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1. different name Press Enter key Incorrect password entered 35 You pressed an inappropriate key for the selected item Time or Temperature values were outside allowed ranges If a cycle is repeated you may not specify an infinite dwell time within the cycle Programming a protocol with more than nine cycles Programming a protocol with a cycle containing more than nine steps Pressing the option softkey when neither a temperature nor time field is selected Errors were detected in execution of the last protocol A protocol is currently being executed The 99 user defined protocol storage limit has been reached You may not delete or overwrite Bio Rad template protocols You pressed Enter prior to naming a protocol A protocol with the same name already exists Service Options are for Bio Rad internal use only Appendix A Specifications Input Power 100 120 VAC 100 120 VAC 10 50 60 Hz Fuse 8 0 A 5 x 20 mm Type T 220 240 VAC 220 240 VAC 10 50 60 Hz Fuse 4 0 A 5 x 20 mm Type T Power 670 Watts 910 VA max Environmental Operating Ambient Storage Block Temperatures Range Cycling Speed Storage Cooling Overshoot Accuracy Uniformity Temperature Gradient Input Gradient Range Functional Gradient Range Minimum Temperature of Gradient Maximum Temperature of Gradient Gradient Accuracy Gradient Uniformity Descriptive Specifications Dimensions Chassis HxW
2. but it can be used at other points as well When an infinite dwell time is specified the MyCycler will pause the protocol at the selected temperature until you terminate or resume execution Clear The Clear key is used to clear the entire entry in an input field For example if you have specified an incorrect duration for a step pressing the Clear key erases the entire entry not just the last character entered Shift The Shift key is located to the left of the alphanumeric keys The Shift key is used in conjunction with the alphanumeric keys to switch between alphabetic and numeric character see the discussion above for the alphanumeric keys when naming a protocol or instrument Directional Arrows lt gt A V The four Directional Arrow keys surround the Enter key and direct the cursor when navigating the screen Normally the right and left arrows are used to move from field to field not within a field The exception is the case when you are assigning a protocol or instrument name using the alphanumeric keys in this instance the right and left arrows move the cursor within the name field and the only way to move out of the field is with the Enter key The up and down arrows are used to move the cursor from line to line within selection boxes or from one field to field when editing or creating protocols In some of the Utilities screens the up and down arrows are used to set the time date and default conditions
3. subsequent sections 1 Power up the MyCycler by either plugging in the instrument or pressing the Standby key on the front panel of the instrument if in Standby mode After a quick diagnostic routine the Home screen will be displayed Press F2 Create from the Home Screen A selection menu will appear Select the Custom option from the selection menu it should be selected by default and press Enter You may also choose to edit a Bio Rad template protocol listed in this menu if the template protocol is similar to your desired protocol Edit the fields of the protocol e The default custom protocol is a simple three step amplification protocol 30 seconds at 95 C 30 seconds at 55 C followed by 0 seconds at 72 C e To add or delete a step or cycle press F4 Add Del and select the appropriate option Note that vertical lines demarcate different cycles and that steps with in the same cycle are not separated by vertical lines Cycles are numbered sequentially in the bottom left corner of their first step s display Use the arrow keys to move the selection box between the different fields for each step of your protocol Set point temperature fields are shown immediately above the temperature plot line whereas dwell time fields are shown immediately below the temperature plot line The repeats field which specifies the number of times a cycle is to occur followed by an x is shown in the bottom right corner of
4. 1 3 2 Fuse Installation and Power Cable Connection Your MyCycler is configured for 100 to 240 V You should install the correct fuse using the following procedure Warning Failure to follow this procedure may result in damage to the unit and invalidation of the warranty 1 Disconnect the power cord from the unit 2 Remove the fuse holder from the rear panel of the instrument with a small flat head screwdriver or similar tool 3 Pull the fuse holder out and install the correct fuse The MyCycler comes with the following two fuses a For 100 120 V operation Use 8 0A 5 x 20 mm Type T fuses b For 220 240 V operation Use 4 0A 5 x 20 mm Type T fuses 4 Reinsert the fuse holder into the rear panel of the instrument and press the fuse holder gently until it snaps into place 5 Insert the power cord plug into the power entry module Plug the power cord into a properly grounded outlet Fuse Power Entry 1 3 3 USB Cable Connection In addition to the power cable connector the rear panel of the MyCycler contains a USB port that may be connected to a personal computer allowing the transfer of protocol files Validation Reports and Run Reports Using this link you may print out any downl
5. 23 6 11 Run Setup Screen 2 eases wiacehivervelniecenaedeiiestaadeedeiaiabecn ages 23 6 1 2 RUM Sree Mnato he a luna rae a aa ane aaa daa 24 6 1 3 Running Gradient Protocols 0 cecceeeeeeeeeeeeeetteeeeeeesteeeeeeenaees 25 6 1 4 Converting a Gradient Protocol sessseeeesseerrreseerrrsseeerrssreense 25 6 2 Options While a Protocol is Running eesseessseseeeseesrrsssrerrreseerrrssrrernssene 26 6 2 1 Displaying the Home Screen while a Protocol is Running 26 6 2 2 A Power Failure while a Protocol is Running 26 6 2 3 Pausing a Running Protocol 0 ceeccceeeeeeceeeeeeeecteeeeeeesteeeeeeenaees 27 6 2 4 Terminating a Running Protocol 0 ccecccceeeeeeteeeeeeeetteeeeeeenaees 27 6 2 5 End of Run Screen cccccccceceeeeeeeeeeeeceeceeeeeeeeeseeeeesensaeaeeees 27 Section 7 REPOMS sisses ivves cdcivedeceniceaeseeteseveed deceveserseaceustevtessvvstiensivectveecnierte 28 FA THe RUN REP OM stetee cecilia tidak iadelcccutelidece atded thegat laladened vai a E sada tecentaghties 28 7 2 The Validation Report cccccceceeceeeeeeeeecceeeeeeeeeeeeeesesecesucsaaeeeeeeeneess 28 7 3 Soft Key Functions for Reports ccccceeeeeeeeeeeeeeecneeeeeeenneeeeeeenaeeeeeeenaees 28 7 4 Uploading Reports c cccecccececeeeeeeeeeeceaaeaeeceeeeeeeeseesecsaccuaeeeeeeeneees 29 SECON S UNAS 5 cise evasive Teveckedeceedadcnieck coteves cocusdarveceeddtesdivestsescvcus
6. 8 1 1 View Reports Choose this option to browse through an index of past runs and to view individual Validation Reports and Run Reports The runs are stamped and sorted by date and time with the most recent runs listed at the top of the list 8 1 2 Instrument Information Choose this option to display the Instrument Name serial number firmware version and the number of user defined protocols saved to memory 8 1 3 Set Date and Time Choose this option to set the current date and time The changes you make will not be saved unless you press F5 Accept Changes You may press F1 Cancel at any time to cancel the changes you have made and to close the Set Date and Time display 8 1 4 Set Display Contrast Choose this option to adjust the display contrast of the LCD screen The changes you make will not be saved unless you press F5 Accept Changes You may press F1 Cancel at any time to cancel the changes you have made and to close the Set Display Contrast display 8 1 5 Service Options For Bio Rad internal use only 8 2 Set Preferences Menu The Set Preferences menu which is accessed from the Utilities menu contains the following options 8 2 1 Default Hot Start Options Choose this option to set the default Hot Start and Hot Start Temperature settings as they appear on the Run Setup Screen The changes you make will not be saved unless you press F5 Accept Changes You may press F1 Cancel at any time to cancel the changes you have
7. F4 Display key to display the information on that help topic 9 1 Soft Key Options for the Help Screen e F1 Previous Selects the previous topic listed in the help index e F2 Next Selects the next topic listed in the help index e F4 Display Index When viewing the index of help topics this softkey is labeled Display and pressing this button displays the information on the selected help topic When viewing the information on a help topic this softkey is labeled Index and pressing this button takes you back to the index of help e F5 Done Brings the display back to the Home screen Section 10 Care and Maintenance 10 1 Cleaning the Unit You should ensure that no liquid is spilled onto or into the MyCycler In addition periodically wipe it clean of dust and other residue that comes with normal operation of the instrument Use a soft lint free cloth and de ionized water 10 2 Replacing a Fuse or Battery The fuse is located on the rear panel of the instrument If the MyCycler does not turn on as indicated by its LED located on the front panel of the instrument when plugged in and the power button is pressed the fuse may need to be replaced To replace the fuse 1 Disconnect the power cord from the unit 2 Remove the fuse holder from the rear panel of the instrument with a small flat head screwdriver or similar tool 3 Pull the fuse holder out and replace the old fuse with one having the correct cur rent rat
8. MyCycler to a PC computer system This utility is included on the CD ROM that is shipped with all MyCycler systems This utility will work with Windows 98 Windows 2000 Windows XP and Windows ME It will not work with Windows NT because that operating system has no native support for USB To install the Upload Utility 1 Insert the Installation CD into a CD ROM drive 2 Select Run from the Start menu 3 Type X Setup where X is the drive letter of the CD ROM drive 4 Follow the instructions on the screen to complete the installation A folder called Report Utility will be created in the MyCycler folder To upload reports to the PC 1 Connect the MyCycler to the PC using the supplied USB cable 2 Select Start gt Programs gt MyCycler gt Report Utility 3 Select the type of Report to upload 4 Click on the report name on the left side of the screen to see the report displayed on the right side of the screen 5 To save the report click Save to File Enter a valid filename in the dialog box followed by TXT 6 Click Save Files are saved in plain text format and can be easily reopened and printed using a word processor program such as Word MyCycler Report Upload Utility ersion 1 000 using MCREMOTE DLL a Click on a Run to View Selected Report Type Validation Report PEVECETS OT Protocol validation validation Date Tuesday September 17 2002 validation 7 validation Begin 2 50 PM End 3 47 PM validation Se
9. cycle the instrument would go to 95 C and then to 55 5 C Finally on the third repeat of the cycle the instrument would go to 95 C and then to 56 0 C Temperature increments or decrements may be as low as 0 1 C and they may be as large as desired so long as they do not result in values outside the legal ranges described in section 4 3 1 If you input an increment or decrement function that would result in an illegal temperature value the thermal protocol will run but the temperature will cease to increment or decrement once the upper or lower limit has been reached Furthermore for every repeat that would result in an illegal tem perature value an error is counted on the End of Run screen and displayed in the Validation and Run reports 13 4 3 2 2 Increment Decrement Time Most protocols call for the exact same dwell time for each repeat of a cycle but in some instances you may wish to program an automatic increase or decrease in the step dwell time after each repeat To input an automatic increment or decrement function for a step the cycle containing the step must have more than one cycle repeat The automatic increment and decrement function updates the dwell time by a specified amount after every repeat starting after repeat one For example you could create a cycle with 3 repeats with a first step at 95 C for 10 seconds and a second step at 55 C for 45 seconds You could then specify a 5 second automatic dwell time de
10. keys 0 9 which are arranged like the keys on a telephone Each numeric key except 1 and 0 is used to represent three or more letters The alphanumeric keys are usually used as number keys for the entry of time temperature and cycle repeats When entering a protocol or instrument name into a screen display the keys automatically shift to alpha mode for the entry of letters The word ALPHA is displayed in the top right corner of the screen You can toggle between alpha and numeric by pressing the Shift key To enter uppercase letters press F2 Caps Lock before pressing the alphanumeric key To specify an alphabetic character press the key until the desired character is displayed For example the 2 key is used for a b or c entries To input the letter a press the 2 key once To input b press the 2 key twice and to input c press the 2 key three times If the 2 key is pressed a fourth time it will display the letter a Decimal Point When entering numeric decimal values press this key to enter values after the decimal co Infinity The 0 key is labeled with an infinity symbol above the 0 to indicate that it has a secondary function of Infinite Dwell Time Like the alphabetic characters this secondary func tion is accessed by first pressing the Shift key The Infinity key is used to indicate dwell times that are to be terminated by user intervention 6 Typically this feature is used at the end of a protocol
11. others end with a 3 the number indicates the number of steps in the amplification cycle of that protocol For either option you choose you will need to enter values for time tempera ture and repeats as described in the following sections To edit an existing protocol press F1 from the Home screen You may then select the desired protocol from the Protocol Library and then select the Edit Protocol option 5 1 Specifying Time Values Time values may fall between 1 second and 99 minutes 59 seconds You must use the mm ss format e g 00 01 to 99 59 When you input a value the numbers will be entered from right to left with implied zeros in the front For example to enter 1 minute 15 seconds press 1 1 5 followed by the Enter or an arrow key Note entering a fifth digit will cause the left most digit to be lost All protocols will have default values in each time field If you want to accept the default value press Enter or an arrow key The Clear key may be used to remove all numbers in the time field 5 2 Specifying Temperature Values Temperature values must be in the range of 4 0 C to 100 0 C Numbers are displayed on the screen as the keys are touched beginning with the position immediately to the left of the decimal point and then they move to the left with each subsequent entry No decimal point will be displayed until you press the deci mal point key Enter or one of the arrow keys If the decimal point key is no
12. step is carried out it is shown in inverse video RUNNING My First Protocol The screen also shows the current temperature of the reaction module block when block monitoring mode is selected or the calculated sample temperature when the temperature is monitored via the algorithm mode The current repeat number and dwell time of the current repeat will also be shown and will count down as the protocol progresses The name of the protocol is displayed to the right of the word RUNNING If the protocol is an unsaved modification of a saved protocol then the name of the saved protocol is displayed and preceded by the letter M for modification in parentheses The current time of day will be displayed along with the time the protocol was initiated and with an estimated time of completion 24 6 1 3 Running Gradient Protocols The temperature gradient will appear in the graphical representation of the protocol The maximum temperature minimum temperature and thermometer icon will be displayed for the gradient segment This graphical presentation of the protocol appears in the run screen while the protocol is running RUNNING MJ My Gradient 6 1 4 Converting a Gradient Protocol The MyCycler Thermal Cycler allows the user to convert an existing gradient protocol to a non gradient protocol To use the conversion feature select the F1 Option to go to the Protocol Library Select the gradient protocol that will be co
13. the Protocol Library as well as the parameters organization and layout of thermal cycling protocols e Section 5 Creating and Editing Protocols This chapter explains how to use the Edit screen and the process of creating and editing protocols e Section 6 Running Protocols This chapter provides instructions on how to run any protocol This includes a number of options for controlling the execution and monitoring the progress of the protocol e Section 7 Reports This chapter describes Validation reports and the Run reports in detail and explains how to read them e Section 8 Utilities This chapter describes the features of the Utilities screen This screen supports a number of features for customizing the environment e Section 9 The Help Screen This chapter describes how to access and use the MyCycler s onboard help screens e Section 10 Care and Maintenance This chapter provides information on cleaning the unit replacing fuses a troubleshooting guide and a list of error messages e Appendix A Specifications This appendix provides the MyCycler system specifications e Appendix B Warranty This appendix includes the MyCycler warranty and technical support information e Appendix C Product Information Section 2 Quick Guide for Running the MyCycler The following procedure is provided for the user wishing to immediately start using the MyCycler Detailed information for using the instrument is provided in
14. the last step of a cycle e To add an increment or decrement option for either time or temperature put the selection box on the desired time or temperature field press F3 Option and select the desired option After selecting the desired option a new field will pop up in the display In this new field input the amount of time or degrees Celsius by which you want to increment or decrement each repeat When you are finished editing the protocol press F5 Done Save the protocol by choosing Save Protocol As from the selection menu Name the protocol using the alphanumeric keys as described in section 1 5 and press Enter when finished The Home screen will appear Press the F1 Protocol Library to access the Protocol Library Using the arrow keys select the protocol you just created and press Enter A selection menu will appear Select Run Protocol The Run Setup screen should appear Specify whether or not you want a hot start and the hot start temperature if you picked YES and which temperature measurement mode you want and the sample volume if you picked Algorithmic Measurement Press F5 Begin Run to begin the run Section 3 The Home Screen The Home screen is the first screen displayed after the instrument is turned on and finishes its self diagnostic routine The Home screen serves as a starting place for all functions of the interface and can be accessed from most other screens via the F4 Home S
15. the set point temperature and dwell time at that temperature A cycle is defined by specifying the times and temperatures for all steps and the number of times the cycle is repeated The MyCycler comes with a set of predefined Bio Rad protocols in the Protocol Library You may also create new protocols by modifying any existing protocol in the library including the Bio Rad protocols or you can create a new protocol from scratch 4 2 The Protocol Library Screen The Protocol Library screen contains the list of all thermal protocols saved on the instrument All user defined protocols appear on the left hand side of the screen in the column labeled My Protocols Bio Rad template protocols appear on the right hand side of the screen in the column labeled Bio Rad Use the arrow keys to select a protocol and then press Enter for more options See Section 4 2 3 Protocol Options Use arrow keys to select a protocol and then press Enter User defined Protocols My Protocols Bio Rad Bio Rad Template My First Protocol STANDARD 2 Protocols RT PCR 2 LONG PCR 2 CYCLE SEQ2 NESTED PRIHM2 TOUCHDOWN STANDARD 3 RT PCR 3 LONG PCR 3 CYCLE SEQ3 Citations Screen Screen Done 4 2 1 My Protocols User defined protocols are displayed in the Protocol Library under the column labeled My Protocols The MyCycler has sufficient memory to store up to 99 total protocols in the library You may run view edit delete or rename any of these p
16. 10 safety certification Create a potential safety hazard Bio Rad is not responsible for any injury or damage caused by use of this instrument for purposes other than those for which it is intended or by modifications of the instrument not performed by Bio Rad or an authorized agent This product conforms to the Class A standards for electromagnetic emissions intended for laboratory equipment applications It is possible that emissions from this product may interfere with some sensitive appliances when placed nearby or in the same circuit as these appliances The user should be aware of this potential and take appropriate mea sures to avoid interference This instrument is intended for research applications only Section 1 1 1 1 2 1 3 1 4 1 5 1 6 Section 2 Section 3 3 1 Section 4 4 1 4 2 4 3 44 4 5 Section 5 5 5 5 6 5 7 Section 6 6 1 Table of Contents Introductio M aeaee eee ee aae Per e eaaa e aa ieie Ea da Saanaa sE aa Eaa 1 OVERVIEW a r bee alt tele the r a tas Tal ne E alee ees daly 1 F atures ss tacit E E etetaa atte tae toy cnn Pela ede seh 2 System SOUP ctiiin eh eA Ain dene th der ities tiered 2 Tat Unpacking ooe e ete nites cae alee ete tie 2 1 3 2 Fuse Installation and Power Cable Connection 0 ee 3 1 3 3 USB Cable Connection cccccccceeeeeeeeeeeeeceeeeceeeeeeeeeeeeeenseaaees 4 1 3 4 Powering Up and Shutting DOWN 000 0 eeeeeeeetteeeeeeenteee
17. 91 Japan 03 5811 6270 Korea 82 2 3473 4460 Latin America 305 894 5950 Mexico 55 52 00 05 20 The Netherlands 0318 540666 New Zealand 64 9 415 2280 Norway 23 38 41 30 Poland 48 22 331 99 99 Portugal 351 21 472 7700 Russia 7 095 721 1404 Singapore 65 64153188 South Africa 00 27 11 4428508 Spain 34 91 590 52 00 Sweden 08 555 12700 Switzerland 061 717 95 55 Taiwan 886 2 2578 7189 2578 7241 United Kingdom 020 8328 2000 Sig 1204 4006219 Rev F
18. MyCycler Thermal Cycler Instruction Manual Catalog Number 170 9703 For Technical Service Call Your Local Bio Rad Office or in the U S Call 1 800 4BIORAD 1 800 424 6723 Safety Information Notice to Purchaser Purchase of this instrument Serial No conveys a limited non transfer able immunity from suit for the purchaser s own internal research and development and for use in applied fields other than Human In Vitro Diagnostics under one or more of U S Patents Nos 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 estop pel 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 The sample block of the MyCycler thermal cycler can reach temperatures of 100 C and the heated lid can be programmed to maintain temperatures up to 110 C The heated lid should remain closed at all times during operation to prevent accidental skin burns Always allow the sample block to return to its idle temperature before opening the lid and removing samples When placing or removing samples open the heated lid all the
19. When a time or temperature field has a default value and that field is highlighted pushing an arrow key is an implied Enter accepting the default entry Enter In the middle of the arrow keys is the Enter key When you press Enter the current selection or input field is accepted Stop Below the LCD screen and to the left of the F1 softkey is the Stop key If the Stop key is pressed while a protocol is running the protocol will be paused as described in section 6 2 3 Pressing the Stop key again while the protocol is paused will terminate the protocol Standby When the instrument is in Standby mode pressing the Standby key once turns the instrument back on When the instrument is on holding the Standby key for 3 to 4 sefonds puts the instrument into Standby mode A warning will appear if you attempt to initiate Standby mode while running a protocol or when unsaved changes have been made to a protocol 1 6 What s in this Manual This manual is organized into the following sections e Section 1 Introduction This chapter provides an overview of the instrument and how to set it up e Section 2 Quick Guide for Running the MyCycler This chapter is a quick guide for the user that wants to start running the MyCycler immediately e Section 3 The Home Screen This chapter describes the Home screen and the functions associated with it e Section 4 Thermal Cycling Protocols This chapter describes how to use
20. agents 1 LCD Display Keypad 1 2 Features e Self adjusting lid and reaction module design accommodate 0 2 ml tubes strips and 96 well plates e Graphical representation of thermal cycling protocols e User friendly software including menu driven software ready made protocol templates and user defined preferences e Run status and history are recorded in run reports and validation reports e Optional sleep mode saves power when the instrument is not in use e USB port enables users to transfer and print protocols or reports with a host computer connected to the instrument and a printer e Compact design saves bench space e Temperature monitoring and control can be specified by instrument algorithm or reaction module block mode e NIST traceable temperature performance 1 3 System Setup 1 3 1 Unpacking The MyCycler is shipped in one box containing the following MyCycler thermal cycler e Power cord e Instruction Manual e Fuses e USB cable for PC interface MyCycler utility CD ROM Carefully remove the contents of the shipping box To remove the thermal cycler lift it out by grasping the underside of the unit Remove the plastic bag and inspect the instrument for any external damage Check off all parts against the supplied packing list Your MyCycler was carefully tested at the factory and was shipped in good working order If any part is missing or damaged contact Bio Rad Laboratories immediately
21. ate are not retained when power is off Operation Not Possible message Bad power cord Circuit tripped Wrong fuse installed Ambient temperature too hot Lid heater turned off Lid heater failed Loose cable connection or instrument failure Not enough tubes in block Poor Adjustment LCD failure loose cable Loose fan cable Failed fan Dead battery Bad LED circuit 34 Replace cord Check outlet reset breaker Check line voltage and install the correct fuse type as described in section 1 3 2 Move to cooler location see specifications Check lid heater prefer ences in Set Preferences Call Bio Rad Call Bio Rad Add 10 extra empty tubes Adjust as described in Section 8 1 4 Call Bio Rad Call Bio Rad Replace battery See Section 10 2 Call Bio Rad 10 4 Error Messages Message Cause No operations allowed for selected item Press Enter key Out of range entry corrected to the nearest valid value Infinite time invalid in repeated cycles Only nine cycles are allowed ina protocol Only nine steps are allowed in a cycle No options available for this option Note The previous run had exceptions Press Enter key Cannot start run Run currently in progress Press Enter key There is no available space to save new protocols Press Enter key No changes are allowed to the Bio Rad protocols Press Enter key Error Name is blank Error Name in use Please use a
22. ay view any protocol in the Protocol Library on the View screen which displays a graphical representation of the protocol While viewing the protocol you may use the arrow keys and the Enter key to scroll through the protocol display In addition a textual display of any increment or decrement option for the currently selected parameter is shown at the bottom of the screen Generally the View screen serves only as a means to browse through an existing protocol Therefore no modifications can be made on the View screen 4 5 1 Soft Key Functions for the View Screen Softkey Option Description F1 lt lt Cycle Shifts the protocol display to the left by one cycle F2 gt gt Cycle Shifts the protocol display to the right by one cycle F3 Run Screen Displays the Run screen F4 Home Screen Displays the Home screen F5 Done Closes the View screen display 16 Section 5 Creating and Editing Protocols To create a new protocol press F2 from the Home screen You will be asked to select whether you wish to e Create a Custom Protocol This is a completely new protocol you will define If you choose Custom a simple three step one cycle protocol is displayed All editing options are available through the softkeys Use one of the Bio Rad protocols as a template Section 4 2 2 contains a list of these protocols You will be able to select from the individual protocols in the Bio Rad folder Some protocol names end with a 2 and
23. creen softkey even while running a protocol The Home screen also displays the current date and time as well as the user defined instrument name The default name is the instrument s serial number The date time and instrument s name may all be configured in Utilities see Section 8 1 Utilities BIO RAD MyCycler Monday January 28 2002 10 35 AM My Personal Cycler Choose an option below Pr otoc ol R un Library Create Screen Utilities Help 3 1 Soft Key Functions for the Home Screen Softkey Option Description F1 Protocol Library Displays the Protocol Library screen allows access to all saved protocols F2 Create Displays a menu of Bio Rad protocol templates Select either the protocol template most similar to the desired protocol to begin editing or select Custom to create a new protocol from scratch F3 Run Screen Displays the Run screen used to monitor the current run status of the MyCycler F4 Utilities Displays the Utilities screen select this option to alter instrument settings or for other miscellaneous functions F5 Help Displays the Help screen You may browse through an onboard collection of help topics 10 Section 4 Thermal Cycling Protocols 4 1 Overview Thermal cycling protocols contain the temperature cycling information to direct the MyCycler A protocol is made up of as many as nine cycles and a cycle is made up of as many as nine steps A step is defined by specifying
24. crement for the second step Thus on the first repeat of the cycle the instrument would hold at 55 C for 45 seconds Then on the second repeat of the cycle the instrument would hold at 55 C for 40 seconds Finally on the third repeat of the cycle the instrument would hold at 55 C for 35 seconds Dwell time increments or decrements may be as low as 1 0 seconds and they may be as long as desired so long as they do not result in values outside the legal ranges described in section 4 3 1 If you input an increment or decrement function that would result in an illegal dwell time value the thermal protocol will run but the dwell time will cease to increment or decrement once the upper or lower limit has been reached Furthermore for every repeat that would result in an illegal dwell time value an error is counted on the End of Run screen and displayed in the Validation and Run reports 4 3 2 3 Temperature Gradient The MyCycler Thermal Cycler offers a temperature gradient option for optimization of assay conditions Gradients may be programmed at any step of any cycle of the protocol The gradient option allows input of a temperature gradient of 1 25 degrees in total temperature span at temperatures as low as 30 C and as high as 99 C Thermal Gradients in the MyCycler are formed from the front to the rear of the sample block resulting in eight specific temperatures for assay optimization This innovative design allows for evaluation of
25. cursor position If Delete step or Delete cycle is chosen the step with the cursor or cycle with the cursor is deleted EDITING My First Protocol Option Add Del Done 5 5 Soft Key Functions for the Edit Screen Softkey Option Description F1 lt lt Cycle Shifts the protocol display to the left by one cycle F2 gt gt Cycle Shifts the protocol display to the right by one cycle F3 Option Adds or removes increments or decrements F4 Add Del Adds or removes cycles and steps F5 Done Allows you to save revisit or reject changes made to the protocol Also allows you to run the protocol without saving changes 5 6 Completing Protocols When you have finished editing the protocol press F5 Done to display a menu of options The choices are e Run Protocol To run the protocol immediately without first saving it The Run Setup screen is displayed This is documented in section 6 1 1 e Save Protocol To save changes made to an existing protocol This option is unavailable when editing a Bio Rad template protocol 21 e Save Protocol as You will be asked to create a name for the protocol You may then select the new protocol from the Protocol Library screen as described in section 4 2 Abandon Edits Reverts the protocol without saving changes e Resume Editing Allows you to return to the protocol edit screen to make further changes The MyCycler can store up to 99 different protocol files i
26. e sample block may be hot to touch while the unit is running 6 1 1 Run Setup Screen When you choose to run a protocol the Run Setup screen is displayed RUN SETUP Protocol M My First Protocol Temperature Measurement Sample Volume Mode 15 100 uL Algorithmic Measurement a 50 HE Hot Start Hot Start Temperature C YES 35 0 Use right left arrows or Enter to move between fields Use up down arrows to change selections Numeric keys may also be used for numeric field entries egin Run In this screen you can choose to specify Hot Start and the hot start temperature If Hot Start is chosen the MyCycler will heat to the hot start temperature when the run is initiated and then go into Pause mode See section 6 2 3 e Temperature measurement mode This is the method of temperature measurement You can choose to monitor the block temperature of the reaction module or the sample temperature by algorithm If you choose the Algorithmic method then you must specify the volume of the sample Sample Volume When the Run Setup options are specified press F5 Begin Run Protocol execution will begin as soon as the heated lid reaches the appropriate temperature 23 6 1 2 Run Screen The Run screen will be displayed as the execution of the protocol begins The Run screen displays the graphical representation of the protocol with the set point temperature and dwell time of each step displayed on the graph As each
27. eeeeeaas 4 13 9 standby Modes mcnaettes etic neti A ia agen edie epee 4 Recommended Tubes and Plates cccceeeeeeeeeeeeeeeeceeeeeeeeeeeteeeees 5 MyCycler Keypad ce ccccececcececeeeeeeeeeeeceaenaecaeceseeeeeeeseeencanaecaeeeeeeeeeees 5 What s in this Manual 2 ccceeceeceeeeecceececeeeeeeeeeeecaeaaeaeeeeeeeeeeeeeeeeeseenaees 8 Quick Guide for Running the MyCycler cccccccesssseeeeeeeeeeeeeeees 9 The HOME SCHON ics cisesveiicsscecs tec estcscteveverccseusdcuessteveidcasescrsveesevads 10 Soft Key Functions for the Home Screen cceccccceeeeeeteeeeeeetteeeeeeenaees 10 Thermal Cycling Protocols cccceccseseeseeeeeeeeeeeeeeeeseeneeeeeeeenees 11 OVEIWIOW EAEE Pose E EEE E E Som fh ac datas ie E saa desea scatnecces tenets 11 The Protocol Library Screen eee ceeeecceeeeeeeeeceee eee eeneeeeeetaeeeeeetneeeeereeea 11 472 1 My Protocols re oap tyes E eee nes ea iceeetis 11 4 2 2 Bio Rad Protocols siseseid a eena ra iae 11 4 2 3 gt Protocol Opting r ebe aa a a Gielen ee a aana aael 12 4 2 4 Soft Key Functions for the Protocol Library ceceeeeeeeeees 12 Protocol Parameters iaaa aa a aa a aai 13 4 3 1 Basic Programming Options sseseeeeeeeeeeeseeeressserrrssrtrrrssreernssent 13 4 3 2 Advanced Programming Options ccccceceeeceeeeeeeeneeeeeeeeneeeees 13 4 3 2 1 Increment Decrement Temperature 00 ceeeees 13 4 3 2 2 Increment Decremen
28. en the you press F3 Option a menu will offer the choices Constant Temp Increment Temp and Decrement Temp Temp Gradient Max Ramp Rate and Set Ramp Rate Figure X X e If the cursor is on a dwell time field when you press F3 Option the choices in the menu are Constant Time Increment Time and Decrement Time e If you press F3 when the cursor is somewhere other than a temperature or dwell time field a message will be displayed advising that no options are available for this item Increment Decrement Temperature When you select one of these options a field will be displayed immediately above the set point temperature field For temperature increments a thermometer icon and an up arrow will appear next to the increment field For temperature decrements a thermometer icon and a down arrow will appear next to the decrement field The specified value will be added to or subtracted from the set point temperature accordingly for each repeat after repeat one Use the number keys to input a temperature increment or decrement value You may set the increment or decrement as low as 0 1 C and as large as you like as long as the combination of the increment or decrement and the number of repeats does not result in a temperature outside the range of the MyCycler 4 0 100 0 C Increment Decrement Time When you select one of these options a field will be displayed immediately below the dwell time field For time increments a clock icon and a
29. he serial number of your instrument The Instrument Name at the time of the run e The thermal cycling protocol in text e The Temperature Measurement Mode selected for the run e The Sample Volume selected for the run if Algorithmic Measurement Mode was specified The Validation Report summary which lists the total number of exceptions and errors Ramp Rates of Gradient Steps 7 2 The Validation Report The Validation Report includes all the details of the Run Report but also includes a list of every step cycle and repeat of the protocol flagged as OK Exceptions or Errors as follows e OK Signifies that the instrument successfully attained the correct set point temperature and held it for the correct amount of time The step will have an OK appended to it e Exceptions and Errors Signifies that an exception or error has occurred or the user has intervened with the progress of the protocol Exceptions and Errors are denoted in the Validation Report with a flag 7 3 Soft Key Functions for Reports Softkey Option Description F1 Begin Brings the display to the first line of the report F2 PageUp Scrolls the report display up by one page F3 PageDown Scrolls the report display down by one page F4 End Brings the display to the last line of the report F5 Done Closes the report display 28 7 4 Uploading Reports An external utility is available to upload Run and Validation reports from the
30. in standby mode To wake the instrument from standby mode simply press the Standby button once Upon waking from Standby mode the Home screen is displayed 8 2 7 Instrument Name Choose this option to input a new Instrument Name for your MyCycler The name may consist of up to 20 characters The instrument name cannot be blank The new Instrument Name will be displayed on the Home screen as well as in Validation Reports and Run Reports for subsequent runs 8 2 8 Beeper Options Choose this option to set the instrument to make a particular sound for a number of different occasions End of Run Sets the beep option for whenever a protocol ends e Error Sets the beep option for errors e Alert Sets the beep option for warnings e Key Click Set to enable or disable audible key presses e Volume Sets the volume of the beeper The changes you make will not be saved unless you press F5 Accept Changes You may press F1 Cancel at any time to cancel the changes you have made and to close the Beeper Options display You may also press F2 Test to sound the beeper with the currently selected volume and tone settings 32 Section 9 The Help Screen The Help screen provides onboard help and information and is displayed when you hit F5 Help from the Home screen From the Help screen you may browse through a list of different help topics which are sorted by category Use the up and down arrow keys to select a topic and then press the Enter or
31. ing a For 100 120 V operation Use 8 0A 5 x 20 mm Type T fuses b For 220 240 V operation Use 4 0A 5 x 20 mm Type T fuses 4 Reinsert the fuse holder into the rear panel of the instrument and press the fuse holder gently until it snaps into place 5 Insert the power cord plug into the power entry module Plug the power cord into a properly grounded outlet 33 The battery will need to be replaced if the time and date do not remain set after the unit is turned off The battery is a 3V lithium coin cell battery number CR2077 Bio Rad catalog 900 1228 To replace the battery 1 Disconnect the power cord 2 Turn the MyCycler over so that the bottom faces up Locate the access panel at the bottom of the front Loosen the screw and remove the panel 3 Remove the old battery and replace it with a new battery A small flat head screwdriver may be used to aid removal The battery terminal flat side must face outwards 4 Replace the access panel on the bottom of the instrument and tighten the screw 5 Reconnect the power cord 10 3 Troubleshooting Procedure Problem Cause Solution No power front panel Blown fuse in power Replace fuse LED does not light entrymodule Fuse blows repeatedly Will not go to 4 degrees Condensation on the tops of tubes or plates menu Lid heater does not work Crushed tubes LCD too light or dark LCD panel blank but fan runs No fan but LCD panel on Time and d
32. k icon and an up arrow for increments or a down arrow for decrements Cycles are demarcated within the plot by vertical bars and are labeled by cycle number in the bottom left corner of their first steps The number of repeats for cycles are displayed in the bottom right corner of their last steps e g 30 repeats would be displayed as 30x and 1 repeat would be displayed as 1x For cycles with an infinite hold the repeats portion of the plot displays 1x The graphical representation of the protocol accommodates a maximum of five steps on the screen at any one time even if this results in a partial display of a cycle Cycle numbers and repeats are shown only in the first step of the cycle whether or not this step gets cut off from the display If the protocol continues off the left edge of the screen a left arrow appears under the bottom left corner of the graphical display Likewise if the protocol continues off the right edge of the screen a right arrow appears under the bottom right corner of the graphical display In either case if the protocol continues off the screen you may use the left and right arrow keys to scroll through the protocol when viewing or editing a protocol 15 Cycle 1 Set Point Temperature and Dwell Time Ramp Up VIEWING My First Protocol Graphical Representation Ramp Down Repeats r Advanced Option Description Run Screen 4 5 Viewing Protocols You m
33. lds within the textual display although it automatically updates to match any option fields edited in the graphical display For example if you added a 30 second dwell time increment to a step and selected the increment field the textual display would read Increase time by 00 30 every repeat If the currently selected parameter contains no increment or decrement then this portion of the screen is empty 5 4 2 Temperature Gradient The MyCycler Thermal Cycler offers a temperature gradient option for optimization of assay conditions Gradients may be programmed at any step of any cycle of the protocol The gradient option allows input of a temperature gradient of 1 25 degrees in total temperature span at temperatures as low as 30 C and as high as 99 C Thermal Gradients in the MyCycler are formed from the front to the rear of the sample block resulting in eight specific temperatures for assay optimization This innovative design allows for evaluation of the maximum assay components at each specific temperature Each row includes twelve wells for evaluation of assay components such as MgC1 or primer concentrations The temperature gradients formed by the MyCycler take a non linear yet highly reproducible shape that allows for excellent prediction of actual sample temperatures at each row Extensive validation of the gradient temperatures indicate that the non linear gradient is both predictable and reproducible Temp Gradient To add a te
34. ler will resume execution of the protocol automatically when power is restored The protocol will resume at the step with the highest set point temperature of the cycle that was interrupted on the same repeat that was interrupted Each power failure is counted as an error at the end of the run and is described in the Validation and Run reports If power is lost more than twice the MyCycler will not resume execution of the protocol If any single power interruption lasts longer than ten minutes the protocol will not resume 26 6 2 3 Pausing a Running Protocol When the STOP key or the Pause F1 soft key is pressed while a protocol is running the MyCycler will go into Pause mode and the temperature of the reaction module block will be brought to the next set point temperature and held there If the MyCycler is counting down a dwell time when the STOP or Pause soft key is pressed it maintains the temperature and the clock stops The soft key options are Resume or End the running protocol If you choose e F1 Resume Run The clock will immediately begin counting down the dwell time or resume counting down at the point at which the protocol was paused e F2 End Run The instrument will be heated or cooled to the idle temperature and you will return to the Home screen 6 2 4 Terminating a Running Protocol To terminate execution of a protocol before it has been completed go into Pause mode as described above and select F2 End Run or p
35. ling rates was conducted to insure reliable and reproducible experimental results The MyCycler features a heated lid This eliminates the need for any oil overlay in the sample tubes as long as lid temperature control is on and the lid remains closed throughout the run The self adjusting heated lid provides the versatility to accommodate a variety of tubes or plates The MyCycler offers two modes of temperature monitoring and control e Algorithm uses the experimentally derived sample temperature given a specific sample volume e Block uses the actual sample block temperature Both modes of temperature control yield excellent results in our test protocols The MyCycler comes with an exceptionally intuitive user interface offering a graphical view of the programmed protocols Each protocol may include as many as 9 cycles with 9 steps each and up to 99 repeats for each cycle Additionally the MyCycler is capable of advanced protocol options such as time and temperature increments and decrements Furthermore every time a protocol is executed a detailed report of the run is recorded and stored on the instrument for 30 days Practice of the polymerase chain reaction PCR process requires a license The MyCycler is an authorized thermal cycler and may be used with PCR licenses available from Applied Biosystems Its use with authorized reagents also provides a limited PCR license in accordance with the label rights accompanying such re
36. made and to close the Default Hot Start Options display 30 8 2 2 Default Temperature Measurement Mode Choose this option to set the default Temperature Measurement Mode as it appears on the Run Setup Screen The changes you make will not be saved unless you press F5 Accept Changes You may press F1 Cancel at any time to cancel the changes you have made and to close the Default Temperature Measurement Mode display 8 2 3 Default Sample Volume Choose this option to set the default Sample Volume as it appears on the Run Setup Screen The changes you make will not be saved unless you press F5 Accept Changes You may press F1 Cancel at any time to cancel the changes you have made and to close the Default Sample Volume display 8 2 4 Idle Temperature Mode Choose this option to specify the temperature control mode in between protocols You may choose to turn off all temperature control when the instrument is idle and allow it to come to ambient temperature or you may choose to maintain a particular Idle Holding Temperature The changes you make will not be saved unless you press F5 Accept Changes You may press F1 Cancel at any time to cancel the changes you have made and to close the Idle Temperature Mode display 8 2 5 Lid Temperature Control Choose this option to specify the heated lid control You may choose between the following options e Set lid temperature to any value from 100 C to 110 C or turn off lid temperature control co
37. mperature gradient to your set point temperatures put the cursor on the desired temperature step of the protocol and press F3 option EDITING STANDARD 2 CHOOSE OPTION Constant Temp Increment Temp tt Decrement Temp 4 Temp Gradient 44 Max Ramp Rate Set Ramp Rate Option Add Del 19 From the menu select Temp Gradient Once selected a default value of 1 C minimum maximum gradient will be displayed Input the desired range of the temperature gradient The display will be updated with the temperatures for each row of samples These values will be recorded in the run and validation reports see Section 7 Note The minimum gradient is 1 0 C the maximum gradient is 25 C The lowest available temperature within any gradient is 30 C the highest allowable temperature within any gradient is 99 C If the first temperature is higher than the second temperature an error mes sage will appear The second temperature will be corrected to the nearest acceptable value In addition any input temperature out of the range of the acceptable values for gradient will be corrected to the nearest acceptable value 5 4 3 Max Ramp Rate Set Ramp Rate The ramp rate is the speed with which the MyCycler changes temperatures between the steps of a cycle or between cycles The default condition is for the MyCycler to adjust temperatures at the maximum ramp rate with the minimum ramp time The MyCycler allows you to change tempera
38. mpletely e Set the lid temperature to 40 C or turn off lid temperature control completely when block temperature is below 25 C Press F5 Accept Changes to save changes or press F1 Cancel at any time to cancel the changes and to close the Lid Temperature Control display Note We do not advise turning off lid temperature control when the block is at 25 C or higher since this will cause evaporation of the samples in most cases 8 2 6 Auto Standby Options Choose this option to enable or disable the Auto Standby feature for your MyCycler and to specify the Length of Idle Time Before Auto Standby within the range of 1 minute to 9 hours and 59 minutes The changes you make will not be saved unless you press F5 Accept Changes You may press F1 Cancel at any time to cancel the changes you have made and to close the Auto Standby Options display The instrument is considered not inuse when it is not running a protocol not receiving input from the keypad not holding temperature for an infinite dwell time or not holding a protocol with unsaved changes in memory 31 When Auto Standby is enabled the instrument will go into standby mode following the specified period of non use The instrument is considered not in use when the instrument is not running a protocol is not receiving input from the keypad is not holding a temperature for an infinite dwell time The advantage to enabling Auto Standby mode is that the instrument saves power while
39. n ceeecccceeeeeeteeeeeeeetteeeeeeenaees 33 Section 10 Care and Maintenance cceeceeeeeeeeeeeeeeeseeeeeeeeeeeeneeneeeeeeeeeeees 33 10 1 Cleaning the Unit aiieieo eii ieia iieii 33 10 2 Replacing a Fuse or a Battery ec eeeeeeeeeeeeeecteeeeeeenneeeeeeenaeeeeeeeaees 33 10 3 Troubleshooting Procedure ceeceeceeeeeeeeeeeeeeecneeeeeeenneeeeeeetseeeeenenaaes 34 10 4 Eror Message Su nren aaa aai an ceded atazate RANE P ARRA 35 Appendix A Specifications wvviccccccsicsiieesearscniseceececsssescsceceecerssersecescersserscorseses 36 Appendix B Product Information cceeceeeceseceeeceeeeeeeeeeeeeeeeeeeeeeeeees 38 Section 1 Introduction 1 1 Overview The Polymerase Chain Reaction PCR has been one of the most important developments in Molecular Biology This technique has greatly accelerated the rate of genetic discovery making critical techniques relatively easy and reproducible The MyCycler thermal cycling instrument provides optimum performance for PCR and other thermal cycling techniques The MyCycler incorporates a Peltier driven heating and cooling system for superb thermal cycling performance See Appendix A Specifications at the end of this manual for detailed information regarding the rates of heating and cooling and accuracy and uniformity of the reaction module s temperature Rigorous testing of the module s accuracy uniformity and consistency in temperature and of heating and coo
40. n its on board memory File management is provided in the Protocol Library screen refer to Section 4 2 The information stored in a protocol file will consist of e the time and temperature for each step of every cycle any gradient or automatic increment or decrement to the time or temperature for each step of every repeated cycle e the number of times each cycle is repeated 5 7 Naming a Protocol A protocol is given a name when Selecting the Save Protocol As option e Selecting the Rename Protocol option Protocols are named using the alphanumeric keys see section 1 5 for details A new protocol is saved as a file under the My Protocols column of the Protocol Library Whenever the protocol is run the name of the protocol appears on the Run screen and in the Validation reports and the Run reports for that run All protocol files names must be unique 22 Section 6 Running Protocols 6 1 How to Run a Protocol To run a stored protocol 1 From the Home screen press F1 to display the Protocol Library 2 Use the arrow keys to highlight the desired protocol Press Enter and from the selection box choose Run Protocol and press Enter 4 Confirm the selections in the Run Setup screen hot start conditions temperature measurement methods and press F5 to Start the Run The Run Setup screen is documented below in section 6 1 1 This symbol on the reaction module indicates a hot surface The reaction modul
41. n up arrow will appear next to the increment field For time decrements a clock icon and a down arrow will appear next to the decrement field The specified value will be added to or subtracted from the dwell time accordingly for each repeat after repeat one Use the number keys to input a time increment or decrement value You may set the increment or decrement as low as 1 0 seconds and as long you like as long as the combination of the increment or decrement and the number of repeats does not result in a dwell time outside the range of the MyCycler 00 00 99 59 18 Constant Temp Time All optional features are reversible To cancel a temperature increment or decrement place the cursor on the set point temperature field or the temperature increment or decrement field and press F3 Option then choose Constant Temp from the list box Similarly to cancel a time increment or decrement place the cursor on the dwell time field or the time increment or decrement field and press F3 Option then choose Constant Time from the list box The set point temperature or dwell time will be made constant and the increment or decrement field will be removed from the display Textual Display of Increments and Decrements After adding an increment or decrement option for either a dwell time or a set point temperature a brief textual description of the increment or decrement will appear at the bottom of the Edit screen There are no editable or selectable fie
42. nverted From the Choose Operation Menu select Convert Gradient A menu will appear that contains a temperature for each row of the gradient Select the conversion temperature from the Choose Row Menu Save the protocol with a unique name Please note that when a gradient protocol is converted to a non gradient protocol the ramp rates associated with the gradient protocol are transferred to the non gradient protocol This is done so that the conversion of a protocol will produce an identical result A black triangle in the upper left corner of a protocol step indicates that the ramp rate has been changed When a step containing an altered ramp rate is highlighted the actual rate is shown below the protocol For more details on changing ramp rates please review Section 5 4 3 in this manual 25 RowB 643 deg C RowC 63 1 deg C RowD 61 2deg C Row E 58 6 deg C Row F 56 9 deg C RowG 55 8deg C Row H 55 0 deg C Ramp rate 1 2 C Second Option AddiDel 6 2 Options While a Protocol is Running 6 2 1 Displaying the Home Screen While a Protocol is Running In the Run screen pressing F4 Home Screen does not affect execution of the current protocol From the Home screen you will be able to perform other functions including programming additional protocols You may return anytime to the Run screen by pressing F3 Run Screen 6 2 2 A Power Failure while a Protocol is Running If a running protocol is interrupted by a power failure the MyCyc
43. oaded protocols or reports if the PC is connected to a printer The USB link is not necessary for running the instrument 1 3 4 Powering Up and Shutting Down Before powering up the MyCycler place it in a location that has sufficient ventilation and access to the reaction module and keypad We recommend at least 4 10 cm clearance to the left right and rear of the instrument For convenience about 14 15 36 38 cm clearance from the bench surface is needed to open the lid To turn the MyCycler on press the Standby button on the front panel of the instrument once A green LED next to the Standby button glows when the instrument is on and receiving power To shut down the MyCycler completely simply unplug the power cord from the power outlet An alternative to system shutdown is Standby mode 1 3 5 Standby Mode To conserve power the MyCycler has a user programmable standby option The green LED next to the Standby button blinks to indicate that the MyCycler is in Standby mode This option will turn off all non essential operations in an idle instrument including the LCD screen heated lid and sample block temperature control The fan will turn off when the internal temperatures have equilibrated Auto Standby settings for the instrument may be programmed as described in Section 8 2 6 When in Standby mode briefly press the Standby button once to turn the instrument back on Standby mode can also be initiated by holding do
44. ocol names are not allowed 4 2 4 Soft Key Functions for the Protocol Library Softkey Option Description F1 Citations PageUp The Citations option is available when the cursor is in the Bio Rad template column This displays a short list of citations that describes the currently selected Bio Rad protocol The PageUp option is available when the cursor is in the My Protocols column This scrolls the My Protocols column up one page from the current page F2 Info PageDown The Info option is available when the cursor is in the Bio Rad column This displays a short description of the currently selected Bio Rad protocol The PageDown option is available when the cursor is in the My Protocols column This scrolls the My Protocols column down one page from the current page F3 Run Screen Displays the Run screen F4 Home Screen Displays the Home screen F5 Done Displays more options for the selected protocol 12 4 3 Protocol Parameters 4 3 1 Basic Programming Options e Set point temperature Temperatures between 4 0 C and 100 0 C may be entered e Dwell time Finite dwell times may be as long as 99 minutes and 59 seconds 99 59 or may be set as short as 0 seconds 00 00 When the dwell time is set to 00 00 the MyCycler will heat or cool until it attains the set point temperature and then immediately begin heating or cooling to the next set point temperature Infinite dwell times may be pr
45. ogrammed for any steps belonging to a cycle with only one repeat When an infinite dwell time is reached the instrument maintains the specified temperature until you intervene If the infinite dwell time is pro grammed for any step other than the last step of the protocol the instrument goes into Pause mode when it reaches that step and holds the set point temperature until you press the Resume Run or End Run soft key You may specify an infinite dwell time by pressing the Shift key followed by the 0 key e Repeat number Any cycle without an infinite dwell time may have 1 to 99 repeats 4 3 2 Advanced Programming Options 4 3 2 1 Increment Decrement Temperature Most protocols call for the exact same temperature for each repeat of a cycle but in some instances you may wish to program an automatic increase or decrease in the step temperature after each repeat To input an automatic increment or decrement function for a step the cycle containing the step must have more than one cycle repeat The automatic increment and decrement function updates the set point temperature by a specified amount after every repeat starting after repeat one For example you could create a cycle with 3 repeats a step at 95 C anda second step at 55 C You could then specify a 0 5 C automatic temperature increment for the second step Thus on the first repeat of the cycle the instrument would go to 95 C and then to 55 C Then on the second repeat of the
46. ress Stop key 6 2 5 End of Run Screen The End of Run screen is automatically displayed after protocol execution It will offer soft key options for getting reports on the protocol These reports are discussed in the following section If there was any problem with the execution of the protocol a message to that effect will be displayed along with the appropriate instructions e g Call your Bio Rad representative 27 Section 7 Reports Reports are textual summaries that record the details and settings of protocols run on the MyCycler These reports are stored in the instrument memory for 30 days and cannot be deleted Following the end of every protocol both a Validation Report and a Run Report are made available by pressing F2 Run Report or F3 Validation Report from the End of Run screen Furthermore you may also access an index of every protocol run for the past 30 days from the View Reports option in the Utilities menu and you may choose to view the reports for any listed run 7 1 The Run Report The Run Report is a subset of the information contained in the Validation Report The Run Report does include the settings of the instrument and protocol but does not track the execution of every step cycle and repeat of the protocol Both the Run Report and the Validation reports include the following details e Protocol name e Date of run e The time at which the protocol started The time at which the protocol ended e T
47. rial number HBrules chrom8 gt Instrument Name Tube Scorcher 16 validation validation apa validation Conditions validation Cycle 1 1x Step 1l 95 0 C for 03 00 validation validation Cycle 2 28x Step 1 95 0 C for 00 30 chrom8 5 chrom8 Step 2 60 0 C for 00 30 validation validation Cycle 3 1x Hold at 10 0 C validation Temp control by Algorithm Sample volume 15 Ul validation Validation Report summary There were no errors or exceptions validation Protocol 1 validation validation Cycle 1 Step 1l 95 0 validation A 3 validation Cycle 2 Step 1 95 for 03 00 OK for 00 30 OK for 00 30 OK for 00 30 OK for 00 30 OK for 00 30 OK C for 00 30 OK C for 00 30 OK i Cancel Operation 0 1 0 Step 2 60 0 Cycle 2 Step 1l 95 0 Step 2 60 0 1 0 2 0 1 i Cycle 2 Step 1l 95 0 60 95 Save to File 8 T 2 z 6 6 6 6 6 6 Pee ee eee ee ee Step Cycle 2 Step li 29 Section 8 Utilities You can access the Utilities menu by pressing F4 Utilities from the Home screen The Utilities menu provides access to basic miscellaneous options related to instrument operation and access to the Set Preferences menu which is a sub menu containing additional options related to preferences and instrument defaults 8 1 The Utilities Menu The Utilities menu contains the Set Preferences option See Section 8 2 Set Preferences Menu as well as the following options
48. rotocols listed in the My Protocols column 4 2 2 Bio Rad Protocols Bio Rad protocols are displayed in the Protocol Library under the column labeled Bio Rad These protocols serve as templates for several different PCR applications These include standard PCR reverse transcriptase PCR RT PCR nested primer PCR PCR with temperature gradients long PCR touchdown PCR and cycle sequencing PCR These Bio Rad protocols may be run directly or modified as needed prior to running or saving If you wish to modify a Bio Rad 11 protocol and save the resulting protocol you must use the Save As option and specify a new name Bio Rad protocols cannot be overwritten or deleted 4 2 3 Protocol Options After selecting the desired protocol and pressing Enter you are presented with the following choices Run Protocol The Run Setup screen is displayed See section 6 1 1 View Protocol The protocol is displayed in the View screen See section 4 5 Edit Protocol The protocol is displayed in the Edit screen See section 5 Delete Protocol Option only available for a user defined protocol You will be asked to confirm that you want to delete the selected protocol from memory Select YES to delete the protocol or select NO to keep the protocol Rename Protocol Option only available for a user defined protocol You will be asked to input a new name for the selected protocol Protocol names are limited to 25 characters Duplicate prot
49. t pressed before the Enter key or an arrow key then a decimal point and 0 are appended to the temperature automatically For example to enter 95 0 C press 9 then 5 and an arrow or Enter key The display will show 95 0 after the last keystroke To enter 95 5 C press 9 5 decimal key 5 Note Entering a fourth digit will cause the left most digit to be lost Entering two digits after the decimal will clear the entire field The Clear key may be used to remove all numbers in the temperature field 5 3 Specifying Cycle Repeats The number of cycle repeats may be between 1 and 99 The number of repeats is entered from right to left similar to time and temperature values For example to specify 35 cycle repeats enter 3 5 Note Entering a third digit will cause the left most digit to be lost 17 The Clear key may be used to remove all numbers in the cycle repeat field 5 4 Creating and Editing Protocols Advanced Options When creating or editing a protocol the system provides additional functionality in the use of the following e Temperature Dwell Time Temperature Gradient Options F3 Option e Changing the Number of Cycles or Steps F4 Add Del 5 4 1 Temperature and Dwell Time Options F3 Option To add periodic increments or decrements to set point temperatures or dwell times put the cursor on the temperature or dwell time that you want to affect and press F3 Option e If the cursor is on a temperature field wh
50. t Time ccceceeeeeeeeeststeeeeeees 14 4 3 2 3 Temperature Gradient c cccccceceeeeeeeeeeeeesecteeeteees 14 Graphical Representation c ccccceceeeeeeeeeeeencecaeceeeeeeeeeeeeseesensaaeeees 14 Viewing Protocols ienai ee i eed 16 4 5 1 Soft Key Functions for the View Screen ececeeeceeeeeeeeenteeeeeees 16 Creating and Editing Protocols ccccceeeeeeeeeeeeeeeeeeeeeeeeeeeees 17 Specifying Time Values tarce iceveadatiecateas aa aaa a a a bes 17 Specifying Temperature Values ccccecceeesecceeeeeceeeeeeeeeeeeeeteeesennisaeeees 17 Specifying Cycle Repeats cccccceceeeeeeeeeeeeeceaeceeeeeeeeeseeeeesensanaeeees 17 Creating and Editing Protocols Advanced Options 2 00eeeeeees 18 5 4 1 Temperature and Dwell Time Options F3 Option 0 08 18 5 4 2 Temperature Gradient ccccccecceeeeeeseeeeececeeeeeeeeeseeeeesessaeaeeees 19 DAS aivedicnuag A E ETA aeveode diel 20 5 4 4 Changing the Number of Cycles or Steps F4 Add Del 21 Soft Key Functions for the Edit SCreen ccc ceeeeeeeeeetteeeeeeentteeeeeeenaees 21 Completing Protocols ccccusseactenqesseccceqeessececacestadelaeeecedecdegteededeeaeestecedes 21 Naming a Protocol acs ccc caceceicces iad eebese i devas A acca aaa ei 22 R nning Protocols sisien nkan aan a raaraa aana aipee irse aasia 23 How to R n a Protocol ioi ieii hin ae a eel en ees
51. taivedseeet s 30 8 1 The Wulitiles Men czcteatcthtaageeee mediated hee ive cited 30 8 1 1 View Reponts vcis cect giire iieiaei aee a bet lageents 30 8 1 2 Instrument Information 0 cccccceeceeeeeeeeeeceeeeeeeeeeeeeeeteeeeensneaeeees 30 8 1 3 Set Date and Time cccccccceceeeeeeeeeeeeeceeeeceeeeeeeeeeeeeeesnceaeeeees 30 8 1 4 Set Display Contrast ccc eeeeceeeeeeeeecneeeeeeeneeeeeeeeneeeeenenaaes 30 8 1 5 Service Options siz itiiti haea eig aiee aa a ehete 30 8 2 The Set Preferences Menu 0 ccccccceeeeeeeccecceceeeeeeeeeseeeeeeaaaeeeeeeeeneeess 30 8 2 1 Default Hot Start Options 0 cece ceeeeeceeceeeeeeeeeeeteeesennneaeeees 30 8 2 2 Default Temperature Measurement Mode 2 0 eeeeeeeeeees 31 8 2 3 Default Sample Volume cece cece cee ceecceeeceeeeeeeeeeeteeeetnntsaeeees 31 8 2 4 Idle Temperature Measurement Mode cceeeeeeeeeeeteteeeeeeees 31 8 2 5 Lid Temperature Control cccccceeeeceeeeeeceeceeeeeeeeeeeteeesenneeaeeees 31 8 2 6 Auto Standby Options ccc eecceeeeeeeenneeeeeeesneeeeeeeeseeeeeeenaaes 31 8 2 7 Instrument Name ccceeceeceeeeeeeeeeeeeeccecaeeeeeeeeeeeseeeeesessaaeeees 32 3 2 8 Beeper Options arreek vee Saad oe ase acs eae eres aaa eds da eds cede 32 Section 9 The Help Sree ins tei ccssicesviceiecevsevcecetsvdesdscesencusvscecesevseievesisessscvessrss 33 9 1 Soft Key Functions for the Help Scree
52. the maximum assay components at each specific temperature Each row includes twelve wells for evaluation of assay components such as MgCl or primer concentrations The temperature gradients formed by the MyCycler take a non linear yet highly reproducible shape that allows for excellent prediction of actual sample temperatures at each row Extensive validation of the gradient temperatures indicate that the non linear gradient is both predictable and reproducible 4 4 Graphical Representation Thermal protocols are displayed graphically as a temperature plot The graphical representation shows a left to right plot of the thermal cycling program and reflects approximate values of the set point temperatures along its y axis The plot displays the set point temperature dwell times and advanced options such as time or temperature increments and decrements for each step At each step the set point temperature in Celsius e g 95 0 C is shown immediately above the temperature plot and the dwell time in mm ss format is shown immediately below the temperature plot Temperature increments and decrements are denoted within 14 the graphical display of a particular step immediately above the set point temperature and followed by a thermometer icon and an up arrow for increments or a down arrow for decrements Time increments and decrements are denoted within the graphical display of a particular step below the dwell time and followed by a cloc
53. tures at a fixed rate less than the maximum Ramp Rate Ramp rates are adjustable to 0 1 C sec Ramp rates must fall within the range of 0 1 to 2 5 C per second for heating and 0 1 to 1 5 C per second for cooling To set the ramp rate make sure a temperature is highlighted Select Set Ramp Rate from the pull down menu of Option F3 A black triangle will appear in the upper left corner and the default ramp temperature will appear below the graphical representation of the protocol Using the key pad input the desired ramp rate then select enter To edit a ramp rate select the step in which the ramp rate has been changed Highlight the black triangle in the upper left corner Using the keypad input the desired ramp rate then select enter To return to the default maximum ramp rate value select the step in which the ramp rate has been changed Select Option F3 choose Max Ramp Rate from the pull down menu then select enter EDITING GRADIENT 2 1 x 30x 6 1 x Gradient H G F E D C B A 55 0 56 1 57 9 60 5 64 3 67 1 69 0 70 0 lt lt Cycle gt jle Option AddiDel Done 20 5 4 4 Changing the Number of Cycles or Steps F4 Add Del The Add Del soft key F4 allows you to change the number of cycles or steps When F4 is pressed a menu of editing choices is displayed Add cycle before Add cycle after Add step before Add step after Delete step and Delete cycle Steps and cycles are added before or after relative to the current
54. uct Description 170 9703 MyCycler Thermal Cycler System includes the MyCycler Thermal Cycler and a box of 0 2 ml Thin Wall Tubes catalog 223 9473 TWI 0201 0 2 ml Tubes With Domed Caps natural 1 000 TFI 0201 0 2 ml Tubes With Flat Caps natural 1 000 TBS 0201 0 2 ml 8 Tube Strips Without Caps natural 125 TCS 0801 Domed 8 Cap Strips for 0 2 ml tubes and plates natural 120 TCS 0803 Optical Flat 8 Cap Strips for 0 2 ml tubes and plates ultraclear 120 TBS 1201 0 2 ml 12 Tube Strips Without Caps natural 100 TCS 1201 Domed 12 Cap Strips for 0 2 ml tubes and plates natural 200 MLP 9601 Multiplate 96 Well 0 2 ml Unskirted PCR Plates natural 25 MSB 1001 Microseal B Adhesive Seals 100 223 9442 96 Well PCR Plate Sealing Mats 5 170 8870 iTaq DNA Polymerase includes 250 U polymerase 10x PCR buffer and MgCl solution 170 8872 MgCl Solution 1 25 ml of 50 mM MgCl 170 8874 dNTP Solution 200 ul of 10 mM of each dNTP 38 Life Science Group Bio Rad Laboratories Inc Web site www bio rad com USA 800 4BIORAD Australia 02 9914 2800 Austria 01 877 89 01 Belgium 09 385 55 11 Brazil 55 21 2527 3454 Canada 905 712 2771 China 86 21 6426 0808 Czech Republic 420 2 41 43 05 32 Denmark 44 52 10 00 Finland 09 804 22 00 France 01 47 95 69 65 Germany 089 318 84 0 Greece 30 210 777 4396 Hong Kong 852 2789 3300 Hungary 36 1 455 8800 India 91 124 2398112 3 4 5018111 6450092 93 Israel 03 951 4127 Italy 39 02 2160
55. ul Note When using individual 0 2 ml tubes in the MyCycler place at least 10 tubes in the reaction block in wells A1 A4 A9 A12 E1 D12 H1 H4 H9 and H12 to ensure that the tubes are not deformed over the course of the protocol Myce aan Pol aa v 1 5 MyCycler Keypad The MyCycler keypad has 26 keys on the front panel These keys are described in the following table Table 1 Table 1 Front Panel Controls Key s Description Softkeys F1 F5 The five function keys referred to as softkeys are labeled F1 through F5 These keys are used to navigate through the software screens and make selections in the screen displays The operations associated with these keys are displayed in inverse video immediately above the softkey These operations change as the display changes For example in the Home screen the F1 softkey will take you to the Protocol Library and the F2 softkey will enable you to Create a protocol Back The Back key will return you to the immediately previous screen or depending on the context to some other more appropriate previous screen From most places in the firmware you can repeatedly press Back until eventually you return to the Home screen When the Home screen is displayed the Back key has no further function When menus or option boxes are presented Back acts as a Cancel key Alphanumeric Keys Centered below the display are ten alphanumeric keys
56. way up to allow maximum clearance and to avoid accidental skin burns AA This symbol on the reaction module indicates a hot surface Always connect the power supply to a 3 prong grounded AC outlet rated 10 A 100 120 V or 5 A 220 240 V using the AC power cord provided with the MyCycler Do not use an adapter to a two terminal outlet Before plugging the instrument in be sure that the correct fuse is installed in the rear panel fuse holder Use the 4A 5 x 20 mm TYPE T fuse for 220 240 V or the 8A 5 x 20 mm TYPE T fuse for 100 120 V Never remove the outer casing of the MyCycler There are no user serviceable parts for this instrument Call your local Bio Rad office for instrument services To insure adequate cooling of the MyCycler place it on a clean flat surface and be sure that there is at least 4 inches 10 cm clearance around each side of the thermal cycler Make sure that the bench space is free of any foreign objects or debris that could block the fan vents Do not operate the MyCycler in extreme humidity or where condensation can short the internal electrical circuits of the thermal cycler Notice This Bio Rad instrument is designed and certified to meet EN 61010 safety standards EN 61010 certified products are safe to use when operated in accordance with the instruction manual This instrument should not be modified in any way Alteration of this instrument will Void the manufacturer s warranty e Void the EN 610
57. wn the blue Standby button once for 3 to 4 seconds The instrument will go into Standby mode unless you are running a thermal protocol or have made unsaved changes to a protocol If you are running a thermal protocol or have made unsaved changes to a protocol you will be asked to verify the standby selection Note Acceptance of standby initiation will terminate or abandon edits for the active protocol 1 4 Recommended Accessories For optimal performance of the MyCycler we recommend Bio Rad tubes plates and accessories as follows Catalog Number Product Description TWI 0201 0 2 ml Tubes With Domed Caps natural 1 000 TFI 0201 0 2 ml Tubes With Flat Caps natural 1 000 TBS 0201 0 2 ml 8 Tube Strips Without Caps natural 125 TCS 0801 Domed 8 Cap Strips for 0 2 ml tubes and plates natural 120 TCS 0803 Optical Flat 8 Cap Strips for 0 2 ml tubes and plates ultraclear 120 TBS 1201 0 2 ml 12 Tube Strips Without Caps natural 100 TCS 1201 Domed 12 Cap Strips for 0 2 ml tubes and plates natural 200 MLP 9601 Multiplate 96 Well 0 2 ml Unskirted PCR Plates natural 25 MSB 1001 Microseal B Adhesive Seals 100 223 9442 96 Well PCR Plate Sealing Mats 5 170 8870 iTaq DNA Polymerase includes 250 U polymerase 10x PCR buffer and MgCl solution 170 8872 MgCl Solution 1 25 ml of 50 mM MgCl 170 8874 dNTP Solution 200 ul of 10 mM of each dNTP The recommended sample volume for 0 2 ml tubes or 96 well plates is 15 100
58. xD Weight Sample Capacity Sample Size Display Chassis 200 Watts typical 18 28 C 20 to 60 C 4 100 C with 20ul sample in a 0 2 ml tube after full warm up when cycling between 50 C and 95 C at least 2 5 C sec maximum heating rate and 1 5 C sec maximum cooling rate Less than 3 minutes to cool from 40 C to 4 C less than 0 5 C 0 5 to NIST traceable standard after 30 seconds at 90 C block mode Well to well uniformity of 0 5 C within 30 seconds after arrival at 90 C 1 25 C 5 25 C 30 C 99 C 0 5 0 5 20 5 x 23 6 x 44 3 cm 8 1 x 9 3 x 17 5 10 kg 22 Ibs 96 wells 0 2 ml each LCD high resolution screen ABS plastic 36 Programming Specifications No of Programs Cycles Protocols Steps Cycles Repeats Cycle Dwell Time Pause Built in Protocols Regulatory PCR Licenses Safety EMC Communications Electrical Approvals 99 on board up to 9 up to 9 up to 99 00 01 99 59 minutes Yes Templates for cycling sequencing Touchdown RT PCR Nested PCR Gradient temperature PCR long PCR Authorized Thermal Cycler Note Use of the MyCycler with authorized reagents also provides a limited PCR license in accordance with the label rights accompanying such reagents Some applications may require licenses from other parties EN 61010 TUV approved Compliance with EN61326 A1 USB ports TUV 37 Appendix B Product Information Catalog Number Prod

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