 If the air supply is inadequate or too hot the machine can overheat causing performance problems software error messages particularly HS Overheating and Slow Block Cycling and even automatic shutdowns Ensuring an Adequate Air Supply Do not block the air intake vents Position the Mini thermal cycler at least 10 cm from vertical surfaces and other thermal cyclers greater distances may be required see below Do not put loose papers under or in front of the machine they can be sucked into the air vents and cause problems Do allow dust or debris to collect in the air intake vents The air vents are particularly liable to collect dust and debris sometimes completely clogging up Check for dust and debris every few months and clean the intake vents as needed Remove light collections of dust with a soft bristle brush or damp cloth Severe collections of dust and debris should be vacuumed out Turn the machine off prior to cleaning or vacuuming air vents Ensuring That Air 15 Cool Enough Do not position two or more thermal cyclers so that the hot exhaust air of one blows directly into the air intake vents of another Make sure the MJ Mini thermal cycler receives air that is 31 C or cooler by measuring the temperature of air entering the machine through its air intake vents Air intake vents are located at the front of the machine see fig 4 Place the thermal cycler where you plan to use
50. enu will be displayed Deleting a Program To delete a program select Delete from the Files Menu then press Proceed Locate the program to be deleted see Locating a Stored Program p 60 then press Proceed A confirmation screen will be displayed Delete ABCD Delete program YES No Select Yes then press Proceed The program will be deleted and the Main Menu will be displayed To cancel the deletion press Cancel or select No and press Proceed Renaming a Program To rename a program select Rename from the File Menu then press Proceed Locate the program to be renamed see Locating a Stored Program 60 then press Proceed A naming screen will be displayed Rename CUSTOM1 New name A Name the new program see Naming the Program chapter 6 then press Proceed The program will be renamed and stored and the Main Menu will be displayed BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Using the Utilities Tools Utilities Use these utilities available under Tools to accomplish the following tasks View the last program run on the instrument View and or change the default settings of the heated lid Perform a self test Use the gradient calculator Check the software version of the instrument Change the contrast of the instrument screen Viewing the Last Program Run To view
51. erature This mode offers more efficient temperature cycling of the reactants and can lead to reduced protocol times since generally 5 10 seconds can be shaved off each temperature incubation step In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com BIO RAD 39 40 To enter Block Temperature Control Mode simply enter 0 in the Sample Vol field In Block Control mode temperature ramping will proceed at maximum ramp speed without the temperature overshoots unless otherwise specified Note When using 0 5 ml tubes we recommend a minimum sample volume of 20 Entering the Program s Steps Once these header fields have been filled you will be able to begin entering your steps You are presented with two options from the Edit Menu New Lid 100 C ABCD Vol 20uL 1 TEMP GRAD TEMP enters a temperature step GRAD enters a gradient step Entering a Temperature Step To enter a temperature step select Temp then press Proceed The first Temp screen will be displayed New Lid 100 C ABCD Vol 20uL The third line of this screen shows the number of the step being programmed 1 is used in the example above The last line of the screen allows a target temperature in degrees Celsius to be entered for the step Use the keyboard to enter any number between O and 99 9 as the target temperature 92 0 is used in the example below Lid 100 C Vol 20uL Temp
52. est simply select the Self Test option from the Tools Menu Upon completion of the self test the Main Menu is displayed If the instrument displays an error or failure message you should contact Bio Rad technical support Gradient Calculator The Gradient Calculator tools allows users to visually recreate the temperature gradient that was used in a gradient cycling reaction From this users can learn the exact annealing temperature that resulted in a successful amplification reaction To visualize the temperature gradient select the Gradient Calculator option from the Tools Menu The first screen will ask you to enter the low end temperature for the gradient BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Using the Utilities GRADIENT CALCULATOR LOWER TEMP C Enter the lower temperature keeping in mind that the lowest value for the gradient is 30 and press Proceed You will then be asked to enter the upper temperature for the gradient GRADIENT CALCULATOR LOWER TEMP C 50 0 UPPER TEMP Enter the lower temperature keeping in mind that the highest value for the gradient is 90 C and that the difference between the upper and lower temperature limits cannot exceed 16 C and press Proceed The following screen will display the temperature used in each row of the sample block The top row corresponds to the back row of the sample block whil
53. etection methods and cleaning procedures for this isotope Consult your radiation safety officer for his or her recommendations If mild cleaning agents do not remove radioactivity harsher cleaners may be used occasionally and carefully Users have suggested the detergent PCC 54 Pierce Chemical Co Rockford Illinois Pierce Eurochemie B V Holland Micro Cleaning Solution Cole Parmer Niles Illinois and Dow Bathroom Cleaner available in supermarkets 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 N surface finish of the blocks 24 BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Running Protocols B nnirig a Protocol es eor SER Lut c tte Er odit e D us 26 Reading he RUNTIME CIS acies AA A RM EEEE 28 Reading the Temperature Display 5 28 Reading the Protocol Completion Screen ooooccccocccooo nenn 29 Manually Stepping Through a Protocol s 30 Pana m Running Protocols pane dee cl Ge ees doth palate AAA 30 Stopping a RUNNING PFOTOCOM tal nalen oR dele hou 31 Resuming a Protocol After a Power Outage oss se e peeta enn 32 Using the Instant Incubation Feature so teiaa E o T eee 32 25 26 Running a
54. g iProof high fidelity polymerase for small intermediate and long templates iPRF1kb Step Temp Time 1 95 2 00 2 95 05 3 72 30 4 GOTO 2 20X 5 72 10 00 6 END iPRF8kb Step Temp Time 1 95 2 00 2 95 05 3 72 4 00 4 GOTO 2 20X 5 72 10 00 6 END iPRF15kb Step Temp Time 1 95 2 00 2 95 05 3 72 7 30 4 GOTO 2 20X 5 72 10 00 6 END Standard 2 step PCR protocol STD 2 Step Temp Time 1 95 4 00 2 95 30 3 65 30 4 GOTO 2 30X 5 4 6 END Standard 3 step PCR protocol STD 3 Step Temp Time 1 95 4 00 2 95 30 3 55 30 4 72 30 5 GOTO 2 30X 6 72 7 00 7 4 8 Touchdown PCR protocol TCHDOWN Step Temp Time 1 95 4 00 2 95 30 3 60 30 Increment 0 5 C cycle 4 72 30 5 GOTO 2 30X 6 95 30 7 45 30 8 72 30 9 GOTO 6 30X 10 72 7 00 11 4 12 Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 2 step RT PCR protocol RTPCR 2 A Preinstalled Protocols 3 step nested primer protocol Step Temp Time 1 37 60 00 2 95 5 00 3 95 30 4 65 30 5 GOTO 3 40X 6 72 7 00 7 4 8 3 step RT PCR protocol RTPCR 3 Step Temp Time 1 37 60 00 2 95 5 00 3 95 30 4 55 30 5 72 30 6 GOTO 3 40X 7 72 7 00 8 4 9 END 2 step nested primer protocol NEST PR2 Step Temp Time
55. ge the sample block One exception to this recommendation involves the use of volatile radioactive 35S nucleotides A small amount of oil in the block can help prevent escape of these compounds See page 24 for important information regarding safe use of these compounds in polypropylene tubes and polypropylene and polycarbonate microplates A second exception involves the use of thick wall 0 5 ml tubes Certain brands of these tubes fit poorly in the block in which case oil may somewhat improve thermal contact Whenever possible use high quality thin wall tubes intended for thermal cycling see page 23 for a tube and plate selection chart 22 BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Tube Microplate and Sealing System Selection Chart Operation The following sample vessels and sealing options are recommended for use with the MJ Mini thermal cycler These items are available from Bio Rad Laboratories Key Reaction vessel fits block sealing option fits reaction vessel without modification gt Reaction vessel sealing option can be cut to fit Table 2 Compatible sample vessels and sealing options Thermal Cycler Reaction Vessels Sealing Options for Oil free Cycling Microseal Microseal Microseal Chill out Bio Rad A Film B Seal F foil Strip caps wax MJ Mini Description Catalog MSA 5001 MSB 1001 MSF 1001 TCS se
56. he 0 5 ml tubes does not allow them to be accommodated in adjacent wells the tubes should be placed in a staggered fashion i e in every other well in the block The tubes should NOT be placed in the spaces between wells Furthermore placement of tubes in the peripheral wells along the edge of the cycler block should be avoided as this may result in compromised amplification due to condensate formation For correct placement of 0 5 ml tubes see Figure 5 When using 0 5 ml tubes thin walled tubes are recommended these are specifically designed for thermal cycling and the higher quality brands provide a good and consistent fit If thick walled 0 5 ml tubes are used ensure that they fit the wells snugly Since these tubes were originally designed for centrifuges some brands may not fit tightly in thermal cycler wells Both thin and thick walled 0 5 ml tubes are available from Bio Rad Figure 5 Wells in which 0 5 and are designed for precise block fit ml tubes should be placed In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com BIO RAD 19 20 Thin Walled Vs Thick Walled Tubes The thickness of sample tubes directly affects the speed of sample heating and thus the amount of time required for incubations Thick walled tubes delay sample heating since heat transfers more slowly through the tubes walls For the earliest types of thermal cyclers this delay mattered little These machine
57. he right Copy lt MAIN gt IPRFikb lt FOLDER1 gt PRF8kb lt FOLDER2 gt iPRF15kb With the appropriate folder on the left side of the screen selected use the right Select key to move the cursor to the second column and toggle up and down to select the appropriate program name then press Proceed File Utilities Use these utilities available from the Files Menu to accomplish the following tasks Create new folders in which to store programs Secure delete or rename existing folders Copy delete or rename existing programs Move a program between folders Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Using the Utilities To display the Files Menu select Files from the Main Menu then press Proceed lt FOLDERS gt PROGRAMS NEW COPY SECURE MOVE DELETE DELETE RENAME RENAME Creating a Folder The MJ Mini cycler can each hold programs in a number of folders including the lt MAIN gt folder New programs are placed in the lt MAIN gt folder by default unless a different folder is specified To create a folder select NEW from the Files Menu then press Proceed A naming screen will be displayed New Folder Name A Name the folder using the instructions found under Naming the Program in chapter 6 then press Proceed The name will be assigned to the new folder the folder will be stored and the Ma
58. his symbol identifies components that pose a risk of personal injury or damage to the instrument if improperly handled CAUTION Risk of Electrical Shock This symbol identifies components that pose a risk of electrical shock if improperly handled CAUTION Hot Surface This symbol identifies components that pose a risk of personal injury due to excessive heat if improperly handled Safety Warnings and Guidelines Warning Operating the Mini Peltier thermal cycler before reading this manual can con stitute a personal injury hazard Only qualified laboratory personnel trained in the safe use of electrical equipment should operate this machine heat pump sample block or other accessory Doing so will void your warranties and can put you at risk for electrical shock Return the MJ Mini cycler to the factory US customers or an authorized distributor all other customers if repairs are needed Warning Do not open or attempt to repair the MJ Mini cycler base the power supply the to cause burns or cause liquids to boil explosively Wear safety goggles or other eye protection Warning The sample blocks can become hot enough during the course of normal operation at all times during operation be available inside the machines even when a fuse has blown or been removed Never open the cycler base you could receive a serious electrical shock Opening the base will also void your warranties Warning The Mini cycler incor
59. id pivots around a central point so it is important to distribute individual tubes evenly load at least four tubes in the center of the block and at least one tube in each of the four corners of the block If using a sealing film or mat apply it to the loaded microplate according to the manufacturer s directions 4 Close the Hot Bonnet lid by pressing down on the top lever Turn the thumbwheel clockwise to lower the inner lid onto the loaded microplate tubes The thumbwheel turns easily at first since the inner lid has not yet come into contact with anything Stop turning the thumbwheel when you feel increased resistance which indicates that the inner lid has touched the microplate tubes In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com RAD 21 5 For microplate sealing films or mats that require additional pressure turn the thumbwheel clockwise an extra half turn past the point of initial contact to set an appropriate lid pressure Caution 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 An extra half to three quarters of a turn ensures the correct pressure for most types of reaction vessels Some empirical testing may be required to determine the optimum pressure required for certain vessels Once this pressure has been determined the thumbwheel position m
60. iew the text and graphical programming screens Status Indicator Lights Block Status lights Indicate whether the sample block is heating red light is illuminated or cooling blue light is illuminated Opening and Closing a Sample Block Grip the front handle of the Hot Bonnet heated lid and pull upward firmly The top lever will pop open to reveal the entire thumbwheel Continue pulling upward to open the Hot Bonnet lid The Hot Bonnet lid will tio backward revealing the entire block Caution Do not pull on the thumbwheel to open the unit This can damage the closing mechanism of the Hot Bonnet lid To close the sample block press down on the top lever The lever will close down over the thumbwheel as the Hot Bonnet lid closes down over the sample block A click signifies that the lid s latch has engaged Selecting the Correct Sample Vessel The MJ Mini cycler accepts both 0 2 ml and 0 5 ml tubes as well as 48 well microplates Keep in mind that differences in tube and plate composition and wall thickness among the many brands available can affect reaction performance Protocols may require some adjustment to ensure optimum performance when using a new vessel type Bio Rad offers a full range of tubes and microplates manufactured to the specifications of the sample block of MJ Mini cycler See Table 2 for a complete list 0 5 ml Tubes It is possible to load up to twelve 0 5 ml tubes in the MJ Mini cycler Since the width of t
61. ilution of bleach in water If using bleach swab wells with water afterward to remove all traces of bleach Clean spilled liquids out of the block as soon as possible dried fluids can be difficult to remove Do not clean the block with caustic or strongly alkaline solutions e g strong soaps ammonia bleach at a higher concentration than specified above These will damage the block s protective anodized coating possibly causing electrical 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 chapter 4 clean the wells whenever the oil has become discolored or contains particulate matter Use a swab to determine whether cleaning is needed Clean the block with 95 ethanol as described above Oil buildup must be prevented Old oil harbors dirt which interferes with vessel seating and diminishes thermal coupling of sample vessels to the block Caution Do not pour any cleaning solution into the block s wells and then heat the block in an attempt to clean it Severe damage to the block the heated lid and the chassis will result Cleaning the Air Vents Clean the air intake and exhaust vents with a soft bristle brush a damp cloth or a vacuum cleaner whenever dust is visible in them The air intake vents are located on the bottom and on both sides of the machine the air exhaust vents are located on back sides see figs 3 and 4 If these vents be
62. imes that this loop will be repeated see below As you scroll through the program certain steps in the graphical display become highlighted to show the user what step is being referenced With GoTo steps the dotted line running under the graphical display becomes animated indicating that this step is selected 94 0 2 35x 95 0 95 0 72 0 GOTO 72 0 In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com BIO RAD 57 58 To change the value of any step highlight that step and retype the numeric value Select Proceed to accept the changes In order to change the time of a particular step select the temperature step and then use the right Select key to move the cursor over the time field Enter a new time and then press Proceed With a GoTo step you can edit both the GoTo step number as well for the number of times the loop will be repeated To exit the graphical mode press the Screen key again You will return to the text display of the protocol From here you can continue to edit the protocol more extensively or you may choose to save or cancel your edits as described below Saving an Edited Program To save an edited program use the right Select key to scroll to the End step of the program Position the cursor on the number for that step then press Proceed A line allowing the editing session to end will be displayed on the last line of the screen Edit
63. in Menu will be displayed Assigning a Password to a Folder Protocols in a password protected folder cannot be edited renamed or deleted nor can new protocols be placed in the folder without the password Users without knowledge of the password can still run copy and view a program Note A password cannot be assigned to the lt MAIN gt folder To assign a password to a folder select SECURE from the Files Menu then press Proceed A list of all folders in the machine will be displayed Select the desired folder other than lt MAIN gt then press Proceed The password assignment screen will be displayed Secure lt FOLDER1 gt New password In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com BIO RAD 61 62 Valid passwords consist of numbers up to four digits long For passwords of three digits or less press Proceed after the password has been entered Passwords four digits long will be automatically accepted as soon as the last digit is typed and the Main Menu will be displayed Passwords can be changed at any time Follow the steps described above to select the desired folder then press Proceed screen asking for the old password will be displayed Secure lt FOLDER1 gt Old password Enter the old password Again if the password is less than four digits in length press Proceed after entering the final digit of the password and you wi
64. ing the GoTo Step to Write Short Programs The GoTo step allows programs of many repetitious steps to be shortened to just a few lines When the program encounters a GoTo step it returns to a specified step repeats that step and repeats all steps that follow back to the GoTo step When the program has returned or cycled back to the step a specified number of times the program moves on to the step that follows the GoTo step For example consider a basic cycle sequencing protocol consisting of 30 repeats of a denaturation and an annealing extension step Rather than listing all 60 steps use a GoTo step to design a short easy to enter program Raw program Thermal cycler program 1 92 for 30 sec 1 92 for 30 sec 2 60 for 3 min 2 60 for 3 min 92 for 30 sec 3 GoTo step 1 29 times i e cycle back to step 1 4 60 for 3 min and repeat steps 1 and 2 29 times 5 92 for 30 sec 4 End 6 60 for 3 min 7 92 for 30 sec continues for total of 60 lines Choosing a Temperature Control Method The MJ Mini cycler can control block temperature in two possible ways and both have different implications for the speed and accuracy of sample heating Calculated control The thermal cycler adjusts the block s temperature to maintain samples of a specific volume in a specific vessel type at programmed temperatures This includes optimized overshoots of the block by a few degrees for a few seconds which bring
65. it and turn it on Try to reproduce what will be typical operating conditions for the machine in that location particularly any heat producing factors e g nearby equipment running window blinds open lights on Run a typical protocol e g BASIC for 30 minutes to warm up the cycler then measure the air temperature at the air intake vents If more than one machine is involved measure the air temperature for each If the air intake temperature of any machine is warmer than 31 C use table 1 to troubleshoot the problem Some experimentation may be required to determine the best solution when more than one cause is involved After taking steps to solve the problem verify that the temperature of the air entering the air intake vents has been lowered using the procedure outlined above Table 1 Troubleshooting air supply problems Cause Possible Remedies Air circulation is poor Provide more space around machine or adjust room ventilation Ambient air temperature is high Adjust air conditioning to lower ambient air temperature Machine is in warm part of room Move machine away from or protect machine from such heat sources as radiators heaters other equipment or bright sunlight Machines are crowded Arrange machines so that warm exhaust air does not enter intake vents In the 5 call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com BIO RAD 15 16 BIO RAD Visit on the Web at www bio r
66. last line Select one of the displayed choices then press Proceed New Lid 100 C ABCD Vol 20uL 1 92 0 FOR 0 30 2 50 0 FOR 0 30 1SEC CYCLE OK YES No Option Yes accepts the Ext value and displays the Enter Menu again Use the Enter Menu to enter the next step in the program No allows reentry of the Ext value Option displays the Options Menu again Use the Options Menu to enter another option for the step Entering a Rate Option To enter a rate step select Rate from the Options Menu The first Ramp screen will be displayed New Lid 100 C ABCD Vol 20 1 92 0 FOR 0 30 2 50 0 FOR 0 30 C SECOND The bottom line of this screen allows a ramp rate in degrees Celsius per second to be entered for the step Use the keyboard to enter any rate up to 2 5 C sec 1 0 C sec is used in the example below BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Creating Programs New Lid 100 C ABCD Vol 20 1 92 0 FOR 0 30 2 50 0 FOR 0 30 C SECOND Note Ifa ramp rate faster than the cycler s maximum rate of heating and cooling is entered the maximum rate will be used Press Proceed The ramp rate will be incorporated under the temperature step is modifies and a confirmation menu will be displayed on the last line New Lid 100 C ABCD Vol 20 1 92 0 FOR 0 30 2 50 0 FOR 0 30 RAMP 1 0
67. lete from the Edit Menu then press Proceed The step will immediately be deleted and the program being edited will be displayed again minus the deleted step To cancel a deletion see Cancelling Editing Changes p 58 Note Be careful when using Delete Once a step has been deleted it cannot be recovered without abandoning all editing changes that have been made in the program This could be inconvenient if the program has been extensively edited Editing a Step Selecting to edit a step allows the fields of that step to be edited in the same manner as if you were scrolling through the protocol using the Select keys Pressing Proceed will likewise allow you to continue to step through all fields in the program Adding an Option To add an option to a step select Option from the Edit Menu then press Proceed The Option Menu will be displayed for the step and include step temperature increments step time extensions ramp rates and beep option Add the desired option to the step see Modifying a Program Step with the Options chapter 6 When the option is complete select Yes from the confirmation menu then press Proceed The steps of the program being edited will be displayed again with the new option appearing in the list BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Editing Programs Editing a Program in Graphical Mode It is possibl
68. ll be brought to the password assignment screen If the password is four digits long the password will automatically be accepted when the fourth digit is entered and the password assignment screen will appear Enter the new password as described above The new password will be assigned to the folder and the Main Menu will be displayed again Deleting a Folder A folder must be empty before it can be deleted After all programs have been moved or deleted from the folder select Delete from the left side of the Files Menu then press Proceed A list of all folders in the machine will be displayed Select the folder to be deleted then press Proceed A confirmation screen will be displayed Delete folder lt FOLDER1 gt lt FOLDER2 gt Erase folder YES No Select Yes then press Proceed The folder will be deleted and the Main Menu will be displayed To cancel the deletion press Cancel or select No and press Proceed BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Using the Utilities Renaming a Folder To rename a Folder select Rename from the left side of the File Menu then press Proceed Select the Folder to be renamed and press Proceed A naming screen will be displayed Rename FOLDER1 New name A Note The lt Main gt folder cannot be deleted Name the new folder see Naming the Program chapter 6 then press
69. mand from the Main Menu and then press the Proceed key You will see a list of Tools features TOOLS LAST RUN DEFAULT SETTINGS SELF TEST GRADIENT CALCULATOR VERSION CONTRAST In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com BIO RAD 43 Select Gradient Calculator and press the Proceed key You will asked to enter the LOWER TEMP C Enter lower limit temperature of the gradient using the number keys and then press the Proceed key You will then be asked to enter the UPPER TEMP C Enter the upper temperature for the gradient using the number keys and Proceed key The following screen will be displayed ROW A 66 0 000000 64 9 000000 C 62 8 000000 0 59 9 000000 56 3 000000 53 4 000000 G 51 2 000000 50 0 000000 Press Proceed to return to the Main Menu Entering a GoTo Step When programming the MJ Mini cycler the option to include a GoTo step becomes available only after a temperature step has been included In other words a GoTo step cannot be the first step of a protocol To enter a GoTo step select GoTo from the Enter Menu The first GoTo screen will be displayed New Lid 100 C ABCD Vol 20uL 1 92 0 FOR 0 30 2 50766 0 30 3 GOTO GOTO STEP 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
70. no condensation occurs But in some circumstances if the lid temperature is too high it can increase the temperature of the reaction Optimizing lid temperature therefore requires finding a balance between preventing condensation and raising reaction temperature The optimal lid temperature for a given experiment will be affected by the reaction volume and the height of the vessel specifically the amount of surface area that rises above the heated block For tall vessels that have a large surface rising above the heated block the greater potential for condensate formation dictates that lid temperatures should be higher When using low profile vessels with reaction volumes approaching the maximum for the vessel e g 50 100 ul in 96 well plates 15 30 ul in 384 well plates the proximity of the reaction solution to the lid means lid temperatures should be lower For very small reaction volumes lt 5 ul the need to limit condensation generally outweighs potential lid effects on reaction temperatures so the lid temperature should be higher Note When using 0 5 ml reaction vessels we recommend a heated lid temperature of 110 C BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Editing Programs Eding a Ster d Pregratmi s sss d east Sc EVO A De 54 Editing a Program n Graphical per ee pie ee rer 57 Saving an Edited Program scs bera a DRA eve o
71. o Gee aww 58 Cancelling Editing Changes iS to Roe Ret bou ehe eR anew 58 53 54 Editing a Stored Program The editing tools available through Edit on the Main Menu make it easy to extensively edit stored programs by Changing individual values in program steps Adding new steps Deleting steps Adding options to temperature steps Note The editing tools do not include a renaming function To create a new program from a stored program begin by copying the program and saving it with a new name see Copying a Program Chapter 8 Note If you only need to change the lid temperature or the sample volume you may do this at the start of any standard run Initiating Editing To initiate editing select Edit from the Main Menu then press Proceed One of two types of screen will be displayed depending on whether your programs have been stored in the lt MAIN gt folder or in custom folders If all programs have been stored in lt MAIN gt The screen will list the contents of lt MAIN gt Edit PROGRAMS lt MAIN gt iPRFikb iPRF8kb IPRF15kb TAQ FST LONG 2 Select the program to be edited then press Proceed If programs have been stored in custom folders The screen will list all the folders residing in the machine on the left hand side As you move your cursor over the list of folders a list of programs that resides in each folder is displayed on the right screen Edit PROGRAM
72. oll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com RAD 27 28 Reading the Runtime Screen When a protocol is running a runtime screen will be displayed Running iPRF1kb Step 1 95 0 2 00 Step 2 92 0 0 01 Step 3 70 0 0 10 The screen lists the protocol name IPRF1kb in the example above protocol step that is running Step 1 and either the block temperature for block control protocols or the calculated sample temperature for calculated control protocols When the step s target temperature is reached a timer starts in the Temp line min sec By pressing the Left arrow button you can view the lid temperature This screen shows only as long as the left Select key is pressed The runtime screen returns when you stop pressing the key By pressing the Right arrow button you can view the total time that the protocol has been running the total time remaining in the protocol and the cycler number that the protocol is currently running This screen is displayed only as long as the key is pressed The runtime screen returns when you stop pressing the key Reading the Temperature Display Screen By pressing the Screen button you can toggle between different screens during a protocol Pressing the button once will bring you to the temperature display screen 90 0 0 09 This screen lists a shorthand version of the protocol On the left the list of the temperature steps a
73. ortening of hold times each time the step is executed in a GoTo cycle Rate modifies the thermal ramping speed for protocols that require less than maximal speed of temperature change Beep modifies a temperature step causing the machine to beep when a specified target temperature is reached Entering an Increment Option To enter an increment option select nc from the Options Menu for a temperature step then press Proceed The first Inc screen will be displayed New Lid 100 C ABCD Vol 20 1 92 0 FOR 0 30 2 50766 0 30 3 GOTO 1 4 END OK YES No The temperature step being modified appears on the bottom line of this screen The plus sign means that the screen 1 set up to enter a progressive increase in temperature per cycle Press the key to switch to a minus sign allowing entry of a progressive decrease in temperature Press to change back to a plus sign BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Creating Programs Enter the numerical value of the temperature increase or decrease 1 2 is used in the example below New Lid 100 C ABCD Vol 20 1 92 0 FOR 0 30 2 50 0 FOR 0 30 CYCLE 1 2 Press Proceed The Inc value will be included in the protocol and a confirmation menu will be displayed on the last line New Lid 100 C ABCD Vol 20 1 92 0 FOR 0 30 2 50 0 FOR 0 30
74. porate neutral fusing which means that live power may still Safe Use Guidelines The MJ Mini thermal cycler is designed to be safe to operate under the following conditions Indoor use Altitude up to 2 000 m Temperature 5 C to 40 C Maximum relative humidity 80 for temperatures up to 31 C decreasing linearly to 50 relative humidity at 40 C Mains supply voltage fluctuations not to exceed 10 of the nominal voltage Installation categories overvoltage categories Pollution degree 2 Electrical Supply 100 240 VAC 50 60 Hz 400 W BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Electromagnetic Interference This device complies with Part 15 of the FCC Rules Operation is subject to the following two conditions 1 this device may not cause harmful interference and 2 this device must accept any interference received including interference that may cause undesired operation This device has been tested and found to comply with the EMC standards for emissions and susceptibility established by the European Union at time of manufacture This digital apparatus does not exceed the Class A limits for radio noise emissions from digital apparatus set out in the Radio Interference Regulations of the Canadian Department of Communications LE PRESENT APPAREIL NUMERIQUE N EMET PAS DE BRUITS RADIOELECTRIQUES DEPASSANT LES LIMITES APPLICABLES AUX APPAREILS NUMERIQUE
75. ppears In this case the denaturation temperature 90 0 is followed by the annealing temperature 64 0 as well as an extension time of 72 0 This temperature pattern is repeated 29 times as indicated by the GOTO step in the protocol as well as the 29x shown at the bottom of the screen This cycling is followed by a final hold step of 10 0 On the right a diagrammatic representation of the protocol is presented In the example above the cycler is currently holding the samples at 64 0 On the left this step is highlighted and on the diagrammatic representation this step is blinking A counter on the top line of this screen marks the amount of time that has passed on this step min sec BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Running Protocols Time Remaining Screen Press the Screen button once more to see the time remaining in the protocol 00 25 55 Time Remaining The time is noted in hours min sec In this case there are 25 minutes and 55 seconds remaining until the program is complete This screen is particularly useful in lab settings where multiple cyclers are being run From the Time Remaining Screen pressing the Screen button returns the user to the Main Menu This is the same screen that we have encountered previously except that the bottom line indicates that the thermal cycler is engaged in running a protocol RUN VIEW NEW FILES EDIT T
76. prevent condensation Sealing with Oil or Wax Mineral oil silicone oil paraffin wax or Chill out liquid wax may be used to seal samples Use only a small amount of oil or wax 1 3 drops 15 50 ul are usually sufficient Include this volume in the total volume when setting up a calculated control protocol see Choosing a Temperature Control Mode in chapter 5 Use the same amount of oil or wax in all sample vessels to ensure a uniform thermal profile Most paraffin waxes solidify at room temperature The wax can then be pierced with a micropipette tip and the samples drawn off from below the wax Silicone oil and mineral oil can be poured off or aspirated from tubes if the samples are first frozen 15 to 20 C The samples are usually pure enough for analysis without an extraction Chill out liquid wax available from Bio Rad Laboratories is an easy to use alternative to oil This purified paraffinic oil solidifies at 10 and is liquid at room temperature By programming a holdstep at low temperature the wax can be solidified at the end of a run A pipette tip can then be used to pierce the wax in the tubes and remove the samples The wax is available in a clear optical assay grade or dyed red to assist in monitoring its use The red dye has no adverse effects on fluorescent gel analysis of reaction products BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Operation
77. ries CHO series gt lt Multiplate unskirted MLP series lt lt lt Y Y 96 well microplates MLL series Y Multiplate unskirted MLP series gt lt gt lt gt lt Y Y 48 well microplates Y Multiplate unskirted MLP 2401 gt lt gt lt gt lt Y Y 24 well microplates gt lt 0 2 ml strip tubes TBS series Y Y Y 8 strip amp 12 strip TLS series Y 0 2 ml individual tubes TFI 0201 Y Y Y TBl series Y 0 5 ml individual TBI series Y tubes w caps Y Reaction vessel fits block sealing option fits reaction vessel without modification Reaction vessel sealing option can be cut to fit In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com 23 Safety Warning Regarding Use Of 35 Nucleotides Some researchers have experienced a problem with radioactive contamination when using 35 in thermal cyclers This problem has occurred with all types of reaction vessels The Problem When 35 nucleotides are thermally cycled a volatile chemical breakdown product forms probably SO This product can escape the vessel and contaminate the sample block of a thermal cycler and possibly the air in the laboratory Contamination has been reported with microplates 0 2 ml tubes and 0 5 ml tubes Polycarbonate Reaction Vessels The largest risk of contamination occurs when using 96 well polycabonate microplates Polycarbonate is somewhat permeable both to water and the 35 breakdown product This problem
78. s 6 767 512 and 7 074 367 Effective February 1 2009 BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Table of Contents Explanation A AA Safety Warnings and Guidelines sa resse rer apus kenra ELETA YES BEES RAKIA Electromagnetic Interference and Warning Documentation COMVENTIONS aa jae eas oS Chapter Te Arodu tO sr er Sah ld A ies el Chapter 2 Layout and Ghiapter 3 Installation eco a nee cR ae re a Ghapter A Operation are rb exec A ERR IN TRO b ooo Chapter RUNNING PFOTOCOIS deret deal ute Ret D D ede e T a ae Chapters Creating Programs A sa aate Ga OP ERRAT ER REAGAN Chapter 7s Editing Programs susi ret ed a e e en Ghapter 8 Using the Utilities s serere Chapter 9 Ghapter 10 Tro bleshootingz saxi Pine ee eae ae Rae ee REM Appendix A Preinstalled Protocols In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com Explanation of Symbols CAUTION Risk of Danger Wherever this symbol appears always consult note in this manual for further information before proceeding T
79. s ramping rates were so slow below 1 that there was plenty of time for heat to transfer through the tube wall to the sample during a given incubation Modern thermal cyclers have much faster ramping rates so the faster heat transfer provided by thin walled tubes allows protocols to be significantly shortened Essentially up to 30 seconds can be saved per cycle by using thin walled tubes for an overall savings of 15 minutes in a 30 cycle run 0 2 ml Tubes All types of thin walled 0 2 ml tubes may be used Bio Rad sells high quality 0 2 ml tubes in a number of styles including individual tubes and strips Microplates A variety of polypropylene 48 well microplates can be used in the MJ Mini cycler as long as they fit the wells snugly In addition the Multiplate line of 96 well plates and Microseal film seals can be cut down to fit in the sample block of this instrument Polypropylene microplates and compatible Microseal film or strip caps for sealing are available from Bio Rad Laboratories Sealing Sample Vessels To avoid changing the concentration of reactants steps must be taken to prevent the evaporation of water from reaction mixtures during thermal cycling Only a layer of oil or wax will completely prevent evaporation from the surface of the reaction fluid However an adequate degree of protection can be achieved by sealing vessels with caps film or adhesive seals then cycling the samples using the heated lid to
80. s to scroll downward to view all protocol steps By selecting Proceed again you are brought back to the previous screen from which you can highlight and select Run to commence the cycling program Tip The MJ Mini thermal cycler comes pre loaded with a series of template protocols for a variety of common applications See Appendix A for a full list of protocols You may chose to run these programs as they are or to adjust certain parameters in order to optimize your reactions Selecting Calculated Temperature Control Mode vs Block Control Mode With the MJ Mini thermal cycler the default setting for running a protocol is calculated temperature control method This temperature control method compensates for the fact that the sample s temperature lags behind the block temperature When creating a new protocol you will be asked to enter a sample volume The cycler will automatically take this volume into account when running the protocol and by employing small temperature overshoots the cycler rapidly brings the sample to its target temperature Every time you select a protocol to run you will be asked to enter a sample volume By entering zero in the Sample Vol field the cycler will enter Block Control Mode this mode does not employ the small temperature overshoots As a result it will take slightly longer for the sample to reach its target temperature and the protocol will generally take a little longer to run In the U S call t
81. serious electrical shock Opening the base will also void your warranty 1 Disconnect the power cord from the back of the instrument Move the power switch to the off position 2 Remove both fuses and replace them with new ones it is impossible to visually determine which fuse is blown You may however test the fuses with an ohmmeter to determine which is defective and replace just that one 3 Reconnect the power cord In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com RAD 71 72 BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 10 Troubleshooting Error Messages Error Message Probable Cause Action Running A C POWER FAILED Displayed when a machine running a No action is necessary Protocol resumes FAILED PLEASE RETURN TO BIO RAD FOR SERVICE working so the protocol was terminated CYCLE X STEP Y RECOVERED protocol has been turned off either running when power is restored Results 27 2 PRESS PROCEED TO intentionally or due to a power outage may or may not be affected depending CONTINUE and then turned on again on whether power failed early or late in the protocol and whether the power was restored before the sample cooled excessively ALL BLOCK SENSORS HAVE None of the temperature sensors are Contact Bio Rad Laboratories ALPHA UNIT HAS OVERHEATED
82. step by selecting the second step by highlighting the step number 2 in the example followed by pressing Proceed New Lid 100 C ABCD Vol 20 1 92 0 FOR 0 30 2 GOTO 1 25 TIMES 3 END Press ENTER to edit BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Creating Programs New Lid 100 C ABCD Vol 20uL 1 92 0 FOR 0 30 2 TEMP GRAD GOTO 3 GOTO 1 25 TIMES 4 END Press ENTER to edit You will be presented with the following options INS DEL EDIT and OPTION Select the INS option to insert a step before the GoTo step New Lid 100 C ABCD Vol 20uL 1 92 0 FOR 0 30 2 TEMP GRAD GOTO 3 GOTO 1 25 TIMES 4 END Press ENTER to edit Select Temp and then enter the temperature and time hold fields as previously described in this chapter Deleting a Program To delete the program Position the cursor on any step number and press Cancel A cancellation confirmation screen will be displayed and you will be asked whether or not you wish to save these changes New Lid 100 C ABCD Vol 20 1 92 0 FOR 0 30 2 50766 0 30 3 GOTO 1 25 TIMES 4 Save changes YES Select No then press Proceed The program will be deleted and the Main Menu will be displayed Keeping a Permanent Record of Programs Occasionally in the course of repairing a defective thermal cycler it is necessary to replace the chip that
83. t is desired select GRAD from the Enter Menu and then press the Proceed key For the purpose of this example a gradient step will be entered as Step 2 New Lid 100 C ABCD Vol 20uL 1 92 0 FOR 0 30 2 TEMP GRAD GOTO END In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com RAD 41 42 The first screen for programming the gradient will appear New Lid 100 C ABCD Vol 20 1 92 0 FOR 0 30 2 LOWER TEMP C Enter the lower limit temperature for the purposes of this example 50 C then press Proceed The upper temperature screen will appear New Lid 100 C ABCD Vol 20 12 92 0 FOR 0 30 2 50 UPPER TEMP Enter the upper temperature for the purposes of this example 66 then press Proceed Use integers only Note The maximum temperature differential that can be programmed along the sample block is 16 C The next screen requires you to enter a hold time for the temperature gradient step New Lid 100 C ABCD Vol 20uL 1 92 0 FOR 0 30 2 50766 TIME Enter the hold time in the form of min sec we have chosen 30 sec for the example below Press Proceed A confirmation screen will appear New Lid 100 C ABCD Vol 20uL 1 92 0 FOR 0 30 2 50766 0 30 OK YES No Option BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723
84. tain four types of steps Two of the steps are mandatory and two are optional 1 Temperature step mandatory Sets a temperature for the sample block as well as the length of time it is held at that temperature The MJ Mini cycler brings the block to this temperature at its maximum rate of heating or cooling unless modifying instructions are added to the program With Calculated Temperature Control Mode the cycler will incorporate small temperature overshoots to rapidly bring the sample to its target temperature these overshoots however do not alter the target temperature or the incubation time for a sample With Block Control the heat pump brings the sample holder rapidly to the target temperature without any temperature overshoots samples therefore take a little longer to reach their target temperature and incubation steps are generally lengthened to accom modate this 2 Gradient step optional Allows you to program a temperature gradient from front to back along the sample block The range of any single gradient can be as great as 16 C The maximum program mable temperature is 99 C the minimum programmable temperature is 35 C 3 GoTo step optional Causes the program to cycle back to an earlier step for a specified number of times up to 9 999 times 4 End step mandatory Instructs the MJ Mini cycler to shut down its heat pump because the program is complete Additional instructions termed options can be add
85. tep stores the program and displays the Main Menu or a folders menu displays the Enter Menu so that additional steps can be added If you have created custom folders for your programs see chapter 8 choosing Yes brings a screen listing the folders SAVE ABCD IN lt MAIN gt lt FOLDER1 gt lt FOLDER2 gt Select the folder you want to store the program in then press Proceed The program will be stored in the folder and the Main Menu will be displayed If all programs are stored in the same main folder pressing yes will save the program and bring you back to the Main Menu In the 5 call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com BIO RAD 45 46 Modifying Program Step with the Options The Options Menu is accessible from the confirmation menus of temperature steps To access the Options Menu select Option from the confirmation menu of a temperature step then press Proceed The Options Menu will be displayed on the bottom line of the screen New Lid 100 C ABCD Vol 20 1 92 0 FOR 0 30 2 50766 0 30 3 GOTO 1 4 END OK YES No Inc modifies a temperature step with an increment option An increment option allows a progressive increase or decrease of temperature each time the step is executed in a GoTo cycle Ext modifies a temperature step with an extend option An extend option allows a progressive lengthening or sh
86. tored To add or delete a step or to modify a step with an option position the cursor on the step number then press Proceed The Edit Menu will be displayed for that step Edit Lid 100 C iPRF1kb Vol 20uL 1 95 0 FOR 0 30 2 95 0 FOR 0 01 3 72 0 FOR 0 10 4 GOTO 2 35X INS DEL EDIT OPTION INS allows a step to be added before the highlighted step DEL deletes the highlighted step EDIT positions the cursor over the various fields of the selected step so that the values may be changed OPTION allows an option to be added to the highlighted step if it is a temperature step In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com BIO RAD 55 56 Inserting a New Step To insert a new step select INS from the Edit Menu then press Proceed The Enter Menu will be displayed for the new step a new step 2 is added in the example below Edit Lid 100 C IPRFikb Vol 20uL 1 95 0 FOR 0 30 2 95 0 FOR 0 01 3 72 0 FOR 0 10 4 GOTO 2 35X INS DEL EDIT OPTION You may select to insert a Temperature step a Gradient step a GoTo step in the program see Entering the Program s Steps chapter 6 When the step is complete select Yes from the confirmation menu then press Proceed The program being edited will be displayed again with the new step appearing among the listed steps Deleting a Step To delete a step select De
87. tructing AN air vents can lead to overheating and increases the risk of electrical shock and fire BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 2 Layout and Specifications FOME e tre tx te odit he ee ba 10 ontrobPanel sie ee A A QUUM eM REUS 10 com AM E 11 Bottom VIEW es eere etu tee ere uo ei e e A E E SD oe RR OE RE 11 12 SDOCITICatIOFIS RR RR ART RUE RC RARI Layout of the Mini thermal cycler Thumbwheel Heated lid closed Control panel Figure 1 Front view of the MJ Mini thermal cycler LCD window Screen hot key m MJ Mini BIO RAD ersonal Thermal Cycler Block heating cooling lights SCREEN Selection keys Pause key Proceed key PROCEED Cancel key Figure 2 Control panel of the MJ Mini thermal cycler 10 BIO RAD Visit on the Web at www bio rad com In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Layout and Specifications Heated lid Power switch USB ports Jack for power cord E Fuses Figure 3 Back view of the MJ Mini thermal cycler Front Air intake vents Air exhaust ven
88. ts Figure 4 Bottom view of the MJ Mini thermal cycler In the U S call toll free at 1 800 4BIORAD 1 800 424 6723 Visit on the Web at www bio rad com RAD 14 Specifications MJ Mini Thermal Cycler Thermal range 0 99 9 C but no more than 30 C below ambient temperature Thermal accuracy 0 2 C of programmed target 90 C NIST traceable Thermal uniformity 0 4 C well to well within 10 sec of arrival at 90 C Ramping speed Average ramp rates are 1 5 C sec with a maximum rate of 2 5 C sec Sample capacity 48 x 0 2 ml tubes 12 x 0 5 ml tubes or one 48 wel microplate Line voltage 100 240 VAC rms no adjustment needed among voltages within these ranges Frequency 50 60 Hz single phase Power 400 W maximum Fuses Two 6 3 A 250 V 5 x 20 mm Displays 64 x 128 backlit LCD Ports Two USB ports for access by service personel from Bio Rad Laboratories Memory 400 typical programs in 12 folders Weight 4 1 kg Size W x D x H 18 x 32 x 20 Specifications Gradient Temp gradient accuracy 0 2 C of programmed target at end rows 10 sec after the timer starts for the gradient step NIST traceable Thermal row uniformity 0 4 C in row well to well within 10 sec of reaching target temperature Calculator accuracy 0 4 of actual row temperature NIST traceable Gradient range 35 99 Thermal Gradient differential range 1 16 12 BIO RAD Visit on the Web at www bio rad com In the U

MJ Mini™ Gradient Thermal Cycler - Bio-Rad

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MJ Mini™ Gradient Thermal Cycler - Bio-Rad