GM-F6000 Thermal Cycler
Contents
1. Use good quality PCR tubes USB flash drive is not TC drive is inserted recognized The USB flash drive incompatible with the cycler Tubes are deformed after Tubes are of poor quality too soft experiment or bad heat resistance Heat lid didn t work or the Turn on the heat lid and set the lid Sample losing because of temperature of lid is set too low temperature to be higher than 105 C evaporation poor quality better quality Press Run on display but no l l Stop the last running program before l Another program is running l action running a new one Message Can t find xx a Touch OK to cancel this message and then A running program on USB flash program on USB flash drive touch OK again to cancel the Warning A drive is restored but the USB and the screen is black when power failure has occurred message flash drive didn t insert on cycler power on Touch Stop to exit Adjust date and time via System Clock should be reset Setting Admin Options gt Date Time Clock is abnormal screen The battery in the cycler should TE EEN be changed Warning message Instrument Improper operation Shut off and contact the maunfacturer failure Error code 01 to 05 Instrument failure GM F6000 Thermal Cycler User Manual 34 PT E GMbiolab Co Ltd www genemarkbio com E mail tech genemarkbio com Gvbiolab2. 1 Installation 1 1 Site Requirements Power supply Environmental Conditions 1 2 Unpacking The Thermal Cycler is intended for indoor use Ensure that the installation site meets conditions below The Thermal Cycler has a universal 85V 265V power supply and is supplied with an appropriate plug Be sure that the instrument is connected to a reliable power outlet that is rated to handle the load of the thermal cycler Table 1 Temperature and humidity conditions Ambient temperature 10 to 30 C 50 to 86 F Relative humidity 20 to 8096 noncondensing Place the Thermal Cycler on a level table or bench Avoid placing the instrument adjacent to heaters cooling instruments water sink or in direct sunlight Keep away from any equipment that vibrates such as a refrigerator or centrifuge The recommended distance between the instrument and the back wall is 20 cm 7 9 in Two thermal cyclers can be placed side by side Remove the packaging materials and keep in case of shipping damage to the unit 2 Inspect the instrument for shipping damage 3 Included in the box should be Thermal Cycler with block Appropriate power cord User Manual this manual including warranty certificate Performance Test Statement or pass card 1f have IMPORTANT If the Thermal Cycler is damaged or some items are missing or damaged contact our company or local distributor 4 Move to the desired installation site 1 3 P
3. 4 Touch Calculate to display calculated temperature gradient from the first column to the twelfth column 5 Touch Time to edit the holding time You can also set Pause or Increment Time as you need The allowable increment time range is 1 sec 120 sec 1 4 Set Cycle In the Edit Program screen select a step that you want to set as the last step of a cycle 2 Touch Goto and the Cycle Step screen opens Cycle Step 4 3 From the Step drop down list box select the start step number of the cycle The steps between the last step and the start step will run repeatedly for the specified cycle numbers 4 Touch Cycles to add additional cycle numbers Note Allowable entered cycle numbers range 1 100 The actual cycle numbers will be N 1 where N stands for the entered cycle numbers To perform a PCR reaction with 30 cycles then you should enter a number of 29 5 Touch OK to accept changes and close the screen GM F6000 Thermal Cycler User Manual 19 D Programming 1 5 Edit Step 1 In the Edit Program screen select a desired step 2 Touch Edit to edit the step parameters 3 Touch OK to accept changes and close the screen 1 6 Delete Step 1 In the Edit Program screen touch a step to select it 2 Touch Delete A pop up window appears 3 Touch Yes in the displayed pop up window to delete the step 1 7 Save Program 1 In the Edit Program screen touch Save or Save As to display the Save A
4. E Run Program Buttons on the Run screen Pauses and Resumes run PP Skips run step Skip Stops run Stop Views bar chart of sample block I Gradient temperature Views real time temperature record uy curve Views run time Runs program again Opens Edit Program screen to edit the program A Views run report Report View Run Timer 1 In the Run screen touch View Timer to view run time Time Elapsed shows the time hour min since the run has started Time Remaining shows the estimated remaining time hour min 2 Touch E3 to return to the Run screen Lid 104 9 Sample 76 7 Cycle 1 8 11 41 53 Folder Public Program 0010 Note The actual remaining time may slightly differ from the shown Time Remaining O1 O6 Run Started 2011 1 14 11 41 47 View Bar Chart 1 In the Run screen touch Gradient to view the temperature of each column of of Sample Block sample block in real time Temperature GM F6000 Thermal Cycler User Manual 25 E Run Program View Temperature Record Curve View Run Report 3 2 Control Run Pause Run Skip Run Step Stop Run Run Program Again 26 Lid 104 9 Sample 76 9 Cycle 1 8 Program 0010 Folder Public Step Time 0 3 36 76 8 76 8 76 8 768 769 769 769 769 77 0 77 0 77 0 77 0 1 2 3 4 5 6 7 8 9 10 11 12 Run pause 2011 1 14 12 5 51 Step Time the countdown holding time of the c
5. GeneMark GM F6000 Thermal Cycler User Manual GMbiolab Co Ltd www genemarkbio com Contents Getting Started 1 Install Thermal Cycler llli 7 1 1 Site Requirements 0 0 eee tenes 7 1 2 Unpack Thermal Cycler 0 0 cece eee ees 7 1 3 Power On and Power On 7 1 4 Open and Close Lid 1 tenes 8 1 5 Block Module Exchange 9 2 Home Screen EE 10 To Manage Folge vie eh ke wee ey Oe REES d adi ROC Reach a ele dex a de 11 1 1 Program Library Scree ass esse escencre E A Ne e ge 11 1 2 Add FOO is ee aust aie Steed es ed Scie od uod ES eure miu reb ee are 12 1 3 Rename Folder sx uiia dwt wwe Kam Ghote ab tee des HERG eee ee o 12 1 4 Delete Folder uan deos Oe eee POE eee ee ag 12 e Manage toL eli ves tos oe Gen bawee othe ae oS eae eee aes SRG Ee Ree pos EE 13 2 1 View Program Screen 1 ce ee nets 13 2 2 Rename Program 5255508052040 90800000804 EROR ARGUS wee eee Ro d 13 23 Gee e ance adhe TTE TS TET T TOT TOTO T T T 14 2 4 Delete ProO alls sauce uie RR Rey de EE e RR EEERTPaI ROSE REGE wi 14 2 5 View Last Run Program 14 Programming 1 Create New Program 15 1 1 Edit Program Screen 0 cc eee eens 15 1 2 Set Temperature Control Mode and Lid Temperature 16 e M M dud eoe eu E Sue es beset e ncaa eae eee aes 255 17 Constant Temperature Gen 17 2 GM F6000 Thermal Cycler User Manual po 407 T n 19 126 dll Ole D ines due
6. To configure shortcuts 1 In the Home screen touch Any button labeled with Shortcut or System Setting then Configure Shortcut The Configure Shortcut screen opens mme Configure Shortcut MJ Select Program Q Delete Program J 2 In the Configure Shortcut screen touch a check box next to a function on the right of the screen to select a function as a shortcut 3 f you want to select a program as a shortcut touch Select Program Select Programs for Shortcut Folder Public vi RTPCR400 2011 01 13 2011 01 13 0010 2011 01 13 2011 01 13 Ua Admin 2011 01 12 2011 01 14 16CW 2011 01 10 2011 01 10 v RTPCR 2011 01 09 2011 01 09 4 In the Select Programs for Shortcut screen select a folder from the Folder drop down list box and programs of the selected folder will appear Touch the header of the first or second column of the table to sort all programs Touch a program to select it and then touch Ok to return to the Configure Shortcut screen The program will appear in the left side list box 5 When you finish touch Ok to return to the Home screen The selected function or program will appear in the Home screen GM F6000 Thermal Cycler User Manual 9 Admin Options 9 1 Access Control F System Setting Note You can select no more than six functions and or programs as Shortcuts To deselect a shortcut on the Home screen you need to touch System Setting again and then touch
7. 9 53 10 2011 1 14 10 7 44 4 Public 0010 2011 1 13 16 54 2 2011 1 14 9 46 43 1 6 Public Admin 2011 1 13 16 6 38 2011 1 13 16 36 34 Public 0010 2011 1 13 15 32 30 2011 1 13 16 4 49 Public 0010 2011 1 13 15 31 23 2011 1 13 15 32 11 vV Show EN Clear j 6 After you finish touch E3 to return to the System Setting screen The Tm Calculator is used to calculate the Tm melting temperature and Ta annealing temperature for a primer pair 1 In the Home screen touch System Setting 2 In the System Setting screen touch Tm Calculator to open the screen Lamm Tm Calculator kd 50 fso nM Primer mM Salt Na Primer 1 5 Primer 2 5 EB calculate JAAHA HA E SAS HA w 3 Enter the salt concentration and the primer concentration 4 Enter each primer sequence and then touch Calculate to view the Tm value of each primer the average Tm value and the Ta value Note In order to develop a successful PCR reaction it may be necessary to select a different Ta value from the value on the screen 5 After you finish touch E3 to return to the System Setting screen GM F6000 Thermal Cycler User Manual 29 F System Setting 7 Check 8 Configure Shortcut 30 This function is reserved for service Shortcuts appear on the Home screen and can access various functions or programs When login is enabled each user can configure different shortcuts
8. TS Deletes a selected folder Delete To add a folder 1 In the Program Library screen touch New 1 2 Add Folder 2 In the New Folder screen enter a folder name 3 Touch OK to accept changes and close the screen Note The folder name is case insensitive 1 3 Rename Folder To rename a folder 1 In the Program Library screen select a folder and then touch Rename 2 In the Rename Folder screen Clear the old folder name enter a new name and then touch Ok to accept changes Note The Preset folder Public folder and USB folder cannot be renamed 1 4 Delete Folder To delete a folder 1 In the Program Library screen select a folder and then touch Delete A pop up window appears 2 Touch Yes in the displayed pop up window to delete the folder Note The Preset folder Public folder and USB folder cannot be deleted IMPORTANT When you delete a folder all programs saved in the folder will be deleted at the same time 12 GM F6000 Thermal Cycler User Manual C Manage Folder and Program 2 Manage Program 2 1 View Program Screen 1 In the Home screen touch Program Library 2 In the Program Library screen select a folder and then double click it or touch View to open the View Program screen Touch the header of the first or second column of the table to sort all programs ed Programs of Preset Created Date Y Last Saved Date 2011 10 12 2011 10 12 2011 10 12 2011 10 12 201
9. Date Time 4 In the Date Time screen enter today s date and current time 5 Touch Ok to accept changes and return to the Admin Options screen The Run time Accuracy function is used to adjust coefficient of estimated remaining run time when the original estimated time is not accurate The User Message function is used to manage user accounts To manage user accounts When login is enabled log in as admin 1 In the Home screen touch System Setting 2 In the System Setting screen touch Admin Options 3 In the Admin Options screen touch User Message 4 The User Message screen lists all accounts currently available Touch the table column header to sort all users Cdi User Message v 2011 04 06 2011 04 01 2011 04 01 2011 04 01 2011 03 31 m b A Create d Edit j G Delete j e admin control all Admin Options functions The default password for admin is admin e Guest can create rename copy modify save delete and run programs that stored in Public Folder Guest Folder and USB Folder e All other users can create rename and delete non system folders create rename copy modify save delete and run programs set his or her shortcuts modify his or her login password in the System Setting screen after login In the User Message screen a To create a new user account touch Create to open the Create User screen Enter user name and password case sensitive of no more than 30
10. Set Date Time 1 eee eee eens 33 94 RUNING ACCUIAGY xx eek coa ke Fouche RR Y PR ER andere dE 33 9 5 User Message 33 GM F6000 Thermal Cycler User Manual About This Manual Please read the manual carefully before using the Thermal Cycler Purpose of This This manual provides instructions on how to set up and use the Thermal Cycler Manual We reserve the right to modify this manual at any time without prior notice Writing This manual uses the following conventions Conventions Bold text indicates user operation For example Touch Ok to accept changes and return to last screen Note Provides instructions that draw your attention or may be helpful For example Note When the instrument is set aside for a long time disconnect the power cable from the socket IMPORTANT Provides information that must be read carefully Failure to follow the information will possibly result in damage to the instrument or the user For example IMPORTANT Turn the lid knob counterclockwise to loose the lid before opening the lid to prevent damage to the lid IMPORTANT To prevent electric shock please turn off the unit and disconnect the power supply prior to cleaning Suggested Operation Gesture For optimum screen performance and visibility the angle shown at the left is suggested for operation a GM F6000 Thermal Cycler User Manual A Instrument Overview A INSTRUMENT OVERVIEW
11. oes adewau et cen ee ene oe ee oe oboe eee eos ee ees 20 1 6 Delete e EEN 20 1 7 Save Program 155655506 0 cen nee nee e ECRIRE EE A ERA 20 le Le nn Ns 2 6 4 5 nae she Oo She pe bane 6 eee EE 21 3 Program Wizard Function 0 00 eee 21 1 Load Samples into the Instrument llli 23 2 elect Program tO FUIT Luosemk er REeTERIDI ESA RR RERGG NE ER RE rv EHE YE 23 3 View Run State and Control un 24 3 1 View Run Gate 24 Run Screen Gegen andes cote eee esau ENEE od eee Sg 24 View RUN NIMC t4e lt ewe yore Zeg pete boe Reb rir eee ws cba Sx PRESE 25 View Bar Chart of Sample Block Temperature 26 View Temperature Record Curve 00 leslie 26 View Run Te MP 26 oralio EE 26 FRU RUN EEN 26 Skip RUN Step eee eee eens 26 weed sae oa dee Senn Gee eee eee ee a oe oe ee es 26 R n Program Agas eebe EK EE ey bor EE SEN 26 1 System Setting Sereen 2 2 es 27 PN POO O 28 S HIE Se EE EE EE E E ENS eens 28 4 Gradient Calculator 0 0 0 0 eee nents 28 2 VIEN PIEDOH cu ras tea ERSTE oe Poe oe E eee oe oe bee se SPINE oe is 29 6 Mab ee EE 29 pelo J L rPr 30 8 Configure SO Lll s sucus n beens peed UR DOW e ern ER LEER E ssdudacas cease 30 9 IE CODIGOS ursa ds ET vk SPP FI PMIPEPUEESCPRI PASO QCRR RGN4 E E 31 9 1 Access Control dz ct emere dw Sed OR e owed ee een dae ar 31 9 2 Thermal Cycler Namen 32 9 3
12. the equation ie a larger sample volume requires a longer time to reach temperature Block mode does not consider sample volume and simply heats the block to the set temperature 16 GM F6000 Thermal Cycler User Manual D Programming Sim tube is the preferred control method especially when reaction steps are 30 seconds less It is important to input sample volumes for the most accurate dwell times For lid temperature control it is recommend to select a temperature five to ten degrees Celsius above the highest temperature of the program steps e g the pre denaturation step to protect sample from evaporation and condensation Note The lid heating will automatically turn off when block temperature is below 30 C The lid will heat to the specified temperature before the actual program starts running Setting a lid temperature below ambient will cause the program to stall 1 3 Add Step A PCR program comprises several steps Each new step will be inserted after the selected step while the initial step will be inserted without selecting a step The maximum amount of steps for a program is 30 Constant 1 In the Edit Program screen touch anywhere in the column for a step to select Temperature it When the step is selected the background becomes blue Step 2 Touch Temp and the Temp Step screen opens Temp Step 2 Le ELI THEBHBBIB 3 Edit Temperature and Time Note The allowable temp
13. 1 Instrument Components Lid Knob Lid Lid Handle Touchscreen USB A Port Air Vent e Figure 1 Front View of Thermal Cycler E a M b Air Vent Power Switch USB B Port Power Inlet Ethernet Port Figure 2 Rear View of Thermal Cycler Table 1 Functions of Thermal Cycler Components Air Vents Allows air to circulate into and out of the instrument GM F6000 Thermal Cycler User Manual 5 A Instrument Overview 2 Menu Overview Table 2 and Figure 3 describe buttons and virtual keyboard common to many of the screens IMPORTANT Nails or the stylus pen supplied by the manufacturer is suggested to touch the touchscreen Table 2 Buttons in the screens of Thermal Cycler Returns to the Home screen Closes current screen and returns to previous screen Moves between pages i e Page Up and Page Down Scrolls left or right to view graph or curve Accepts present parameters setting and closes the screen Close the screen without changing any parameters Runs a selected program or incubation mode Figure 3 Virtual keyboard in the screens of Thermal Cycler Texts are entered with the virtual keyboard Enter a letter A letter button Touch abc ABc to change between lowercase letters and uppercase letters Delete the last character in an input field Erase all characters 6 GM F6000 Thermal Cycler User Manual B Getting Started B GETTING STRATED
14. 1 10 12 View Program Screen Buttons Views and or edits program steps see chapter D for details Creates a new program see chapter D for details Renames a selected program Copies program between folders Deletes a selected program Runs a selected program see chapter E for details 2 2 Rename Program To rename a program 1 In the View Program screen select a program and then touch Rename 2 In the Rename Program screen Clear the old program name enter a new name and then touch OK to accept changes Note The program name is not case insensitive Programs in the Preset folder cannot be renamed GM F6000 Thermal Cycler User Manual 13 C Manage Folder and Program 2 3 Copy Program 2 4 Delete Program To copy a program 1 In the View Program screen select a program and then touch Copy to open the Copy Program screen 2 In the Copy Program screen select a Target Folder in the drop down list box and then touch Copy to copy the program If you want to a Rename the program before copy Touch Clear to clear the old Program Name and then enter a new name b Create a new target folder to copy the program to Touch New Folder to open the New Folder screen enter a folder name and then touch OK to return the Copy Program screen c Touch Export to copy the program to a USB flash drive To delete a program 1 In the View Program screen select a program and then touch Delete A
15. Configure Shortcut In the Configure Shortcut screen unselect the check box for deleting a function shortcut or select the program from the program list and then touch Delete Program for deleting a program shortcut The Admin Options is used to control access mode set thermal cycler name IP address set date time set run time accuracy and manage user accounts When A login is enabled only admin can see the Admin Options button To use Admin Options functions In the Home screen touch System Setting then Admin Options The Admin Options screen opens ee KE a it ei a a be 5 Access Thermal Cycler Set Run time Control Name IP Date Time Accuracy A User Message The Access Control is used to protect personal programs and folders and limit ordinary users to modify instrument parameters To enable the Access Control When login is enabled log in as admin 1 In the Home screen touch System Setting 2 In the System Setting screen touch Admin Options 3 In the Admin Options screen touch Access Control The Access Control screen opens GM F6000 Thermal Cycler User Manual 31 F System Setting 9 2 Thermal Cycler Name IP 32 nn E3 v d Require Login Allow Create New Account by Anyone Enable Guest Account Allow Login without Password WS OK jJ 4 To enable the Access Control function touch Require Login a To allow anyone to create a new account in the Login
16. characters b To edit user password select a user and then double click it or touch Edit to open the Edit Password screen Enter new password and touch OK c To delete a user account select a user and then touch Delete Touch Yes in the displayed pop up window to delete the user GM F6000 Thermal Cycler User Manual 33 Appendix I Troubleshooting APPENDIX I TROUBLESHOOTING No display and no fan moving No line Nolievolage Wait Wait for power eer power restore sound Power cord unreliable Check power cord and plug when power on Unstable bench Move to a stable bench xu EE Move to a stable foot Fasten the screw Normal display but can t heat Heat pump fails or no current is Shut off and call service or cool supplied No display but fan is moving LCD fails or LCD related circuit Shut off and call service when power on fails When power on a message Lost power or power off the Touch OK to cancel the message Stop the Warning A power failure has cycler when the last program is last program to start a new one occurred still running eg Holding at 4 C Running the block temperature to 93 C The cycler is running under 4 C Water accumulated in sample for at least 30 minutes for a long time while the ambient wells Recommend to raise the storage humidity is high temperature to 10 C Power lost after the USB flash Remove the USB flash drive and insert it Try another USB flash drive
17. dle or when running program which set temperature control mode as Block or sample temperature when running program which set temperature control mode as Sim tube and estimated remaining run time b Shows date day and time GM F6000 Thermal Cycler User Manual 9 B Getting Started Home Screen Buttons When login is enabled touch this button to logout the current user Opens Run screen Go to list of the last 10 run programs LastRun Programs Go to list of folders which contain all saved Program Library programs A A Creates new program quickly A Program Wizard Sets instrument parameters and shows other y N V9 System Setting tools SI Configures shortcut for functions or Empty Shortcut programs La Shows a selected program shortcut a Program Shortcut 10 GM F6000 Thermal Cycler User Manual C Manage Folder and Program C MANAGE FOLDER amp PROGRAM 1 Manage Folder 1 1 Program Library Screen In the Home screen touch Program Library The Program Library screen opens ram tte X A Program Library Created Date_ _ System Folder 2011 01 12 2011 01 12 2011 01 10 2011 01 05 2011 01 05 ey Rename ii Delete The table lists all available folders Folder names include the number of programs in parentheses Touch the header of the first or second column of the table to sort all folders Touch 4 Page Up and Page Down to move between pages The Preset folder conta
18. e view and edit program After adding several steps the screen looks like below Edit Program 3STEP1000 Folder Preset Step 1 Step 2 Step 3 94 0 C 94 0 C 0 5 0 55 0 C 0 0 30 Head j vA Temp J iul Gradient Q Goto 9 Edit Delete J 3 Sayed Save ge R r Items in the Edit Program screen a Step number b Temperature for a constant temperature step c Step holding time hour min sec d The start step number and amounts of additional repeats for cycles GM F6000 Thermal Cycler User Manual 15 D Programming Edit Program Setting steps of a program are carried out via the buttons Screen Buttons Sets temperature control mode and lid temperature P4 Adds a constant temperature step ul Adds a gradient temperature step Gradient Returns a former step and repeats Edits a step Deletes a step Saves th created program Saves another copy of the opened J Save as program Runs the program 1 2 Set Temperature Control Mode and Lid Temperature 1 In the Edit Program screen touch Head The Head screen opens Temperature Control Sim tube Sample volume v 10 100 Lid Temperature Control 1050 C 30 112 JEEE JEEE TJERE E 2 Select temperature control mode and lid temperature control mode and then touch Ok to accept changes Note The Sim tube mode controls the process of heating the sample block to include the sample volume in
19. erature range is from 0 0 C to 99 9 C with 0 1 C interval The allowable time range is from 00 00 00 to 09 06 06 hour min sec f you touch Pause the program will automatically pause as soon as the desired step temperature is reached and the instrument will beep once Touching Resume will continue the program running Pause can be used to add reagents ie hot start or when adding or removing tubes during a step Touching Forever will cause the program to hold indefinitely after reaching this step until it is stopped manually Steps cannot be added after a forever step GM F6000 Thermal Cycler User Manual 17 D Programming 4 You can also set options for a step Increment Temp adds temperature increments to step with each cycle To set the Increment Temp function Touch to shift between and to increase or decrease temperature for each cycle and then enter the number of degrees of temperature in the textbox The allowable temperature range is 0 1 C 10 0 C Note Parameters cannot be set that would cause a step to fall outside of the operating range of the instrument 1e below 0 C or above 99 9 C Increment Time Adds time increments to the holding time within the step for each cycle To set the Increment Time function Touch e to shift between and to increase or decrease time for each cycle and then enter the seconds in the textbox The allowable time range i
20. face of the sample block or lid surface because they may be very hot 105 C 221 F or higher Note The cap of tubes or film on microplate must be sealed tightly to prevent sample evaporation Tubes or microplate should have heat resistance up to about 120 C For best results use thin walled tubes designed for PCR The sample wells of the sample block should be kept clean The height of tubes should be the same so that the lid can keep balance and apply even pressure on each tube 2 Close the lid and turn the lid knob clockwise see the Tighten arrow symbol on the top surface of the lid knob until you hear click sound 2 Select Program to Run From the Home screen 1 To select a last run program Touch LastRun Programs select a program and then touch Run To select a program saved in a folder Touch Program Library select the desired folder and then touch View to open the View Program screen Select a program from the list and touch Run After you touch Run the Set Run Options screen opens Set Run Options Temperature control wi startRun j GM F6000 Thermal Cycler User Manual 23 E Run Program 2 In the Set Run Options screen edit Temperature Control and Lid Temperature Control 3 Touch StartRun to begin the run The Run screen opens 3 View Run State and Control Run 3 1 View Run State Run Screen You can view the status of the program running using the Run screen bel
21. ins eleven preinstalled programs e 3Step_2000 3Step_1000 3Step_500 for amplifying less than 2kb 1kb 500bp nucleic acid templates using three step PCR e 2Step_PCR two step PCR e Gradient for optimizing annealing temperature of PCR reaction This program is only available with Gradient Thermal Cycler e Touchdown and Touchdown2 Touchdown PCR e Long_PCR for amplifying of extra long nucleic acid chain e RT_PCR for synthesizing DNA from RNA by reverse transcriptase e Ligation_16 C for connecting segmental DNA with vector DNA at 16 C e Enzyme_37 C for ordinary enzyme reaction at 37 C Note Programs in the Preset folder cannot be renamed or deleted To modify a program in the Preset folder edit the program and then save to another folder see chapter D Or copy the program to another folder see 2 3 Copy Program and then modify it The Public folder is a system folder and is used as the default folder for saving programs Note When login is enabled all users have access to the Public folder GM F6000 Thermal Cycler User Manual 11 C Manage Folder and Program When plugging a flash drive into the USB port a USB icon ER appears Touch this icon to open the USB folder The USB folder contains programs that are stored in the USB flash drive Programs can be copied to and from the USB flash drive Program Library Screen Buttons Button o Fenton o Es View ES New Renames a selected folder
22. ns There are two screens touch Next and Last to shift between them ple Program Wizard 1 4 Temperature Control p e pa Denaturation oa Anealing 5 5 Extension 72 2 In the first screen edit Temperature Control mode and Lid Temperature Control mode You can leave these parameters as default because the default parameters is suitable for most PCR applications 3 In the second screen touch and edit parameters of each step Keep parameters of a step empty to exclude the specified step You can touch Graph to view the graphical representation of the program GM F6000 Thermal Cycler User Manual 21 D Programming Program Wizard 2 Step 2 Step 3 Step 4 Step 5 Step 6 Step 7 94 0 C 72 0 C GoTo 72 0 C 55 0 C SE 0 1 0 Note e Allowable temperature range 0 0 C to 99 9 C Allowable time range 00 00 to 99 59 min sec Allowable number of cycles 0 101 The actual cycle numbers will be equal to the entered cycle numbers So if you would perform a PCR reaction with 30 cycles then you should enter a number of 30 4 Touch Save to save program or touch Run and then select whether or not to save the program before running according the displayed message in a pop up window 22 GM F6000 Thermal Cycler User Manual E Run Program E RUN PROGRAM 1 Load Samples 1 Place PCR tubes or microplate in the sample wells of the sample block IMPORTANT Do not touch the sur
23. ow Lid 104 9 Sample 76 7 Cycle 1 8 11 41 53 Program 0010 Folder Public 4 Step 2 Step 3 Step 4 88 0 C 0 1 55 66 0 C GoTo 44 0 C 5 0 C Cyc ES S Cyc 1 0 C S Ti rasoj D oe Q Stop J iul Gradient zu Curve G View C 224 Edit J Run Started 2011 1 14 11 41 47 d v Report The items displayed on the Run screen a In the top bar are the colored status light the colored status lights stays green during running changes to orange after touching Pause button changes to red when error arises and changes to white after stopping a run and the run Status Lid lid temperature Block or Sample block temperature when the instrument is idle or when temperature control mode is Block or sample temperature when temperature control mode is Sim tube Cycle current cycle numbers total cycle numbers 11 41 53 Current Time b Program Folder name and Creator of program when login is enabled Note If you create a new program to run but did not save it the program will be given a default name Admin and will be saved in a temporary folder Temp After run the temporary program will not be recorded in the list of the Last Run Programs screen c Options Pause preset pause X C Cyc Increment or decrement temperature X S Cyc Increment or decrement time X C S Ramp rate d The recent run message 24 GM F6000 Thermal Cycler User Manual
24. ower On and Power Off 1 Connect the power cable to the power inlet in the rear of the instrument 2 Connect the plug of the power cable to the socket Make sure the power cable has connected to both power inlet and socket firmly To power on Turn the power switch to position 1 To power off Turn the power switch to position 0 GM F6000 Thermal Cycler User Manual 7 B Getting Started 1 4 Open and Close Lid The lid of the Thermal Cycler can be adjusted to come into contact with and apply pressure to the tops of the reaction vessels Heating of the lid protects samples from condensation IMPORTANT Temperature of the lid can be very high 105 C 221 F or higher Never touch the inner surface of the lid when the temperature is above 43 C To open the lid 1 Turn the lid knob counterclockwise see the Loosen arrow symbol on the top surface of the lid knob to raise the pressure plate 2 Grasp the lid handle so that the handle clamp is pulled toward to the lid handle Lid Handle Lid Knob A Handle Clamp Chassis 3 Lift up the lid handle until the lid keeps opening vertically You can then place reaction vessels in the sample block or remove samples from the block To close the lid 1 Place reaction vessels into the wells of the sample block 2 Hold the lid handle and handle clamp and then let the lid touch the chassis until you hear click sound The lid will be locked in
25. place 3 Turn the lid knob clockwise see the Tighten arrow symbol on the top surface of the lid knob to reduce the lid height until resistance us felt Then continue to turn the lid knob clockwise until you hear click sound The lid is now pressing on the reaction vessels 1 5 Block Module Exchange Block module exchange can be performed within seconds without needing any tool IMPORTANT Please power off and disconnect the power cord from the socket before replacement of the block 8 GM F6000 Thermal Cycler User Manual B Getting Started To remove the block module 1 Open the lid 2 Put your hand on the left and right side of the block module and lift it up vertically 3 Store the block module in a clean secure box To insert the block module Put your hand on the left and right side of the block module with the arrow on block module pointing to another arrow on the chassis Place the block into the hollow cavity of the chassis and press tightly and evenly 2 Home Screen When the instrument powers on the boot screen is displayed for several seconds The Home screen is displayed see below Remaining 0 Oe MN DW S LastRun Program Program System Program Library Wizard Setting Ci Al sott ST Shortcut Shortt About Touchd ownl 2011 6 2 Thu 14 11 2 b a Information Bar lid temperature block temperature when the instrument is Items in the Home screen i
26. pop up window appears 2 Touch Yes in the displayed pop up window to delete the program Note Programs in the Preset folder cannot be deleted 2 5 View Last Run Program 14 In the Home screen touch Last Run Programs The Last Run Programs screen opens Last Run Programs 0010 Public 2011 1 14 10 7 53 4 Admin Public 2011 1 14 9 53 9 001 FF 2011 1 13 15 31 4 iis RTPCR400 Public 2011 1 13 14 16 11 RTPCR Preset 2011 1 13 11 56 10 Kg P 4 Viewed E New A Rename E Copy EN Clear bond The Last Run Programs screen has the same appearance as the View Program screen but shows the recently run ten programs for quick viewing and repeat runs Touch Clear to clear the program list Note The Rename and Copy buttons are not available in the Last Run Programs screen GM F6000 Thermal Cycler User Manual D Programming D PROGRAMMING 1 Create New Program 1 1 Edit Program Screen 1 In the Program Library screen select a folder and then double click it or touch View to open the View Program screen 2 In the View Program screen touch New to open the Edit Program screen Edit Program Admin Folder Public Head y4 Temp J iul Gradient C Soin 9 Edin Gy Delete Save Save As nung Note To open the Edit Program screen more quickly you can put the New Program shortcut in the Home screen see Configure Shortcut for details The Edit Program screen is used to creat
27. rd curve by touching Curve and run time by touching View Timer You can stop running by touching Stop Note The Pause Skip RunAgain Edit Report buttons are not available in the Run screen under Incubation mode 1 In the Home screen touch System Setting 2 In the System Setting screen touch Gradient Calculator The Gradient Calculator screen opens 3 In the Gradient Calculator screen touch Left and Right to enter the low temperature and high temperature of the left 1st and right 12th column of the sample block The temperature range 30 0 C lt Left Right lt 99 9 C The difference between the Left and Right temperature lt 30 C 4 Touch Calculate to display calculated temperature gradient from the first column to the twelfth column Gradient Calculator JE ERE EE g Clear Both e ERIS a RB at llli 5 To leave touch Exit to return to the System Setting screen JR Gd GM F6000 Thermal Cycler User Manual 5 View Report 6 Tm Calculator F System Setting 1 In the Home screen touch System Setting 2 In the System Setting screen touch View Report to open the screen 3 Select a report and double click it or touch Show to open the Run Report screen 4 After you finished touch E3 to return to the View Report screen 5 In the View Report screen you can touch Clear to clear all reports el View Report Run Started Run Aborted Public Admin 2011 1 14
28. s Program screen Save As Program Folder Public VI NewFolder J 2 The current date and time are used as a default name A new name can be entered The name is case insensitive and can be up to 30 characters Note Default program name 10 04 18 Deg N N 1 1 last two digits of year x N b BT month day hour minute 3 From the Folder drop down list box select a folder to save the program to e To create a new folder to save the program touch New Folder and enter a folder name of up to 30 characters 4 Touch Run to both save and run the program Or touch Save to save but not run the program Or touch Export to save the program to a USB flash drive 2 Edit Program To edit a program 1 In the Home screen touch Program Library 2 In the Program Library screen select a folder and then double click it or touch View 20 GM F6000 Thermal Cycler User Manual D Programming 3 In the View Program screen select a program to be edited and then double click it or touch View Edit 4 In the Edit Program screen you can edit the program and then save and or run it following the instructions described above 3 Program Wizard Function The Program Wizard function provides a quick method to create a standard three step or two step PCR program and perform running 1 In the Home screen touch Program Wizard The Program Wizard screen ope
29. s 1 sec 120 sec Note Parameters cannot be set that would allow the dwell time to fall below zero e Slow Ramp Adjust the heating or cooling ramp rate The default ramping rate is the fastest rate To set the Slow Ramp function Enter the value of ramp rate in the textbox Input range is 0 1 6 0 C sec Note The actual maximum ramp rate of heating and cooling varies with block module type Refer to the instrument specifications for the maximum value If a value larger than the block s maximum rate is entered the block s maximum rate will be used If you do not want to slow the running leave this option empty 5 Touch Ok to accept changes and close the screen Gradient 1 In the Edit Program screen select a step after which you want to add the Temperature gradient temperature step Step 2 Touch Gradient and the Gradient Step screen opens 18 GM F6000 Thermal Cycler User Manual D Programming Gradient Step 3 65 5 66 0 Left ban SES 1 63 8 61 6 59 0 56 3 3 4 53 7 51 0 Right 66 0 o 5 6 48 4 S E 46 2 a 44 0 44 5 7 g 8 a Calculate DH el 1 2 3 4 n h 7 8 9 10 11 12 9 E Time Hrs Min 30 Sec Increment Time a Sec 3 Touch Left and Right to enter temperature of the left 1st and right 12th column of sample block The allowable temperature range 30 0 C lt Left lt Right lt 99 9 C Difference between the Left and Right lt 30 C
30. screen touch Allow Create New Account by Anyone b To allow an anonymous user to login touch Enable Guest Account c To allow login without password touch Allow Login without Password 5 Touch Ok and restart the instrument by powering off the power switch After enabling the Access Control you must login as a user on the Login screen see below before you can use the instrument EX em e Create User Guest User 2011 4 29 Fri 9 45 10 6 After you finished experiment touch Qo in the Home screen to log out To enable network control function you need to set the IP address and a unique Thermal Cycler Name for each instrument When login is enabled log in as admin 1 In the Home screen touch System Setting 2 In the System Setting screen touch Admin Options 3 In the Admin Options screen touch Thermal Cycler Name IP 4 In the Thermal Cycler Name IP screen set a unique Thermal Cycler Name and IP address The name can be up to 30 characters 5 When you finish touch Ok to return to the Admin Options screen GM F6000 Thermal Cycler User Manual 9 3 Set Date Time 9 4 Run time Accuracy 9 5 User Message F System Setting The date and time appear on the Home screen and the Run screen To set Date Time When login is enabled log in as admin 1 In the Home screen touch System Setting 2 In the System Setting screen touch Admin Options 3 In the Admin Options screen touch
31. tor Report rt 4 d Configure Admin Shortcut Options Shows product information Performs a constant temperature incubation experiment Calculates gradient temperature of each column of the sample block Views stored run reports Calculates Tm value of a primer pair This function is reserved for service Configures functions or programs shortcuts Sets instrument parameters When a user other than admin login the Admin Options icon will change to Login Password s icon The user can edit their login password using this function 27 F System Setting 2 About 3 Incubation 4 Gradient Calculator 28 To view product information about the Thermal Cycler 1 In the Home screen touch System Setting 2 In the System Setting screen touch About and the About screen appears 3 When you finish touch Ok to return to the System Setting screen The Incubation function is used to perform a constant temperature incubation experiment such as DNA ligation or RNA digestion 1 In the Home screen touch System Setting 2 In the System Setting screen touch Incubation 3 In the Incubation screen enter the required incubation temperature If you select Lid On the lid will heat to reach 10 C above the incubation temperature by default 4 Touch StartRun to run the Incubation program and the Run screen opens 5 In the Run screen you can view block temperature by touching Gradient view temperature reco
32. urrent step after the step temperature reached the setting value 2 Touch E3 to return to the Run screen 1 In the Run screen touch Curve to view the temperature record curve 2 Touch E3 to return to the Run screen 1 In the Run screen touch Report to open the Run Report screen The report contains records of run start time run stop time and manual operations during running Touch Export to export the report in BMP format to a USB flash drive 2 Touch E3 to return to the Run screen In the Run screen touch Pause and the system will beep for two times Note The temperature will continue to increase or decrease until it reaches the setting temperature of a step When paused the Pause button changes to Resume button and you must touch Resume to continue the program In the Run screen touch Skip to skip the current running step and run the next step In the Run screen touch Stop and then touch Yes in the displayed pop up window In the Run screen if the running program stopped touch Run Again to run it again GM F6000 Thermal Cycler User Manual F System Setting In the Home screen touch System Setting 1 System Setting Screen LL About AN Tm Calculator System Setting Screen Buttons Login Password GM F6000 Thermal Cycler User Manual The System Setting screen opens d CD PN System Setting X Le Incubation Check iu E Gradient View Calcula
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