Prime and PrimeG OPERATOR’S MANUAL Version 1.
CONTENTS INTRODUCTION BEFORE USE Unpacking SAFETY INFORMATION English Français Deutsch Italiano Español CONTACT INFORMATION PRIME SPECIFICATION INSTALLATION GENERAL SOFTWARE FEATURES Introduction Template programs Incremented/decremented time and temperature Gradient (PrimeG only) Oligonucleotide Tm calculator PROGRAMMING TEXT, TEMPERATURE AND TIME Text entry Temperature entry Time entry INSTRUMENT SETTINGS AND DEFAULTS User preferences Instrument settings Program defaults Service settings Gradient calcula
The run screen Searching for a program not in the shortcut list Running a program not on the shortcut list EDITING A PROGRAM Editing saved programs Editing templates Editing password-protected programs CURRENT STATUS VIEW FILES File searching Viewing a program file Viewing a temperature log file Copying files Deleting files UPDATING THE PRIME SOFTWARE UPGRADING FROM PRIME TO PRIMEG REPLACING BLOCKS FAQs TECHNICAL SUPPORT AND SERVICING ADDITIONAL INFORMATION User Maintenance Fault Finding Fuses Insulation Te
INTRODUCTION The Prime is a stand-alone, flexible and versatile thermal cycler designed to accurately control the 1 temperatures of samples between 4ºC and 100°C. It has many scientific applications including PCR , reverse transcription, ligation and sequencing. It has a flexible range of block options to allow for most commonly used consumables including 0.2ml x 96 well plates, 0.2ml tubes, 0.5ml tubes and 384 well plates. A Combi-Block version is also available which can accept either 33 x 0.
BEFORE USE Before using the Prime please ensure you have read this manual carefully. If there is any doubt relating to the proper use of this equipment, the staff at Bibby Scientific Ltd. or your supplier will be happy to assist you.
SAFETY INFORMATION Please read all the information in this manual before using the Prime. WARNING HIGH TEMPERATURES ARE DANGEROUS: they can cause serious burns to operators and ignite combustible material.
ENVIRONMENTAL CONDITIONS The Prime is designed operate under the following conditions: • Indoor use • Ambient temperature range +5ºC to +40ºC • Altitude to 2000m • Relative humidity not exceeding 80% • Mains supply fluctuations not exceeding 10% • Over voltage category II IEC 60364-4-443 • Pollution degree 2 Note: The control specifications are quoted at an ambient temperature of 20ºC. The specification may deteriorate outside an ambient temperature of between 10ºC and 30ºC.
L'INFORMATION DE SÛRETÉ Veuillez lire attentivement toutes les instructions de ce document avant d’utiliser le Prime. AVERTISSEMENT Les TEMPÉRATURES ÉLEVÉES SONT DANGEREUSES car elles peuvent provoquer de graves brûlures chez l’opérateur et enflammer les matériaux combustibles. Les utilisateurs doivent porter une attention toute particulière aux points suivants : • PROCEDER AVEC PRUDENCE ET PORTER DES GANTS POUR SE PROTEGER LES MAINS • NE PAS utiliser de matériaux combustibles auprès d’objets chauds.
Câble de rechange S’il s’avère nécessaire de remplacer le cordon d’alimentation, utiliser un câble de 1 mm² conforme à la norme H05VV-F relié à une prise IEC320. EN CAS DE DOUTE, CONSULTER UN ELECTRICIEN QUALIFIE.
SICHERHEITS- INFORMATIONEN Lesen Sie diese Anleitung vor Verwendung des Prime bitte sorgfältig durch. ACHTUNG HOHE TEMPERATUREN STELLEN EINE GEFAHRENQUELLE DAR. Sie können schwere Brandverletzung verursachen und brennbare Stoffe entzünden.
Ersatzkabel 2 Bei einem eventuellen Austausch des Netzkabels wird ein Kabel vom Typ H05VV-F mit 1 mm Adernquerschnitt und Europastecker (IEC 320) benötigt. IM ZWEIFELSFALL EINEN ELEKTROFACHMANN HINZUZIEHEN.
INFORMAZIONI DI SICUREZZA Leggere attentamente il presente manuale prima di usare il Prime. AVVERTENZA Le ALTE TEMPERATURE SONO PERICOLOSE in quanto possono provocare serie ustioni agli operatori e dare fuoco al materiale combustibile.
7. Accendere lo strumento per mezzo dell'interruttore situato sulla parte retro dell'unità. Cavo di ricambio 2 Qualora occorra sostituire il cavo di rete, si dovrà utilizzare un cavo di 1mm codice armonizzato H05VV-F collegato ad una spina IEC 320. IN CASO DI DUBBIO, RIVOLGERSI A UN ELETTRICISTA QUALIFICATO. CONDIZIONI AMBIENTALI Il Prime è stato progettato per funzionare nelle seguenti condizioni: • uso interno • range di temperatura ambiente da +5ºC a +40ºC • altitudine massima 2000 m.
INFORMACIÓN DE SEGURIDAD Lea atentamente este manual antes de utilizar el Prime. ADVERTENCIA LAS ALTAS TEMPERATURAS SON PELIGROSAS, ya que pueden ocasionar quemaduras graves a los operarios y prender el material combustible.
7. Encienda el instrumento usando el interruptor situado en la parte posterior de la unidad. Cable de repuesto 2 Si es necesario sustituir el cable de alimentación, se debe utilizar un cable de 1mm de código armonizado H05VV, conectado a un enchufe IEC320. EN CASO DE DUDA, PÓNGASE EN CONTACTO CON UN ELECTRICISTA.
CONTACT INFORMATION For technical, sales or servicing information, contact your local Techne dealer or: UK Bibby Scientific Ltd. Beacon Road Stone Staffordshire ST15 0SA UK Tel: +44 (0)1785 812121 Fax: +44 (0)1785 810405 E-mail: sales@bibby-scientific.com www.techne.com North and South America Bibby Scientific US Inc. t/a Techne Inc. 3 Terri Lane, Suite 10 Burlington, N.J. 08016 USA Toll Free (in NA): 800-225-9243 Tel: +1 609 589 2560 Fax: +1 609 589 2571 E-mail: labproducts@techneusa.com www.techneusa.
PRIME SPECIFICATION TEMPERATURE Block temperature range Block uniformity (at 55ºC) Temperature accuracy (at 55ºC) Gradient availability (PrimeG only) Maximum gradient (PrimeG only) Minimum gradient (PrimeG only) Column uniformity with a 10ºC gradient (PrimeG only) Pre-run sample cooling Temperature set point adjustment 4ºC (10°C during cycling) to 100ºC <±0.3ºC <±0.25ºC Between 30ºC and 80ºC 29ºC (25°C Combi-Block; 19ºC 384-well block) 1ºC <±0.3ºC Yes, 4ºC 0.
COMMUNICATION PORTS USB port on front of unit USB port on rear of unit Connection for USB memory stick Connection for servicing and calibration only DIMENSIONS Height (mm) Width (mm) Length (mm) Weight (kg) 240 240 420 9.
INSTALLATION See also the Safety Information sections on pages 5 to 14. Front view 1. 2. 3. 4. Lid adjustment knob. Lid release latch. 5.7” colour VGA LCD touch screen display. USB port for memory stick. Rear view 1. 2. 3. Mains cable inlet. On/Off rocker switch USB port for service and calibration only. Installation 1. Place the unit on a suitable flat bench, ensuring that the air inlet vents on the sides are free from obstruction. 2.
6. Release the heated lid by lifting the latch forward and use it to lift the lid. To close the lid, lower the lid onto the block and press the latch to secure in place. 7. Place the samples in the block. If individual tubes or strip tubes are being used, space these out evenly across the block to equalise the pressure from the heated lid. 8. The heated lid has a rotating knob to adjust the lid pressure on the samples, allowing for a variety of consumables to be used. To adjust the pressure: a.
GENERAL SOFTWARE FEATURES INTRODUCTION The Prime software allows the user to quickly and easily create thermal cycling programs using a simple and clear touch screen format. The software is structured into five modules which are accessed from the Home Screen. These allow the user to: • Run an existing program, selecting from templates or programs saved on the unit. • Create a new program. • Set instrument and program defaults and preferences. Includes calculator tools. • View the current status of the unit.
The Ice Bucket and Ligation programs are simple temperature holds, with the former having an infinite hold at 10ºC and the latter at 15ºC. In both of these programs the heated lid is switched off and the initial denaturation, hot start and final extension functions disabled. INCREMENTED/DECREMENTED TIME AND TEMPERATURE The software allows the user to either increment or decrement the time and/or temperature of a step within a cycling stage.
OLIGONUCLEOTIDE TM CALCULATOR One of the most important parameters in a PCR is the annealing temperature of the reaction. This can be determined theoretically using various software programmes to calculate the melting temperature (Tm) of the primers. The Tm is defined as the temperature at which half the DNA strands are single stranded and half are double stranded when base paired to a complimentary strand.
PROGRAMMING TEXT, TEMPERATURE AND TIME This section gives instructions for the basic programming of text, temperature and time which are required in later sections. TEXT ENTRY When giving a name to a program or stage, or when entering a keyword or a password, a text entry screen will be opened. Touch individual characters to create the name. • For words with all upper case letters touch CAPS. • Touch SHIFT if only the first letter is required in upper case. • For numbers touch 123.
Advanced temperature entry • First ensure the number of cycles for the stage has been set then enter the required hold temperature as described above. Note: Increase/Decrease Per Cycle will be inactive unless the number of cycles set is greater than 1. To increase the step temperature per cycle: • For an increase in temperature per cycle, touch the button below Increase Per Cycle to turn this function on. Next touch the temperature entry button below this.
The temperature value will now appear orange in the programming screen indicating that it contains a modified function. To decrease the step temperature per cycle: • For a decrease in temperature per cycle, touch the button below Decrease Per Cycle to turn this function on. Next touch the temperature entry button below this. A new screen will open which is similar to the simple temperature entry screen.
The temperature value will now appear orange in the programming screen indicating that it contains a modified function. Note: It is not possible to both increase and decrease the temperature of the same step. To enter a temperature gradient on a step (PrimeG only): On the PrimeG an additional Temperature Gradient button is available. • Touch the button below Temperature Gradient to turn this function on. Next touch the temperature entry button below this.
The temperature value will now appear orange in the programming screen indicating that it contains a modified function. TIME ENTRY When touching a time parameter a time entry screen will open. There are two forms of time entry screen: • A simple form for adjusting the time of the program parameters such as initial denaturation and final extension.
To increase the step hold time per cycle: • For an increase in hold time per cycle, touch the button below Increase Per Cycle to turn this function on. Next touch the time entry button below this. A new screen will open which is similar to the simple time entry screen. The maximum increase in hold time per cycle (based on the number of cycles and the time limits of the unit) will be shown. • Enter the required value using the + and - buttons.
To decrease the step hold time per cycle: • For a decrease in hold time per cycle, touch the button below Decrease Per Cycle to turn this function on. Next touch the time entry button below this. A new screen will open which is similar to the simple time entry screen. The maximum decrease in hold time per cycle (based on the number of cycles and the time limits of the unit) will be shown. • Enter the required value. • If an entered decremented time is invalid, a prompt will indicate the acceptable range.
INSTRUMENT SETTINGS AND DEFAULTS Touch the Settings button to access the instrument Settings menu. • Touch any of the buttons to view and edit the settings. • Touch More Settings to access further options. • Once all the settings and defaults have been set as required, touch Save to save the changes and return to the Home Screen. • If you do not wish to change any settings, touch Cancel to return to the Home Screen. USER PREFERENCES Language • Touch the language button to set the required language.
INSTRUMENT SETTINGS Temperature Log Recording To record the temperature logs (block temperature profile) of each run, touch the button to set this to Always. If temperature logs are not required, set to Never. Auto Resume On Power Loss This determines whether the unit will restart after a power failure. Setting Auto Resume to Always will always allow the unit to re-start irrespective of the length of the power failure.
Date Format Touch the date button to set the required date format. The options are dd/mm/yy or mm/dd/yy. • Touch More Settings for further date and time settings or Back to return to the Settings menu. Administrator Settings This allows an administrator to remove passwords from password-protected programs, change the Administrator password and restore the unit to its factory settings. • Touch None and enter the administrator password. The default password is 1234.
Restore Factory Settings All changes to the instrument defaults and settings can be removed and the unit returned to its factory settings. • From the Administrator menu touch Restore Factory Settings. • Touch the None button and enter the administrator password. • Touch Restore Settings and the unit will be reset to factory defaults. • Touch Cancel to return to the Settings menu without making any changes. PROGRAM DEFAULTS The program default settings will apply to every new program created on the Prime.
Initial Denaturation Use this to denature the sample and/or activate the enzyme before the thermal cycling program begins. • Touch On/Off to toggle between settings. • Touch the time button to set the required hold time. • Touch the temperature button to set the required temperature. Hot Start This will cause the unit to pause at the set temperature. The program will not continue until the unit is manually un-paused. • Touch On/Off to toggle between settings.
GRADIENT CALCULATOR (PRIMEG ONLY) The Gradient Calculator can be used to calculate the temperature for each column of the block for a user-specified temperature and gradient range. • Touch the Target Temperature button and enter the required temperature. • Touch OK. • Touch the Temperature Gradient button and enter the required gradient range followed by OK. • Touch OK. The calculated temperatures for each of the columns of the block will now be displayed.
• Enter the primer concentration in the PCR mix. • Enter the monovalent salt concentration of the PCR mix. • Touch Calculate to calculate the Tm of the primer. • To check the Tm of another primer with the same primer and salt concentrations, touch Back and enter the new primer sequence. • Touch Reset to clear the entries. • Touch Back to return to the Settings menu. • Once all the settings and defaults have been set as required, touch Save to save the changes and return to the Home Screen.
CREATE A NEW PROGRAM From the Home Screen, touch the Create A New Program button. This will open a screen where you can build a program by adding stages and steps and define the temperatures and hold times. The function of each of the buttons on this screen is described below. NAME THE PROGRAM • Touch this button to give the program a name. • Type in the required name using the text entry screen. • Once the name is complete, touch OK to return to the programming screen.
INSERT/DELETE A STAGE A stage is a section of a program that consists of a number of individual steps that can be cycled (repeated) a defined number of times. Insert a new stage • To insert a stage in a program, touch Insert a new stage. A stage with one step will be inserted. Stage 1 • Touch this to give the stage a name (optional). Enter the name using the text entry screen. 1 cycle • Touch this to edit the number of cycles (repeats) for the stage. Enter the required number of cycles then touch OK.
INSERT/DELETE A STEP Insert a new step • Touch Insert a new step to insert the next step in the current stage. • Edit the new step temperature, hold time and ramp rate as required. Delete a step • To delete a step, touch the step area to highlight it and then touch Delete. INSERT/DELETE A PAUSE Insert a pause • To insert a pause between stages, touch Insert a pause. The hold temperature will be that of the previous step.
User User names can be entered and linked to the program to help in searching and identifying programs. • To enter a user name, touch the None selected button next to User. • User names that have already been created will then be listed. • To create a new user name, touch the Create a new user button. • Type in the user name and touch OK. The new user name will be added to the list. • To select a user name, touch the button to highlight it. Touch it again to de-select it.
Keywords Keywords can be entered and linked to the program to help in searching for related programs. • To enter a keyword, touch the None selected button next to Keywords. • Other keywords that have already been created will then be listed. • To create a new keyword, touch the Create a new keyword button. • Type in the keyword and touch OK. The new key word will be added to the list. • To select a keyword, touch the button to highlight it. Touch it again to de-select it.
Passwords A password can be created to protect the program from being edited and deleted by other users. The password will be requested if a user attempts to edit or delete the program. • To create a password, touch the None button next to Password. • Enter the required password then touch OK. The password is case-sensitive. • Touch Cancel to return to Program Options without entering a password. • Touch the Program button to return to the Programming screen.
SETTINGS • Touch the Settings button to view the instrument defaults as set up in the instrument Settings module. Any of these parameters can be edited by touching the appropriate button and will be saved for the current program only. • Touch Program to return to the programming screen. VIEW • Touch View to see a graphical representation of the program. • If the program has more stages and steps than are displayed on the screen, scroll through the program by dragging a finger across the touch screen.
DELETE This is used to delete an entry. First touch the required segment followed by Delete. UP AND DOWN ARROWS Use these buttons to scroll through a program. SAVE Touch this button to save the program. CANCEL Touch this button to cancel changes to the program and return to the Home Screen.
RUN A PROGRAM From the Home Screen, touch one of the shortcuts to run one of the listed programs, or touch Run a program to search and select from other programs and templates saved on the unit. Selected programs can be run directly or edited before running. RUNNING A PROGRAM FROM THE SHORTCUT LIST On the Home Screen, the Run a program area displays shortcuts to four programs.
THE RUN SCREEN The Run Screen will be displayed after a program has been started. It shows the instrument status and the progress of a run. Once the program has been started, the timers in the top right hand corner of the screen will indicate how long the program has been running and the total run time. The progress bar at the top of the screen also indicates how far the run has progressed.
Viewing a running program From the Home Screen: • Touch Current status. • Touch the area for the instrument. • Touch View. SEARCHING FOR A PROGRAM NOT IN THE SHORTCUT LIST There are four ways to search for a program if it is not in the shortcut list: • • • • Search from the complete list of saved programs. Search by keyword. Search by user. Search by both keyword and user. Search from a list • To search for a program saved on the unit, touch Run a Program to open the Program Selection Screen.
Search the programs by user • Touch Search by User and this will open the list of user names stored on the unit. • Select the required user name by touching the appropriate button to highlight it. Touch again to de-select. • When the user name has been selected, touch Done to return to the Program selection screen. Only the programs with the selected user name saved with them will be listed. • To clear the user name search, touch Clear User Search.
RUNNING A PROGRAM NOT ON THE SHORTCUT LIST • Once the required program has been identified, touch it to highlight it. The Program Selector Screen will show a summary of the program, the instrument settings and a graphical representation of the thermal cycling program. • Touch Edit to edit the program if required. • Touch Back to return to the Home Screen. • Touch Start to proceed to the Pre-run Screen. • From the Pre-run Screen, touch Start to run the program.
EDITING A PROGRAM EDITING SAVED PROGRAMS First select the required program by searching the Run a program module. • To edit a selected program, touch the Edit button. Any of the Program Options, Settings or thermal cycling parameters can be edited. • Once all the required changes have been made, touch Save. Note: this will overwrite the existing program. To copy a program for editing, please see section VIEW FILES.
EDITING PASSWORD PROTECTED PROGRAMS If the edited program is password protected, touching Save will open the message box shown opposite. To save the changes either: • Touch the None button next to Password and enter the correct password followed by Save. Note: this will overwrite the existing program. or • Touch the None button next to New Program Name and enter a new name for the edited program, followed by Save as a New Program.
CURRENT STATUS The Current Status area of the Home Screen provides status information on the Prime and is used to access the Run Screen. On the Home Screen, the Current status area shows the versions of software and firmware loaded on the unit. • Touch the Current status button to view the status of the Prime. The Prime status will be shown. If a unit is running a program, as shown by the status, the Run Screen can be viewed. Runs can then be paused or stopped as required.
VIEW FILES The View files module opens the File Manager and allows access to all the program and temperature log files. From here it is possible to copy program files to the unit for editing. Files can also be deleted or copied to a USB memory stick for transfer to a PC or storage. FILE SEARCHING There are four ways to search for a file: • Search program files or temperature logs from the complete list of saved files. • Search by keyword. • Search by user. • Search by keyword and user.
Search the files by user • Touch Search By User and this will open the list of user names stored on the unit. • Select the required user name by touching the appropriate button to highlight it. Touch again to de-select. • When the user name has been selected, touch Done to return to the File Manager screen. Only the programs with the selected user name saved with them will be listed. • To clear the user name search, touch Clear User Search.
VIEWING A PROGRAM FILE • Touch Programs And Logs to display Only Programs. • Search for the required program file and touch it to highlight it. • Touch View to open the temperature profile (Prerun Screen) of the program. • Touch Start to start the program. • Touch Edit to edit the program. • Touch Back to return to the previous screen. Note: The temperature log will remain blank until the program has been started.
When opening a temperature log file, the Temperature Log Monitor screen will be displayed. To view the complete temperature log, drag the mouse across the screen to scroll through the data points. The view will show a graphical representation of the actual temperature changes, second by second, throughout thermal cycling program. Clicking on the Program View button of this screen will display the program that generated the temperature log.
To copy files to a USB memory stick: • Insert a USB memory stick into the port on the front of the unit. A message screen will appear confirming that the USB memory stick has been inserted. • Touch Cancel to return to the File Manager Screen. • Select one or more files for copying by touching the appropriate file button. or • Touch Select All to select all files. • Touch Copy. A message screen will appear giving the option of saving the files to the unit or to the USB memory stick.
DELETING FILES Unused or old files can be permanently deleted from the unit or a USB memory stick. • Select one or more files for deleting by touching the appropriate file button. Note: Multiple file selection is optional and can be set up in the User Preferences section of the Settings Module. or • Touch Select All to select all files. • Touch Delete. A message box will appear asking for confirmation of delete. • Touch Yes to confirm the delete. • Touch Cancel to abort the delete.
UPDATING THE PRIME SOFTWARE The Prime software can be updated by downloading the latest version from the Techne website www.techne.com. You will need a USB memory stick on which to save the update. Note that the update tool requires at least Windows XP SP2 and the Microsoft .Net Framework 3.5 SP1, which, if needed, can be downloaded from: http://www.microsoft.com/downloads/details.
UPGRADING FROM PRIME TO PRIMEG The standard Prime thermal cycler can be easily and quickly upgraded to the gradient PrimeG version by purchasing the PrimeX/USB upgrade. The upgrade consists of a license certificate printed with a unique upgrade code which allows gradient functionality to be installed on any non-gradient Techne Prime thermal cycler.
REPLACING BLOCKS Please note that thermal blocks in Prime and PrimeG thermal cyclers are not interchangeable. Thermal blocks can be replaced under warranty in case of product breakdown and mechanical or electrical failure, but this must be performed by a Qualified Bibby Scientific Service Engineer and may require the unit to be returned to the factory.
FAQs Q1 A1 How do I adjust the pressure of the heated lid for my tubes or plates? For thermal cyclers with lid adjustment knobs, rotate the knob anticlockwise until there is no pressure on the consumable, then close the lid and latch it. To obtain the correct pressure gently rotate the knob clockwise until it is possible to just feel the pressure being applied. Finally, rotate the knob a further quarter of a turn; the lid is now at the correct pressure for use with the consumable.
TECHNICAL SUPPORT AND SERVICING If you require further technical or application assistance please contact Techne at: E-mail: technehelp@bibby-scientific.com. Phone: +44 (0)1785 810433 Fax: +44 (0)1785 810405 For servicing information please contact: Service Department Bibby Scientific Ltd. Beacon Road Stone Staffordshire ST15 0SA E-mail: service@bibby-scientific.com. Phone: +44 (0)1785 810475 Fax: +44 (0)1785 810405 In the USA please contact service@techneusa.com or call +1 609 589 2560.
ADDITIONAL INFORMATION USER MAINTENANCE Before cleaning your unit, disconnect it from the power supply. The outer case of the Prime may be cleaned with a cloth dipped in water or ethanol (hexane or 50% methanol can also be used). No part of the case or cover should be immersed in the solvents. Do not use aggressive solvents such as acetone or abrasive cleaners. The block may be wiped with water, ethanol or propan-2-ol and may be decontaminated by wiping with 2% Neutracon or 1% bleach solution.
ACCESSORIES The following accessories can be obtained from Bibby Scientific Ltd. or your Techne distributor: Product code PrimeX/USB Description Prime base gradient upgrade REPLACEMENT PARTS The following replacement parts can be obtained from Bibby Scientific Ltd. or your Techne distributor: Note that block removal can only be performed by a qualified service engineer.
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