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MJ Research DNA Engine Dyad PTC-220 Operation Manual Download Page 47

5-9

Creating Programs

Considerations During Program Creation

Once you have written the body of your raw program, there are decisions to make before
creating your Dyad program. They concern how your steps should be implemented. These
decisions involve the following:

•

Temperature control mode

•

Lid control mode

•

Temperature ramping rate (advanced mode only)

•

Temperature hold time

•

Temperature time extend (advanced mode only)

•

Temperature increment (advanced mode only)

•

Temperature gradient (available with the 96-well Alpha unit only).

•

Outside of the example protocol: other considerations

Choosing a Temperature Control Mode

The Dyad cycler can control incubation temperature in three possible ways, each of which
has different implications for the speed and accuracy of sample heating. These include

Calculated Control

, 

Block Control

, and 

In-Sample Probe Control

.

Calculated Control

When using calculated control, the Dyad cycler estimates 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 or probe control.

Since the sample temperature will always lag behind the block temperature, the Dyad
cycler can adjust the block temperature to bring samples of a specific volume in a spe-
cific vessel type to programmed temperatures. This is done through optimized “over-
shoots” of the block temperature by a few degrees for a few seconds, which bring
samples to the desired temperature more quickly.

Calculated control is also the method of choice for most types of programs because it
yields the most consistency, reliability, and speed. Calculated control provides for shorter
protocols in three ways:

1. Brief and precise block temperature overshoots are used to bring samples to

desired incubation temperature rapidly.

Summary of Contents for DNA Engine Dyad PTC-220

Page 1: ...PTC 220 DNA Engine Dyad Peltier Thermal Cycler Operations Manual Version 1 3 Boston San Francisco Tahoe Copenhagen Seoul i ...

Page 2: ...Thermal cyclers can be used for a number of purposes including the polymerase chain reaction PCR PCR is covered by patents owned by Hoffmann La Roche Inc and F Hoffmann La Roche Ltd who have granted exclusive and nonexclusive licenses for some types of applications Roche and its licensees provide end user licenses within their respective fields These licenses have different terms depending on the ...

Page 3: ...d Editing Programs 6 1 Running Programs 7 1 Using the Utilities 8 1 Maintenance 9 1 Troubleshooting 10 1 Part II Accessories Alpha Units and the Remote Alpha Dock System 11 1 Appendix A Safety Warnings and Guidelines A 1 Appendix B How a Peltier Heat Pump Works B 1 Appendix C Shipping Instructions for US Residents C 1 Appendix D Warranties D 1 Index In 1 Declaration of Conformity DoC 1 iii ...

Page 4: ...ms or buttons such as Calculated Block and Tracking Typically these will be parameter selection items Select is meant to be synonymous with click on point and click and any phraseol ogy implying selection of menu or option items with a mouse Particularly with the Dyad cycler select should symbolize any physical selection on the Dyad input devices touch pad mouse numeric keypad arrow keys to access...

Page 5: ...Introduction 1 Meet the DNA Engine Dyad Cycler 1 2 Using This Manual 1 2 Important Safety Information 1 3 ...

Page 6: ...file man agement and much more Choice of calculated temperature control for highest speed and accuracy or of block or probe temperature control for compatibility with protocols designed for a variety of instrument types Instant Incubate feature for continuous temperature incubations Using This Manual This manual contains instructions for operating your DNA Engine Dyad cycler safely and productivel...

Page 7: ... the instrument Warning The DNA Engine Dyad cycler can generate enough heat to inflict serious burns and can deliver strong electrical shocks if not used according to the instructions in this manual Please read the safety warnings and guide lines in Appendix A and exercise all precautions outlined in them Warning Do not block the Dyad cycler s air vents see figs 2 1 and 2 4 for loca tion Obstructi...

Page 8: ...1 4 DNA Engine Dyad Operations Manual ...

Page 9: ...tions 2 Front View 2 2 Control Panel 2 2 Back View 2 3 Bottom View 2 3 Alpha Units 2 4 Single Block Models 2 4 Dual Block Models 2 4 Slide Block 2 4 Power Bonnet Accessory 2 4 Specifications 2 5 Gradient Specifications 2 5 ...

Page 10: ... l t i e r T h e r m a l C y c l e r D N A E n g i n e M J R e s e a r c h Touch pad Air intake vents Display screen Air exhaust vents Dual block Alpha unit lid closed P e l t i e r T h e r m a l C y c l e r D N A E n g i n e D Y A D Numeric keypad Touch pad Keypad Touch pad mouse keys Cursor keys 1 4 VGA display screen ...

Page 11: ...reen contrast adjustment knob External mouse port External mouse touch pad selection switch Back View Bottom View Figure 2 3 Figure 2 4 Dyad cycler front Dyad cycler rear Alpha unit handles Power cord jack Ethernet port Power switch RS 232 port Fuses ...

Page 12: ... Holds customer designed adapter through four screw down points Dual Block Models 30 30 Dual Holds 2 x 30 x 0 5ml tubes 30 48 Dual Holds 1 x 30 x 0 5ml tubes and 1 x 48 x 0 2ml tubes 48 48 Dual Holds 2 x 48 x 0 2ml tubes or half plates Slide Block Twin Towers Holds 2 x 16 standard slides Power Bonnet Accessory Permits remote control of Alpha unit lid opening available for Alpha unit models 96 384 ...

Page 13: ... with installed Alpha unit Line voltage 200 240VAC Frequency 50 60Hz Power 1600W maximum Fuses Two 6 3A 250V 5 x 20mm Displays One 1 4 size VGA screen 320x240 16 colors Ports One 9 pin RS 232 serial port One ethernet port Memory 8 MB Weight 11kg base only Size 48 x 29 x 15cm l x w x h base only Gradient Specifications 96 Alpha unit only Accuracy 0 4 C of programmed target at end columns 30 seconds...

Page 14: ...2 6 DNA Engine Dyad Operations Manual ...

Page 15: ... 2 Optional External Mouse Device 3 2 Environmental Requirements 3 3 Power Supply Requirements 3 3 Air Supply Requirements 3 4 Ensuring an Adequate Air Supply 3 4 Ensuring That Air Is Cool Enough 3 4 Requirements for Robotics Installations 3 5 384 Well Microplate Specifics 3 6 ...

Page 16: ...r location of jack then plug the cord into a 220V electrical outlet With the machine switched off mount the Alpha units see the Installing an Alpha unit section in Chapter 4 Caution Do not insert or remove an Alpha unit with the Dyad cycler turned on electrical arcing can result Read the safety warning in Appendix A re garding electrical safety when inserting or removing an Alpha unit Optional Ext...

Page 17: ... Environmental Requirements Ensure that the area where the DNA Engine Dyad cycler is installed meets the following conditions for reasons of safety and performance Nonexplosive environment Normal air pressure altitude below 3000m Ambient temperature 5 31 C Relative humidity of 10 90 noncondensing Unobstructed access to air that is 31 C or cooler see below Protection from excessive heat and acciden...

Page 18: ...ons of dust with a soft bristle brush or damp cloth Severe collections of dust and debris should be vacuumed out Turn the instrument off prior to cleaning or vacuuming air vents Use a solid non perforated support material when using the Dyad cycler on a wire rack Ensuring That Air Is Cool Enough Do not position two or more DNA Engine Dyad cyclers or other thermal cyclers so that the hot exhaust ai...

Page 19: ...o r c e r a s e n i h c a M e k a t n i r e t n e t o n s e o d r i a t s u a h x e m r a w t a h t o s s e n i h c a m e g n a r r A s t n e v Requirements for Robotics Installations Robotics installations require special attention to airflow and air temperature Typically in these installations DNA Engine Dyad cyclers and other thermal cyclers are restricted to a small area along with other heat ...

Page 20: ...s needed probably about once every 10 to 20 runs Your experience will be the best guide in establishing the frequency for re coating As you will see a very thin coat is sufficient to eliminate any sticking TFE tetra fluoroethylene dry lubricant is available from many sources One source in the United States is Miller Stephenson Chemical Co Inc in Danbury CT 203 743 4447 in Morton Grove IL 847 966 2...

Page 21: ...bes 4 7 Microplates 4 7 Sealing Sample Vessels 4 8 Sealing with Oil or Wax 4 8 Sealing with the Hot Bonnet Lid 4 8 Adjusting the Hot Bonnet Lid s Pressure 4 9 Loading Sample Vessels into the Block 4 10 Using Oil to Thermally Couple Sample Vessels to the Block 4 10 Using the Optional Probe 4 11 Customizing the Probe Vessel 4 11 Adding the Oil 4 12 Loading and Connecting the Probe 4 12 Detecting a F...

Page 22: ...conds During the boot sequence the user is presented with several options including 1 Selftest choose the number 1 on the numeric keypad to instruct the Dyad cycler to perform a diagnostic system test and report any errors 2 Send Files choose the number 2 on the numeric keypad to prepare the Dyad cycler to transfer stored program files to another Dyad cycler see Chapter 8 for instructions on trans...

Page 23: ...tion Keys Cursor keys left right up and down arrows Use to move around within the display screen Numeric keypad Use to enter numeric values Enter key below keypad Use to accept specific programming additions and modifications Touch pad Use to move the display screen pointer with the movement of a finger tip Once the pointer is positioned over a menu or selection item on the display screen a single...

Page 24: ...ng and closing Alpha units with Power Bonnet lids Installing an Alpha Unit Caution Do not insert or remove an Alpha unit with the DNA Engine Dyad cycler turned on electrical arcing can result Read the safety warning in Appen dix A regarding electrical safety when inserting or removing an Alpha unit 1 Turn the DNA Engine Dyad cycler off see the Caution above 2 Hold the Alpha unit at its front and b...

Page 25: ...aution above 2 Pull upward on the handle When the lock releases you will hear a click and the Alpha unit will slide a little toward the back of the DNA Engine Dyad cycler The electrical connectors of the Alpha unit and the DNA Engine Dyad cycler are now disengaged so there is little danger of electrical shock 3 Slide the Alpha unit toward the rear of the DNA Engine Dyad cycler about 3cm 4 Grasp th...

Page 26: ...in choosing sample vessels Keep in mind that differences in tube and plate composi tion 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 MJ Research offers a full range of tubes and microplates manufactured to the specifications of each type of Alpha unit to ensure a p...

Page 27: ...ster heat transfer provided by thin walled tubes allows protocols to be significantly shortened 0 2ml Tubes All types of thin walled 0 2ml tubes may be used MJ Research offers high quality 0 2ml tubes in a number of styles including individual and strip tubes Microplates A variety of polycarbonate or polypropylene microplates can be used in Alpha units as long as they fit the wells snugly Polyprop...

Page 28: ... 14 C and is liquid at room temperature By programming a hold at low temperature the wax can be solidified at the end of a run A pipette tip can then be used to 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 Sealing ...

Page 29: ...neous material can decrease thermal conduction and interfere with the proper seating of a microplate or tubes 2 Open the Hot Bonnet lid Turn the blue 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 lid pivots around a central point so it is important to distribute individual tube...

Page 30: ... for cleaning instruc tions 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 MJ Research 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 ...

Page 31: ... Chapter 5 for information on programming protocols for probe control Probe control cannot be used with heated lid protocols Note Because the thermal characteristics of a probe never precisely match those of an actual sample calculated control is often a better choice than probe control Customizing the Probe Vessel For the most precise control of sample temperatures install the probe s thermistor ...

Page 32: ...sed It is important to use the correct amount of oil so that the representative sample changes tem perature at the same rate as the actual samples To add the oil open the sample tube and pipette in the appropriate amount The oil must completely cover the thermistor Light and heavy silicone oil may also be used but necessitate more complex calculations to determine the amount to add to the probe tu...

Page 33: ...ocol begins running the protocol s temperature control method is automatically switched from probe control to calculated control and the following message is immediately displayed Probe Sensor Failure Used Calc Control If the probe malfunctions during a protocol run the temperature control method is also switched to calculated control When the run finishes the following message is displayed Calc c...

Page 34: ...a m M 1 0 0 1 M S M l a e s o r c i M d a p P 1 0 0 1 P S M p i r t S 8 s p a c 1 0 8 0 S C T p i r t S 2 1 s p a c 1 0 2 1 S C T t u o l l i h C x a w s e i r e s O H C d e t r i k s l a e s o r c i M s e t a l p o r c i m l l e w 4 8 3 s e i r e s P S M d e t r i k s l a e s o r c i M s e t a l p o r c i m l l e w 6 9 s e i r e s P S M d e t r i k s l l e h S d r a H s e t a l p o r c i m l l e ...

Page 35: ...re sealed for oil free thermal cycling 0 2ml Polypropylene Tubes and Polypropylene Microplates These tubes 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 perme able to the 35 S breakdown product Either way there have ...

Page 36: ...ion methods and cleaning procedures for this iso tope Consult your radiation safety officer for his or her recommendations If mild cleaning agents do not remove radioactivity harsher cleaners may be used occa sionally 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 ...

Page 37: ... Viscosity 50cs Volume to use 1 7 x volume of buffer in individual sample tube plus one volume of oil overlay Dow Corning 200 heavy silicone oil dimethypolysiloxane Sigma DMPS V Density 0 97g ml Viscosity 5cs Volume to use 2 7 x volume of buffer in individual sample tube plus one volume of oil overlay Note Use these oils only in the proportions outlined above Using them in any other proportion for...

Page 38: ...4 18 DNA Engine Dyad Operations Manual ...

Page 39: ...hoosing a Temperature Ramping Rate Advanced Mode Only 5 11 Choosing a Temperature Hold Time 5 12 Choosing A Thermal Gradient 5 12 Beyond the Example Protocol Other Considerations 5 13 Entering Program Steps 5 14 The Status Window 5 14 Entering a Program Using Graphical Mode 5 15 Using the Mode Selection Window 5 16 Using the File Save As Window 5 17 The Graphical Programming Window 5 19 Selecting ...

Page 40: ...wer up procedures Let s review The control panel components include Display Screen This is a 1 4 VGA display screen approximately 10cm x 12 5cm located at the left side of the control panel It displays all Dyad cycler operating parameters and can be controlled by the cursor buttons touch pad or external mouse and the numeric keypad Caution Unlike the touch pad the display screen is not a touch scr...

Page 41: ...ioned over a menu or selection item on the display screen a single tap of the touch pad with a fingertip will implement the command The only exception is during the editing of programming steps Selection of programming steps for editing re quires a double tap Tapping the touch pad has the same effect as the left touch pad button Tip When programming we recommend not to rest your finger on the touc...

Page 42: ... protocol requirements Note The procedures involved in actually entering these steps will be described in subse quent pages but please familiarize yourself with the types of steps used to create Dyad programs The considerations behind choosing various elements will be explained further in the Con siderations During Program Creation section The following is a summary of the individual program eleme...

Page 43: ...ature is useful when annealing stringency is a consideration such as in a touchdown program In a touchdown program the annealing temperature begins higher than the cal culated temperature and incrementally decreases each cycle first reaching and eventually falling below the calculated annealing temperature With the reaction beginning at a temperature favoring high stringency in hybridization and i...

Page 44: ...ps Does not contain temperature or gradient steps that contain modifications i e increment temp extend time slow ramp beep Does not contain more than one goto step Does not contain a temperature incubation below 0 C Does not contain a step with an incubation lasting more than 1 hour 39 minutes and 59 seconds 99 59 Forever incubations excepted In addition to the speed with which they can be entered...

Page 45: ...can be opened in basic mode see Opening a Program in Chapter 6 for more information To create an advanced program refer to the Entering a Program Using Advanced Mode section below Designing a New Program The first step in designing any program is the translation of your experimental protocol into Dyad program steps We suggest writing all steps until you are reasonably comfortable with Dyad program...

Page 46: ...ing like this Raw program 1 92 C for 30 seconds 2 60 C for 3 minutes 3 92 C for 30 seconds 4 60 C for 3 minutes 5 92 C for 30 seconds 6 60 C for 3 minutes continues for a total of 60 lines The Goto Option At 60 lines our program is large unwieldy and would take time to input At step 3 repetition can be reduced with the addition of a goto statement Raw program 1 92 C for 30 seconds 2 60 C for 3 min...

Page 47: ...hen using calculated control the Dyad cycler estimates 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 or probe control Since the sample temperature w...

Page 48: ...rature to maintain the probe at programmed temperatures You may purchase an in sample probe from MJ Research Inc The in sample probe is comprised of a temperature probe placed inside a typical capped tube A thin cable exits the top and may be plugged into the Alpha unit Probe control is available for unusual circumstances that may require it Ordinarily though it should be used with caution While t...

Page 49: ...example program Tracking Mode Offsets the temperature of the heated inner lid a minimum specified number of degrees Celsius in comparison to the temperature of the sample block Track ing is useful for protocols with long incubations in the range of 30 70 C where it may be undesirable to keep the lid at a very high temperature An offset of 5 C above block temperature is adequate for most protocols ...

Page 50: ...tion involves repeating a reaction at several different annealing temperatures which requires a great deal of time and monopolizes the instrument while several experiments are run in tandem To complicate matters further similar time consuming experiments may also be required for denaturing temperature optimization The Dyad cycler programmable temperature gradient feature allows for optimization of...

Page 51: ...denatured and prepped for annealing In some protocols after the final elongation step a slow temperature ramp can also be included to ensure proper product annealing In addition some protocols can include a sustained incubation at sub ambient temperatures to preserve the integrity of the products We will choose an initial incubation at 94 C for 1 minute before cycling and a final incuba tion of th...

Page 52: ...convenience of the operator along with the current cycle number The time remaining in the current step and in the program are also indicated At the screen bottom the program control buttons Run Instant Stop Pause Skip and Graphs allow the operator global or line by line control of the program currently loaded into memory These will be covered in more detail in Chapter 7 The Graphs button can be us...

Page 53: ...hical mode essentially in volves editing the graphically displayed TEMPLATE program The TEMPLATE program will be the last graphical program that was saved In this section we will address both creating an initial graphical program and editing a preexisting template Select Programs Note As described earlier this involves positioning the screen cursor over Pro grams with a fingertip on the touch pad ...

Page 54: ...ted in the Lid Mode field To change the control or lid mode select the box in front of that field In either case the Mode Selection window appears Using the Mode Selection Window For the purposes of this example we have decided to use Calculated for our Temperature Control Mode Select Calculated We have decided to use Constant for our Lid Control Mode Select Constant Constant mode will allow the o...

Page 55: ...ll add steps using the Temp Gradient and Goto options Additionally buttons running across the window bottom provide options to De lete Step Save Run Save or Save As programs and Cancel the current programming session Using the File Save As Window The Save and Save As buttons are probably the most important buttons in the graphical programming window since a program that is saved can be used or edi...

Page 56: ...folder in which to store your new program Select New Folder In this Edit KeyPad window you can select letters that will compose the name of your new folder Folder names cannot be longer than eight characters The virtual keyboard will be presented in situations where a combination of let ters and numbers should be entered Select the characters F O L D E R 1 in succession The backspace key can be us...

Page 57: ...H 1 now appears in the Program field The Graphical Programming Window Before we begin entering program steps let s explore the graphical programming win dow The graphical programming window displays the steps of graphical programs in an arrangement of six wide columns separated by seven narrow columns The narrow columns depict the transition phases between steps while the wide columns depict the t...

Page 58: ...ccept the change and move to the next field If you have selected a step such that the field you wish to edit is highlighted use the number keys to enter the desired temperature time or number of cycles Tap the touch pad or click the mouse once to accept the changes If an inappropriate value is entered such as an incubation temperature of 110 C the change will be rejected and the default value or l...

Page 59: ...t Temp A temperature step will be added as the first step in the protocol with a default temperature of 55 0 C and a duration of 30 seconds Proceed to scenario 3 for instructions on editing step parameters 2 If the first step displayed is a gradient step Select the gradient step step 1 Select Temp This will add a new temperature step to the protocol as step 2 with a default temperature of 55 0 C a...

Page 60: ... backspace key on the numeric keypad to delete the cur rent temperature if it is not 94 0 C Enter 94 from the numeric keypad Tap or click once to accept the change Position the cursor text pointer in the time minute field of step 1 and select by tapping clicking once Use the backspace key to delete the current value if it is not 01 Enter 01 from the numeric keypad and tap or click once to accept t...

Page 61: ...m is also a temperature step but with an incubation temperature of 92 0 C and a duration of 30 seconds If step two in the displayed protocol is a temperature step follow the instructions in scenario 3 and in the Editing Step Parameters section to alter the parameters of the displayed step If step two is not a temperature step Select step 1 Select Temp A new temperature step will be added after ste...

Page 62: ...e limit of 65 C and the default lower temperature limit of 50 C The default duration is 30 seconds The maximum temperature range for a gradient is 24 C and the minimum is 1 C Frac tional degrees are not accepted Recall that in our example protocol the gradient step should specify a range of 45 C to 65 C and a duration of 3 minutes Position the cursor text pointer in the higher limit temperature fi...

Page 63: ...step 3 and select by tapping clicking once Use the backspace key to delete the current value if it is not 00 Enter 00 from the numeric keypad and tap or click once to accept the change Entering a Goto Step Step 4 of our program incorporates a goto step designed to cycle a portion of the program a predetermined number of times We have chosen to cycle back to step 2 and repeat steps 2 and 3 an addit...

Page 64: ...bation Step 5 of our program is a forever incubation at 10 0 C to help maintain the integrity of our samples until they can be processed Please note that the instrument can maintain samples at lower temperatures if desired e g 4 C but colder temperatures require considerably more power to maintain and are unnecessary in most circumstances in the opinion of MJ Research scientists Adding a forever i...

Page 65: ...in the fifth temperature gradi ent step column Our completed program appears as follows Select Save to save the completed program GRAPH 1 Note If your completed graphical program still bears the name TEMPLATE select Save As and enter an appropriate name for the program see the Using the File Save As Window section in this chapter A graphical program with the default name TEMPLATE can not be run St...

Page 66: ... that you will choose the Temperature Control Mode and Lid Control Mode for the program Refer to the Considerations During Program Creation section earlier in this chapter for information on temperature and lid control modes We have decided for the purposes of this example to use Calculated for our temperature control mode and Constant for our lid control mode Refer to the Using the Mode Selection...

Page 67: ...ant buttons since a program that is saved can be used or edited at a later date Select Save As As the File Save As window is identical in both graphical and advanced pro gramming mode follow the instructions in the Using the File Save As Window section above to create a new folder named FOLDER2 and a new program named ADV 1 After selecting OK you will be returned to the advanced programming win do...

Page 68: ...4 An incubation at 10 C forever 5 END The first actual step in the protocol is the incubation at 94 C for 1 minute We will use the maximum rate of temperature ramping to this step and we would like the instrument to beep upon reaching the target temperature Position the cursor over the Lid Control Mode step and tap the touch pad ONCE Tapping twice will select the step for editing which will be cov...

Page 69: ...ime Min field Additionally we want the cycler to beep after reaching the target temperature Select Beep on Target At this point in the Temperature Step window all selections have been made according to our protocol Select OK In the advanced programming window the program listing now appears as follows Temperature Control Mode Calculated Lid Control Mode Constant at 100 C 1 Incubate at 94 C for 00 ...

Page 70: ... in the Temperature Step window all selections have been made according to our protocol Select OK In the advanced programming window the program listing now appears as follows Temperature Control Mode Calculated Lid Control Mode Constant at 100 C 1 Incubate at 94 C for 00 01 00 Beep on Target 2 Incubate at 92 C for 00 00 30 Beep on Target End The 92 C denaturation is the first step in the cycling ...

Page 71: ...and the minimum range is 1 C Below the Extend Time option allows for an increase or decrease in incubation time per cycle similar to the option available for temperature steps Since our hypothetical target is 60 C we will choose 45 C for the lower limit and 65 C for the higher limit Additionally we will enter 3 minutes for the incubation hold time Select the Lower Temperature field Enter 45 C Sele...

Page 72: ... the geometry of the Peltier Joule heaters that underlie the block and is normal Rest assured that the temperatures displayed are quite accurate for each well in that column 0 4 C of actual column temperature Select Close Select OK The program listing should now appear as follows Since the program step listing field is limited please use the directional arrow keys to navigate through the steps to ...

Page 73: ...This is typically used during an extension step to allow for diminishing activity of an enzyme or to allow an enzyme to do its job among an ever increasing quantity of product Assume for example that we required a 60 C step with a 1 minute incubation and that we wished to increase the incubation time by 5 seconds per cycle In the Temperature Step window you would implement the following Enter 60 C...

Page 74: ... What we really want it to do is run 30 cycles total This involves the insertion of a goto step Goto steps are useful for cycling your commands a predetermined number of times We have decided to cycle the steps in ADV 1 twenty nine more times Select GoTo The GoTo Step window appears Position the cursor in the Goto step number field and select Enter 2 in the field Note We do not want to include ste...

Page 75: ... are described below should they be needed in other protocols Entering a Lid Control Step When using a single block Alpha unit fitted with a Power Bonnet motorized lid it may be desirable to include steps in the Dyad program that direct the lid to open or close This can be particularly useful in robotic installations To include a lid control step in a program Select Lid in the programming window S...

Page 76: ... for modifying a temperature step to allow a per cycle increase or decrease of temperature each time the step is executed see The Elements of a Program near the beginning of this chapter for more information Move from the programming window to the Temperature Step window using the Temp button as before Enter the appropriate incubation Temperature enter 60 as an ex ample and Time enter 30 seconds a...

Page 77: ...ctions are similar to adding a temperature step with the exception of selecting Forever rather than entering an incubation Time The final program should appear as follows Temperature Control Mode Calculated Lid Control Mode Constant at 100 C 1 Incubate at 94 C for 00 01 00 Beep on Target 2 Incubate at 92 C for 00 00 30 Beep on Target 3 Gradient from 45 C to 65 C for 00 03 00 4 Cycle to step 2 for ...

Page 78: ...DNA Engine Dyad Operations Manual 5 40 ...

Page 79: ... Editing a Program 6 4 Editing a Graphical Program 6 5 Editing an Advanced Program 6 6 Highlighting and Selecting Program Steps 6 6 Deleting a Step 6 6 Inserting a Step 6 7 Editing a Step 6 7 File Utilities 6 8 Saving an Edited Program 6 8 Copying a Program 6 9 Deleting a Program 6 10 Moving a Program 6 11 Deleting a Folder 6 11 ...

Page 80: ...ed to disk as the programs GRAPH 1 and ADV 1 were in the previous chapter it can then be opened for editing or running From the Status window menu bar Select Programs Select Open An additional menu appears allowing you to choose Advanced Mode or Ba sic Mode Opening a Program in Advanced Mode To open our example advanced program ADV 1 Select Advanced Mode You are presented with the open program win...

Page 81: ...pened and edited in advanced mode only a subset of advanced programs can be opened and edited in basic mode Advanced programs that meet the criteria outlined for graphical programs in the Types of Programs section of Chapter 5 can be opened in basic mode Our advanced program ADV 1 can not be opened in basic mode because it con tains the step modification option Beep on Target If an advanced progra...

Page 82: ...o longer be opened or edited in basic mode We will open our example graphical program GRAPH 1 in basic mode The procedure is similar to that described above for opening a program in advanced mode and is summa rized here Select Programs Select Open Select Basic Mode The open program window will appear Select the folder FOLDER1 Select the program GRAPH 1 Select OK GRAPH 1 will be displayed in the gr...

Page 83: ...cal Mode in Chapter 5 specifically The Graphical Programming Window section for more information To replace step 3 the gradient step with a temperature incubation at 60 C first open the program GRAPH 1 in basic mode as described above Select the gradient step Select Delete Step Select step 2 the temperature incubation at 92 C Recall that new steps are added AFTER the selected step Select Temp The ...

Page 84: ... Selection can also be done via the left touch pad button In order to insert or edit steps the Dyad user should become familiar with these conventions By default in this manual we use the single touch pad tap mouse click to highlight a step and a double tap click to select it Deleting a Step The Delete Step button will allow us to delete a program step To begin the process of changing step 3 of ou...

Page 85: ...r as follows Temperature Control Mode Calculated Lid Control Mode Constant at 100 C 1 Incubate at 94 C for 00 01 00 Beep on Target 2 Incubate at 92 C for 00 00 30 Beep on Target 3 Incubate 60 C for 00 03 00 Beep on Target 4 Cycle to step 2 for 29 more times 5 Incubate at 10 C forever End Editing a Step Step 2 of the program ADV 1 includes a 30 second incubation We wish to change that incubation to...

Page 86: ... You can also delete a folder These functions with the exception of saving can be accessed from the Programs drop down menu on the Status window menu bar Saving an Edited Program The decision required here is whether to save the program under the same or different filename In Chapter 5 we discussed the Save As button which allows the creation of a new filename In this instance we will simply save ...

Page 87: ... want to create separate folders to organize them Perhaps you will use separate folders for different us ers or experimental series To copy a program Highlight the From Folder and To Folder locations for the copy Highlight the program in the Copy Program list to be copied Select Copy The program now resides in the destination folder Select Exit to return to the Status window ...

Page 88: ...open program window We provide a conve nient program listing at the bottom of the window so that you can determine whether you truly wish to delete the program Highlight the Folder containing the program to be deleted Highlight the Program Select Delete Before a program is deleted you are presented with a confirmation screen asking you to verify the deletion If you wish to delete the program selec...

Page 89: ...ram is maintained in the To Folder The copy in the From Folder is deleted You will not be prompted with a verification step for this move so exercise some caution Deleting a Folder No command set would be complete without a folder maintenance window Folders must be empty before deletion Select Programs in the Status window Select Delete Folder from the drop down menu To delete a folder highlight i...

Page 90: ...hapter we have utilized editing tools to add and subtract steps from our example programs In addition we learned to utilize file and folder tools to maintain our program lists In subsequent Chapters we will learn more about the menu bar of the Status window and how to navigate the utilities and functions located there We will also learn how to run our new program ...

Page 91: ...tant Incubation Feature 7 2 Running Programs 7 4 The Run Program window 7 5 During the Run 7 6 Run Status 7 6 Terminating a Run 7 7 Pausing Resuming a Run 7 7 Skipping a Step 7 8 Inaccessible Features 7 8 Running Multiple Programs 7 8 ...

Page 92: ...0 C to 105 C 4 C to 100 C with the Twin Towers block This feature can be used for performing ligations digestions etc or with slides overnight humidified hybridizations Note The Twin Towers block can be used as a humidified chamber for steady state incuba tions e g hybridizations color development reactions To humidify a block push one labo ratory tissue into the bottom slot and inject 1ml of deio...

Page 93: ...e desired block s Select OK The block s will now incubate at the desired temperature The Status window will display the status of the selected block Use the block selection menu to select a block To stop the incubation select the appropriate sample block from the block selection menu Select Stop at the bottom of the window A confirmation window will appear asking you to verify termination of the i...

Page 94: ...ical program the program must be assigned a name other than the default name TEMPLATE by performing a save as Graphical programs with the default name TEMPLATE can not be run The Run Program window will appear allowing you to specify the block on which the proto col should be run and the calculated control parameters for the run if applicable as de scribed below To run previously created programs ...

Page 95: ...reparing to run a program using calculated temperature control selecting OK will display a Select Calculated Mode Parameters window that is appropriate for the type of program and Alpha unit that you are using Parameters entered here will allow precise temperature calculations by the Dyad cycler for your specific protocol and Alpha unit For example for a 96 well Alpha unit the following selection ...

Page 96: ...graph the Block Temp Sample Temp and or Lid Temp over time select the appropriate options near the bottom of the Graphs window The estimated Time Remaining in the program and the amount of Time Elapsed since the program was initiated are also indicated Select Status to return to the Status window The Status window will display Block Sample and Lid temperatures correlating to the program running on...

Page 97: ...un log including the date and time that a program was initiated by a user select Cycler Log from the View menu Terminating a Run To terminate a run prior to completion select the appropriate block from the block selection menu in the Status window and select Stop Alternatively select the Command menu in the Status window and then select Stop and either All to terminate all programs run ning on all...

Page 98: ...ll be replaced with Probe temperature Additionally programs with lid temperature steps will not run with probe control Gradient step Alpha units other than 96 well Alpha units will be grayed out Lid step Alpha units will be grayed out if a lid step is included in the protocol but there is no Power Bonnet lid installed Lid mode Alpha units will be grayed out if the lid mode is not set to OFF when u...

Page 99: ...n the Running Protocols section in this chapter to initiate an independent run To summarize we have learned how to run programs on the Dyad cycler We have learned how to select our options based on the type of Alpha unit and sample vessels used in our experiment We have learned how to terminate a program run Finally we have learned how to use the most versatile feature of the Dyad cycler by runnin...

Page 100: ...Using the Utilities 8 About 8 2 User Name 8 3 Set Date Time 8 3 Remote 8 4 Auto Remote 8 4 Update Soft Network Config 8 5 Ping 8 7 Additional Utilities 8 8 Transferring Program Files 8 8 ...

Page 101: ...ilities of the Dyad cycler providing access to user name control remote command mode and the date and time settings The Utilities submenu is selectable from the Status window Here is a review of the available submenus About When this item is selected a screen like the following will appear This screen indicates the Dyad system software version The software version information on this screen can be...

Page 102: ...manner any potential user can determine the owner of a block the person running a program as their name will be displayed when the block is selected in the Status window To delete a user name highlight the name and select Delete User Name Select OK to exit from this screen Set Date Time Choosing this option will allow the setting of the Dyad system time Enter the appropriate information in the fie...

Page 103: ...on by exiting the Remote Mode window will cancel this protocol A confirmation screen will ask you to confirm your intent to exit the Remote Mode window Log on to www mjr com for the latest syntax of the remote command set Auto Remote Select Auto Remote from the Utilities menu to direct the Dyad cycler to automatically enter remote mode upon subsequent power up This feature is particularly useful i...

Page 104: ...ew the current software versions Front end software version 1 07 or greater is required to use the Update Soft and Network Config utilities To view the available software upgrades and or perform an upgrade begin by establishing internet access via an Ethernet 10BaseT connection Connect the ethernet cable to the ethernet port located at the rear of the Dyad cycler see figure 2 3 Then select Update ...

Page 105: ...pear directing you to power cycler the instrument in order to implement the connection information To update the engine or front end software Select Update Soft from the Utilities menu to access the HTTP Update Software Utility window Select Display Versions to view the available software upgrades Click on the arrow button to the right of the Select Software Version field to display the available ...

Page 106: ...dow Select a host name using the up down cursor keys Enter the number of times that you wish to ping the host the interval between pings ms and the lost interval the amount of time sec before the request times out Select OK to return to the Ping window Select PING to run the ping program The results will be displayed in the DL Sockets TCP IP Kernel window A tally at the bottom of the window will l...

Page 107: ... cycler see the Turning the DNA Engine Dyad Cycler On section in Chapter 4 several options are available for transferring pro gram files Options 2 Send Files and 3 Receive Files can be used to establish a Dyad cycler to Dyad cycler transfer of all program files in all folders To perform a Dyad cycler to Dyad cycler file transfer 1 Use a standard DB9 null modem cable to connect the Dyad cyclers via...

Page 108: ...file transfer select Proceed Exit when completed by entering 1 on the numeric keypad of the sending instrument Once the transfer is complete the TRANSFER COMPLETE message will be displayed and the instrument will proceed with the boot sequence ...

Page 109: ...DNA Engine Dyad Operations Manual 8 10 ...

Page 110: ...intenance 9 Cleaning the DNA Engine Dyad Cycler 9 2 Cleaning the Chassis and Block 9 2 Cleaning the Air Vents 9 2 Cleaning Radioactive or Biohazardous Materials Out of the Block 9 3 Changing the Fuses 9 3 ...

Page 111: ...k 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 coating possibly causing electrical shorting If you use oil in the block a practice not recommended by MJ Research Inc see Using Oil to Thermally Couple Sample Vessels to the Block in Chapter 4 clean the wells whenever the oil has bec...

Page 112: ...rning The DNA Engine Dyad 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 Dyad base You could receive a 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 0 off position 2 Insert ...

Page 113: ...9 4 DNA Engine Dyad Operations Manual ...

Page 114: ... System Problems 10 2 Error Messages 10 3 Problems in Power Up 10 8 Problems with System Performance 10 9 Problems with an Alpha Unit 10 10 Problems Related to Protocols 10 10 Problems due to Environmental Conditions Setup and Maintenance 10 13 ...

Page 115: ... Frequency of the problem i e is the problem repeatable Steps already taken to troubleshoot the problem i e controls performed System Problems The Status window was reviewed in Chapters 5 6 and 7 covering the creation editing and running of programs For a review of the basic menus of this window please review these chapters In the Status window the View submenu allows the user to view the Error Lo...

Page 116: ... the run and you will be notified if any persistent problem is found No action required at this time 19 BSF LI An irregularity was detected in the block s left temperature sensor The sensor will be checked automatically during and after the run and you will be notified if any persistent problem is found No action required at this time 17 BSF RI An irregularity was detected in the sensitivity of th...

Page 117: ...ached a temperature higher than normal and the program was automatically stopped Adequate airflow is necessary to prevent the heat sink from overheating Please observe the following guidelines 1 place instruments at least 10cm apart 2 avoid placing instruments in any location where hot air might enter the intake vents 3 place instrument on a hard surface with no debris or paper underneath 4 clean ...

Page 118: ...ms or call 888 MJ CYCLE in the US or Canada or your local distributor outside the US or Canada 18 PSF A possible fault was detected in the in sample probe The thermal control method has been switched to Calculated Mode Results may have been affected Check probe and connections If problem reoccurs please call 888 MJ CYCLE in the US or Canada or your local distributor outside the US or Canada 9 PSO ...

Page 119: ...ature sensor The sensor will be checked and you will be notified if any problem is found No action required at this time 12 SBC CAF The block took slightly longer than expected to achieve the programmed temperature This condition may be caused by inadequate airflow or a problem with the Alpha unit itself Please observe the following guidelines 1 place instruments at least 10cm apart 2 avoid placin...

Page 120: ...The thermal gradient has not been achieved as quickly as expected This may indicate a possible problem with the Alpha unit Call 888 MJ CYCLE in the US or Canada or your local distributor outside the US or Canada 10 UF The instrument has detected unexpected temperature readings This may indicate a problem with the Alpha unit Replace fuse on instrument and confirm that instrument is functional If pr...

Page 121: ...on In this case a problem should be consistent and repeatable Is the fan on Turn power on Did you h ear a beep Is unit plugged In Are fuses good Unit defective Does the initialization screen appear 220Vac Secure Alpha Replace fuses 5x20mm 6 3A Was hit o enter Selftest Selftest Pass Does the About screen appear Unit ready y n y n n y y n y n n y y n y n y n units Plug cycler into Are Alpha units in...

Page 122: ...icated on the display Select last block Are temperatures indicated on the display n n y Re boot and runself test program Pass y n Unit defective return for service Front end software may have become corrupted Re load software Re Test Problem corrected y n Front nd OK proceed Are the number keys working Try an Instant Incubate Are the cursor keys working Try navigating a window with them Is the tou...

Page 123: ...ing point for further investigation Should the Dyad system check out OK we recommend posi tive controls for troubleshooting purposes Following is a general description of some common problems related to the protocols and reaction components in sequencing and thermal cycling applications For a more detailed discussion of protocols and reactions see Current Protocols in Molecular Biology F Ausubel e...

Page 124: ...m e t g n o r W d e s u d o h t e m k c e h c o t y t i l i t u t s i L e s U r o f d o h t e m l o r t n o c e r u t a r e p m e t d e d e e n f i e g n a h c l o c o t o r p o t e n i h c a m g n i s u a c d e l i a f e b o r P d e t a l u c l a c r e d n u l o c o t o r p n u r l o r t n o c e r u l i a f e b o r p r o f n e e r c s k c e h C d e e n y a m e b o r P e g a s s e m r o r r e J M ...

Page 125: ... r o s t c u d o r p n e e s r u c c o n o i t a z i d i r b y h c i f i c e p s n o N p u t e s g n i r u d g n i r e h t o t n i t r a t s t o h a m a r g o r P l o c o t o r p n o i t a r t n e c n o c t n e n o p m o c n o i t c a e R w o l o o t r o h g i h o o t o p m o c f o s n o t a r t n e c n o c k c e h C e z i m i t p o e r o t d e e n y a M s t n e n n o i t a r t n e c n o c m u i s...

Page 126: ...a t n i r i a e r u s e k a M s i r b e d t s u d y b d e t c u r t s b o t o n c e l l o c t h g i l e v o m e R r e p a p r o h t i w s i r b e d d n a t s u d f o s n o i t y v a e h t u o m u u c a V h t o l c p m a d s r e p a p y n a e v o m e R s n o i t c e l l o c i s o P e n i h c a m e h t r e d n u d e c a l p m o r f m c 0 1 t s a e l t a e n i h c a m n o i t s e c a f r u s l a c i ...

Page 127: ...DNA Engine Dyad Operations Manual 10 14 ...

Page 128: ...pha Dock System 11 Alpha Units Available from MJ Research Inc 11 2 About the Remote Alpha Dock System 11 4 Packing checklist 11 5 Requirements 11 5 Environment 11 5 Power Supply 11 6 Air Supply 11 7 Installation 11 7 Operation 11 8 ...

Page 129: ...optimize reaction conditions in a single ex periment The 384 for 384 well Plates ALS 1238 MJ Research Inc has worked with several genome centers to develop a high density format for automated operation The result is the 384 well Alpha unit a true 4X version of the 96 well format The wells have the same V profile and are spaced on 4 5mm centers The Flat Block for Microarrays and Customized Attachme...

Page 130: ...nt blocks each of which can hold 16 slides in isothermal chambers that ramp at rates up to 1 2 C second Slides can easily be sealed with either Self Seal reagent or Frame Seal chambers and the blocks can double as humidified chambers for hybridizations The 96 with a Power Bonnet motorized lid ALP 1296 This sample format can hold either one 96 well microplate or 96 x 0 2ml tubes or strips of 0 2ml ...

Page 131: ...m the PTC 220 base enabling more efficient use of space and facilitating robotic operation The basic system the RAD 200 comprises a dock connector which mounts in the cycler base and a Remote Alpha Dock base into which the Alpha units are mounted Additionally the fan power supply along with the cables to run up to four Remote Alpha Dock fans from a single thermal cycler base must be purchased sepa...

Page 132: ...200 One wall plug power cord RPS 0200 Three round jack power cords RPS 0200 Product registration card US and Canada only Extended warranty application US and Canada only Requirements Environment The Remote Alpha Dock system allows for custom installations The following placement configurations are recommended by MJ Research Inc Figure 11 2 Remote Alpha Dock base and dock connector bottom view ...

Page 133: ...s than that resulting from the unit being placed on a solid horizontal platform A minimum top clearance is also required to allow access to and operation of the Alpha unit lid Remote Alpha Dock units can be flush mounted i e with the feet removed to facilitate robotic operation as long as the airway beneath the unit is equivalent to the airway the unit would have with the feet attached Usually a h...

Page 134: ...labeled DATA and the other POWER Connect the multi pin power cable s male end to the female socket labeled POWER and slide the latch to lock the pins in place Both of the data cable s multi pin connectors are male one is labeled CONNECTOR DATA and the other DOCK DATA Attach the CONNECTOR DATA end to the fe male connector labeled DATA on the circuit board and slide the latch to lock the pins in pla...

Page 135: ...to the initial Remote Alpha Dock unit via the round jack power cords supplied Attach one end of the cord to the initial unit s free round connector Attach the other end to either of the round connectors on the back of the next Remote Alpha Dock unit in the series and so on fig 11 4 When the Remote Alpha Dock system has been completely set up connect the fan power supply s wall plug to a power sour...

Page 136: ...11 9 Alpha Units and the Remote Alpha Dock System Figure 11 5 Flush mounting template ...

Page 137: ...11 10 DNA Engine Dyad Operations Manual ...

Page 138: ...lpha unit blocks can become hot enough during the course of nor mal operation to cause burns or cause liquids to boil explosively Wear safety goggles or other eye protection at all times during operation Warning The PTC 220 DNA Engine Dyad cycler incorporates neutral fusing which means that live power may still be available inside the machine even when a fuse has blown or been removed Never open t...

Page 139: ...cations Operation of these machines in a residential area is likely to cause harmful interference in which case the user will be required to correct the interference at his or her own expense In addition the PTC 220 DNA Engine Dyad thermal cycler designs have been tested and found to comply with the EMC standards for emissions and susceptibility established by the European Union at time of manufac...

Page 140: ...lectrical current is passed through the blocks electrons in the N type blocks and the holes or empty electron spaces in the P type blocks are excited at one conductor semicon ductor interface which absorbs a small amount of heat The electrons and holes flow through the crys talline blocks and return to a low energy state at the other conductor semiconductor interface with the re lease of the previ...

Page 141: ...that is excessively oily or that emits ionizing radiation upon arrival at our factory PLEASE ELIMINATE ALL BIOHAZARDS AND RADIA TION 3 Pack the machine in its original packaging If this has been misplaced or discarded call MJ Research to request shipment of packaging materials You can also request a loaner machine which will be provided if available a rental fee may apply You can use the loaner s ...

Page 142: ......

Page 143: ...warranty lasts so the above limitation may not apply to you The warranty and remedies set forth above are exclusive and in lieu of all others oral or written expressed or implied No MJ Research dealer agent or employee is authorized to make any modification addition or extension to this warranty except in the form of the extended warranty outlined below MJ Research is not responsible for special i...

Page 144: ...mal cycler the opportunity to purchase an extension of the warranty coverage explained above for an additional two years The coverage must be purchased through a purchase order received by MJ Research within 30 days of receipt of the offer of extended warranty or the offer to renew the extended warranty These offers apply only to machines sold and used in the U S A and Canada ...

Page 145: ...6 5 37 gradient step entering 5 33 5 35 increment temp option 5 38 5 39 inserting a step 6 7 lid control step entering 5 37 opening 6 2 6 3 slow ramp option 5 37 specifications 5 7 temperature step entering 5 30 5 33 Advanced programming window 5 29 Air exhaust vents location of 2 2 Air intake vents location of 2 2 2 3 Air supply requirements ensuring adequate air supply 3 4 ensuring air is cool e...

Page 146: ...wing holds 4 8 Constant mode 5 11 Constant temperature incubator use as 7 2 Contrast adjustment knob location of 2 3 Control panel 2 2 4 3 5 2 block status lights 4 4 cursor buttons 4 3 5 2 display screen 4 3 5 2 layout 2 2 numeric keypad 4 3 5 3 touch pad 4 3 5 3 touch pad buttons 4 3 5 3 using 4 3 Conventions programming 5 4 Copying programs 6 9 Cursor buttons See Control panel Cycler log 7 7 D ...

Page 147: ...l requirements 3 3 3 5 Error log 7 7 10 2 Error messages 10 3 Ethernet port location of 2 3 Example program 5 8 Extend time option 5 5 5 35 5 36 F FCC warning A 2 File save as window using the 5 17 5 19 File transfer 8 8 Dyad cycler to Dyad cycler 8 8 File utilities 6 8 copying programs 6 9 deleting folders 6 11 deleting programs 6 10 moving programs 6 11 saving edited programs 6 8 Folder creating...

Page 148: ...adding a step 5 20 deleting a step 5 20 editing 6 5 6 6 See also Editing a program editing a step 5 20 forever incubation entering 5 26 goto step entering 5 25 5 26 gradient step entering 5 24 5 25 opening 6 4 selecting a step 5 20 specifications 5 6 temperature step entering 5 21 5 24 Graphical programming window 5 19 5 20 adding a step 5 20 deleting a step 5 20 editing a step 5 20 forever incuba...

Page 149: ...5 11 tracking mode 5 11 Lid control step advanced program 5 5 5 37 Loading sample vessels 4 10 M Maintenance 9 2 Microplates removing 3 6 selecting 4 7 Microseal A film 4 8 Microseal B adhesive seals 4 9 Microseal M sealing mat 4 9 Microseal P pads 4 14 Mode selection window 5 16 5 17 5 28 Monitoring the run 7 6 Mouse device connecting 3 2 selection switch 2 3 Mouse keys 2 2 4 3 See also Touch pad...

Page 150: ...8 8 Ports 4 4 ethernet 2 3 RS 232 2 3 8 4 Power Bonnet lid 2 4 Power cord location of jack 2 3 plugging in 3 2 Power supply requirements 3 3 acceptable power cords 3 3 Power switch location of 2 3 Probe adding representative sample calculating amount of oil to add 4 12 choosing type of oil 4 12 how to add oil 4 12 silicone oil as representative sample 4 17 connecting to block 4 12 customizing prob...

Page 151: ...temperature gradient 5 12 See also Gradients choosing temperature hold time 5 12 choosing temperature ramping rate 5 11 example 5 8 other considerations 5 13 editing 6 4 6 8 See also Editing a program advanced 6 6 6 8 graphical 6 5 elements end step 5 5 go to step 5 5 gradient step 5 5 lid control mode 5 4 temperature control mode 5 4 temperature step 5 5 graphical 5 15 5 27 adding a step 5 20 del...

Page 152: ...aning 4 16 problem with 35 S nucleotides 4 15 solutions to 35 S problem 4 15 Ramping rate 2 5 5 11 Receive files 4 2 8 8 Remote Alpha Dock system air supply requirements 11 7 environmental requirements 11 5 installation 11 7 operation 11 8 packing checklist 11 5 power supply requirements 11 6 Remote operation 8 4 Remote utility 8 4 Removing microplates See Microplates Resuming a run 7 7 7 8 Roboti...

Page 153: ... thick walled 4 7 Use of oil to improve thermal contact with block 4 10 Save run 7 4 Saving a program 5 17 5 19 Saving edited programs 6 8 Selftest 4 2 Send files 4 2 8 8 Service utility 8 8 Setting machine up 3 2 See also Alpha units installing Shipping instructions C 1 Skipping a step 7 8 Slow ramp option 5 37 5 38 Software update 8 5 8 6 Software version 8 2 Specifications DNA Engine Dyad cycle...

Page 154: ...racy 2 5 Thermal uniformity 2 5 Thermoelectric unit B 1 Time Date setting 8 3 Touch pad See Control panel Touch pad buttons See Control panel Touch pad location of 2 2 Touch pad mouse selection switch location of 2 3 Touchdown 5 5 See also Increment temp option Tracking mode 5 11 Transferring program files 8 8 Dyad cycler to Dyad cycler 8 8 Troubleshooting error messages 10 3 problems in power up ...

Page 155: ...Index In 11 service 8 8 set date time 8 3 update soft 8 5 8 6 user name 8 3 V Virtual keyboard 5 18 W Warranties D 1 ...

Page 156: ...DNA Engine Dyad Operations Manual In 12 ...

Page 157: ...Declaration of Conformity DoC 1 ...

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