Subscribe to Our Youtube Channel
Related Manuals for Cole Parmer Alpha Cycler Series
Summary of Contents for Cole Parmer Alpha Cycler Series
- Page 1 Alpha Cycler Series PCR-300-S, PCR-300-D and PCR-300-Q Operation Manual GS100-001-CPB rev 2.9...
-
Page 2: Table Of Contents
Contents Introduction Alpha Cycler configurations Before Use Unpacking Fuse removal and replace Safety Information Consignes de sécurité Sicherheitsinformationen Informazioni sulla sicurezza Información de seguridad Contact Information Alpha Cycler specification Installation and operation Installation Operation General software features Introduction Basic Android commands and data/text input Template programs Gradient Creating user Profiles Creating a new user account To log in as an existing user Logging out Changing a user password... - Page 3 Contents Using the File Manager Search for a file Reports Deleting a program or report from the File Manager Copying and transferring Programs and reports Copying a program to a USB memory stick Transferring a program from a USB memory stick to the Alpha Cycler Instrument settings and defaults Preferences Instrument settings Temperature log Auto-restart Date and time Program defaults Updating the Alpha Cycler software Procedure Technical support and servicing Replacing blocks Additional information User maintenance Fault Finding Fuses Insulation testing...
-
Page 4: Introduction
Introduction The Alpha Cycler thermal cyclers are standalone systems with flexible block options (96 or 384 well formats being available). The range includes both a single block, the PCR-300-S, a dual block variant, the PCR-300-D and a quad block variant, the PCR-300-Q. The Alpha Cyclers range of block options allow for use of the most commonly used consumables including 0.2ml x 96 well plates, 0.2ml tubes, 0.2ml strip tubes and 384 well plates. All combinations of base unit and block include a gradient feature, manually adjustable heated lid and programming features such as touchdown, active sample cooling, advanced reporting and health check options as standard to allow for most applications to be performed easily. -
Page 5: Before Use
Before use Before using the Alpha Cycler please ensure you have read this manual carefully. If there is any doubt relating to the proper use of this equipment, please contact your local distributor or Cole-Parmer via the website: www.Cole-Parmer.com or email cpenquiries@antylia.com. UNPACKING When unpacking the unit please ensure that the following have been removed from the packaging: Alpha Cycler with block(s). Mains cables (UK, EU, China and US). USB stick containing operator’s manual and default protocols. PCR-300-Q 2x 15A Fuse which must be changed in certain territories and power supplies, see below. PCR-300-D 2x 12.5A Fuse which must be changed in certain territories and power supplies, see below. The user is advised to keep the original packaging in case the instrument ever needs to be returned for service or repair. Cole-Parmer accepts no responsibility for damage incurred unless the unit is correctly packed and transported in its original packaging. IMPORTANT NOTE: IF USING THE PCR-300-D / PCR-300-Q AT 120V, BEFORE THE UNIT IS CONNECTED TO THE MAINS AND SWITCHED ON FOR THE FIRST TIME REPLACE THE FUSES. FOR PCR-300-Q REPLACE 8A FUSES WITH 15A ANTI-SURGE FUSES. - Page 6 Before use REMARQUE IMPORTANTE : EN CAS D’UTILISATION DES MODÈLES PCR-300-D OU PCR-300-Q SOUS UNE TENSION DE 120 V, REMPLACEZ LES FUSIBLES AVANT DE BRANCHER L’APPAREIL À L’ALIMENTATION SECTEUR ET DE LE METTRE SOUS TENSION POUR LA PREMIÈRE FOIS. POUR LE MODÈLE PCR-300-Q, REMPLACEZ LES FUSIBLES 8 A PAR DES FUSIBLES TEMPORISÉS 15 A.
- Page 7 Before use NOTA IMPORTANTE: SE SI UTILIZZA L’PCR-300-D / L’PCR-300-Q A 120 V, PRIMA CHE L’UNITÀ SIA COLLEGATA ALL’ALIMENTAZIONE DI RETE E ACCESA PER LA PRIMA VOLTA, SOSTITUIRE I FUSIBILI. PER L’PCR-300-Q SOSTITUIRE I FUSIBILI DA 8 A CON I FUSIBILI RITARDATI DA 15 A. PER L’PCR-300-D SOSTITUIRE I FUSIBILI DA 5 A CON FUSIBILI RITARDATI DA 12,5 A.
-
Page 8: Safety Information
Safety information Please read all the information in this manual before using the Alpha Cycler. WARNING HIGH TEMPERATURES ARE DANGEROUS: they can cause serious burns to operators and ignite combustible material. Users should be aware of the following potential hazards: • USE CARE AND WEAR PROTECTIVE GLOVES TO PROTECT HANDS. • DO NOT use combustible substances near hot objects. • DO NOT operate the instrument in the vicinity of inflammable liquids or gases. • DO NOT place any liquid directly into the instrument. • DO NOT touch the heated lid when system is running or within 10 minutes of the system completing a run. • DO NOT touch the block when the system is running or within 10 minutes of the system completing a run. OPERATOR SAFETY All operators of Cole-Parmer equipment must have available the relevant literature needed to ensure their safety. It is important that only suitably trained personnel operate this equipment, in accordance with the instructions contained in this manual and with general safety standards and procedures. If the equipment is used in a manner not specified by Cole-Parmer. the protection provided by the equipment to the operator may be impaired. - Page 9 REPLACEMENT CABLE Should the mains lead need replacement, a cable of 1.5 mm of harmonized code H05VV-F 3G connected to an IEC320 plug should be used. IF IN DOUBT CONSULT A QUALIFIED ELECTRICIAN. ENVIRONMENTAL CONDITIONS The Alpha Cycler is designed operate under the following conditions: • Indoor use • Ambient temperature range +5°C to +35°C • 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 20°C ±2°C. The instrument has been tested for radio frequency interference and is certified under EN61326. WARRANTY Cole-Parmer Ltd warrants this instrument to be free from defects in material and workmanship, when used under normal laboratory conditions for two (2) years. In the event of a justified claim, Cole-Parmer will replace any defective component or replace the unit free of charge. This warranty does not apply if damage is caused by fire, accident, misuse, neglect, incorrect adjustment or repair, damage by incorrect installation, adaption, modification, fitting of non-approved parts or repair by unauthorised personnel. Cole-Parmer liability is limited to the cost of repair or replacement of the product and excludes in particular, indirect and consequential loss, damage, costs or expenses, including but not limited to wasted time, materials and expenditure or loss of use, profit, production, revenue, expected savings or goodwill. To make a claim please contact the supplier of the instrument. This warranty is in addition to,...
-
Page 10: Consignes De Sécurité
Consignes de sécurité Veuillez lire toutes les informations contenues dans ce manuel avant d’utiliser l’appareil Alpha Cycler. AVERTISSEMENT LES TEMPÉRATURES ÉLEVÉES SONT DANGEREUSES : elles peuvent être à l’origine de graves brûlures et enflammer les matériaux combustibles. Les utilisateurs doivent tenir compte des dangers potentiels suivants : • FAITES PREUVE DE PRUDENCE ET PORTEZ DES GANTS DE PROTECTION. • N’UTILISEZ PAS de substances combustibles à proximité d’objets chauds. • N’UTILISEZ PAS l’appareil à proximité de gaz ou de liquides inflammables. • NE PLACEZ AUCUN liquide directement dans l’appareil. • NE TOUCHEZ PAS le couvercle chauffant lorsque le système est en marche ou dans les 10 minutes qui suivent son utilisation. - Page 11 CÂBLE DE REMPLACEMENT Lorsque le cordon d’alimentation doit être remplacé, utilisez un câble constitué de conducteurs d’1,5 mm2 de type H05VV-F 3G harmonisé, connecté à une fiche IEC320. EN CAS DE DOUTE, CONSULTEZ UN ÉLECTRICIEN QUALIFIÉ. CONDITIONS D’UTILISATION L’appareil Alpha Cycler est conçu pour fonctionner dans les conditions suivantes : • Utilisation en intérieur • Température ambiante comprise entre +5 °C et +35°C • Altitude jusqu’à 2 000 m • Humidité relative ne dépassant pas 80 % • Variations d’intensité de l’alimentation secteur ne dépassant pas 10 % • Catégorie de surtension II CEI 60364-4-443 • Degré de pollution 2 REMARQUE : les caractéristiques de contrôle sont indiquées pour une température ambiante de 20 °C ± 2 °C. L’appareil a fait l’objet de tests d’interférences radioélectriques et a reçu une certification EN61326. GARANTIE Cole-Parmer France garantit cet appareil contre tout défaut de pièces et de fabrication, dans des conditions d’utilisation normale en laboratoire, pour une période de deux (2) ans. En cas de réclamation dûment justifiée, Cole-Parmer s’engage à remplacer gratuitement la pièce défectueuse ou l’appareil.
-
Page 12: Sicherheitsinformationen
Sicherheitsinformationen Bitte lesen Sie vor der Verwendung dieses Alpha Cycler alle Informationen in diesem Handbuch. WARNUNG HOHE TEMPERATUREN SIND GEFÄHRLICH: Sie können zu schweren Verbrennungen des Bedieners führen und brennbare Materialien entzünden. Die Benutzer sollten die folgenden möglichen Gefahren kennen: • SEIEN SIE AUFMERKSAM UND TRAGEN SIE SCHUTZHANDSCHUHE, UM IHRE HÄNDE ZU SCHÜTZEN. • Verwenden Sie KEINE brennbaren Stoffe in der Nähe heißer Objekte. • Bedienen Sie das Gerät NICHT in der Nähe brennbarer Flüssigkeiten oder Gase. • Füllen Sie KEINE Flüssigkeiten direkt in das Gerät. • Berühren Sie den beheizten Deckel NICHT während des Betriebs des Systems oder innerhalb von 10 Minuten nach Betrieb des Geräts. • Berühren Sie den Block NICHT während des Betriebs des Systems oder innerhalb von 10 Minuten nach Betrieb des Geräts. BEDIENERSICHERHEIT Alle Bediener von Cole-Parmer müssen Zugang zu den Dokumenten haben, die für die Gewährleistung der Sicherheit relevant sind. Es ist wichtig, dass nur entsprechend geschultes Personal diese Ausrüstung gemäß den Anweisungen in dieser Gebrauchsanweisung und den allgemeinen Sicherheitsstandards und -verfahren bedient. Wenn die Ausrüstung auf eine nicht von Cole-Parmer spezifizierte Weise verwendet wird, kann der Schutz des Bedieners beeinträchtigt werden. Alle Cole-Parmer erfüllen internationale Sicherheitsanforderungen und sind mit einem Übertemperatur- Ausschalter ausgestattet. Sollte ein Sicherheitsproblem auftreten, schalten Sie das Gerät an der Netzsteckdose aus und entfernen Sie den Stecker aus der Stromversorgung. - Page 13 7. Stellen Sie sicher, dass der Fuß des Geräts nicht über die Tischkante hinausragt. 8. Stecken Sie das Stromkabel in die Anschlussdose auf der Rückseite des Geräts. An den Geräten PCR- 300-D und PCR-300-Q befindet sich die Dose an der Seite des Geräts. 9. Schalten Sie das Gerät mit dem Schalter auf der Rückseite des Geräts an. An den Geräten PCR-300-D und PCR-300-Q befindet sich der Schalter an der Seite des Geräts. ERSATZKABEL Bei einem eventuellen Austausch des Netzkabels wird ein Kabel vom Typ H05VV-F 3G mit 1,5 mm² Adernquerschnitt und Europastecker (IEC 320) benötigt. IM ZWEIFEL EINEN QUALIFIZIERTEN ELEKTRIKER ZU RATE ZIEHEN. UMGEBUNGSBEDINGUNGEN Der Alpha Cycler kann unter den folgenden Bedingungen arbeiten: • Verwendung in Innenräumen • Umgebungstemperatur zwischen +5°C und +35°C • Höhenlage bis zu 2000 m • Relative Luftfeuchtigkeit maximal 80 % • Netzspannungsschwankungen maximal 10 %...
-
Page 14: Informazioni Sulla Sicurezza
Informazioni sulla sicurezza Si prega di leggere tutte le informazioni contenute in questo manuale prima di utilizzare l’Alpha Cycler. AVVERTENZA LE TEMPERATURE ELEVATE SONO PERICOLOSE: possono provocare bruciature gravi agli operatori e causare l’accensione di materiale combustibile. Gli utenti devono essere a conoscenza dei seguenti pericoli potenziali: • PRESTARE ATTENZIONE E INDOSSARE GUANTI PER PROTEGGERE LE MANI. • NON usare sostanze combustibili in prossimità di oggetti caldi. - Page 15 Cavo di ricambio Qualora occorra sostituire il cavo di rete, si dovrà utilizzare un cavo di 1,5 mm2 armonizzato H05VV-F 3G, collegato ad una spina IEC320. IN CASO DI DUBBI, RIVOLGERSI A UN ELETTRICISTA QUALIFICATO. Condizioni ambientali L’Alpha Cycler è progettato per operare nelle seguenti condizioni: • uso interno • temperatura ambiente compresa tra +5°C e +35°C • altitudine massima 2000 m • umidità relativa non superiore all’80% • oscillazioni dell’alimentazione di rete non superiori al 10% • categoria di sovratensione II IEC 60364-4-443 • grado di inquinamento 2 Nota: le specifiche di controllo sono indicate per una temperatura ambiente di 20°C ± 2°C. Lo strumento è stato collaudato per interferenze da radiofrequenze ed è certificato secondo la norma EN61326. Garanzia Cole-Parmer Ltd garantisce questo strumento da difetti di materiali e fabbricazione per un periodo di due (2) anni, se utilizzato in normali condizioni di laboratorio. In caso di reclamo giustificato, Cole-Parmer sostituirà gratuitamente qualsiasi componente difettoso o l’intera unità. Questa garanzia non copre i danni provocati da incendi, incidenti, uso non conforme, negligenza, errori di regolazione o di...
-
Page 16: Información De Seguridad
Información de seguridad Lea toda la información incluida en este manual antes de usar el Alpha Cycler. ADVERTENCIA LAS TEMPERATURAS ELEVADAS SON PELIGROSAS: pueden causar quemaduras graves a los operarios y prender fuego aL material combustible. Los usuarios deberían ser conscientes de los posibles peligros indicados a continuación: • TENGA CUIDADO Y USE GUANTES PROTECTORES PARA PROTEGER LAS MANOS. • NO utilice sustancias combustibles cerca de objetos calientes. • NO utilice el instrumento cerca de líquidos o gases inflamables. • NO coloque ningún líquido directamente en el instrumento. • NO toque el bloque cuando el sistema esté funcionando o durante los 10 minutos siguientes a la finalización de la serie por parte del sistema. • NO toque el bloque cuando el sistema esté funcionando o durante los 10 minutos siguientes a la finalización de la serie por parte del sistema. - Page 17 8. Conecte el cable de red en la toma de la parte trasera del instrumento. Para el PCR-300-D / AC- 4 la toma de entrada se encuentra en un lado del instrumento. 9. Encienda el instrumento usando el interruptor ubicado en la parte trasera del instrumento. Para el PCR-300-D / AC- 4 el interruptor está un lado del instrumento. CABLE DE SUSTITUCIÓN En caso de que sea necesario sustituir el cable de alimentación, utilice un cable de 1,5 mm2 de código armonizado H05VV-F 3G conectado a un enchufe IEC320. EN CASO DE DUDA, PÓNGASE EN CONTACTO CON UN ELECTRICISTA CUALIFICADO. CONDICIONES AMBIENTALES El Alpha Cycler ha sido diseñado para funcionar en las siguientes condiciones: • Uso interior • Intervalo de temperatura ambiente +5 °C a +35°C • Altitud máxima de 2 000 m • Humedad relativa no superior al 80% • Fluctuaciones de corriente no superiores al 10% • Categoría de sobrevoltaje II IEC 60364-4-443 • Grado de contaminación 2 Nota: Las especificaciones de control se indican a una temperatura ambiente de 20°C ±2°C. El instrumento ha sido sometido a las pruebas de interferencia por radiofrecuencia y está certificado según la norma EN61326. GARANTÍA Cole-Parmer Ltd. garantiza que este equipo se encuentra libre de defectos de material o de fábrica, siempre que se utilice en condiciones normales de laboratorio, durante un plazo de dos (2) años. Si...
-
Page 18: Contact Information
Contact Information For technical, sales or servicing information, contact your local Cole-Parmer distributor or Antylia Scientific directly at: Antylia Scientific Ltd. Beacon Road Stone Staffordshire ST15 0SA Tel: +44 (0)1785 812121 E-mail: cpenquiries@antylia.com Help: cptechsupport@antylia.com Web: www.Cole-Parmer.com... -
Page 19: Alpha Cycler Specification
Alpha Cycler Specification Temperature Block temperature range 4°C (10°C during cycling) to 100°C Block uniformity (at 55°C) ≤±0.3°C Temperature accuracy (at 55°C) ≤±0.25°C Gradient availability Between 10°C and 100°C Maximum gradient 29°C on a 96 well block and 19°C on a 384 well block Minimum gradient 1°C Column uniformity with a 10°C gradient ≤±0.3°C Final store 4°C to 100°C Temperature set point adjustment 0.1°C Heating/Cooling Rate Maximum heating rate 3.4°C/s Minimum heating rate 0.1°C/s Maximum cooling rate 1.0ºC/s Minimum cooling rate 0.1ºC/s Heated lid Selectable heated lid temperature 35 to 115°C or off Lid uniformity ±5°C Pre-heat lid Warm up time from ambient <2 min Over-temperature cut-out Regulated heated lid pressure... - Page 20 Incremented/decremented temperature Incremented/decremented time Pause facility Program naming Alpha numeric plus symbols Password protection Keyword selection Run completion time Auto resume on power failure Yes, always, never or user-defined Oligonucleotide Tm calculator Yes, based on the Nearest-Neighbour method Software updates Free of charge from www.Cole-Parmer.com Communication ports USB port on the front of the PCR-300-S Connection for USB memory stick USB port on side of the PCR-300-D / PCR-300-Q Connection for USB memory stick Type B USB port on rear of unit For Internal use only. Dimensions PCR-300-S PCR-300-D PCR-300-Q Height (mm) 330 330 Width (mm) 260 535 Length (mm) 430 470 Weight (kg) Power PCR-300-S PCR-300-D PCR-300-Q Voltage 100-230V, 50/60Hz 100-230V, 50/60Hz...
-
Page 21: Installation And Operation
Installation and operation See also the Safety Information sections on pages 5 to 15. Front view 1. Heated lid pressure knob 2. Lid release. 3. Android HD touchscreen interface 4. USB port for memory stick. Rear view 1. Mains cable inlet. 2. On/Off rocker switch Note: On the PCR-300-D / PCR-300-Q the mains cable inlet, On/Off rocker switch and USB port are situated on the side of the instrument for easier access. INSTALLATION 1. Place the unit on a suitable flat and level bench, ensuring that the air inlet vents on the sides are free from obstruction, as per the guidelines in the Safety Information sections. Note: Ensure a 250mm gap to the side of the PCR-300-D / PCR-300-Q power lead to allow disconnect of the electrical supply from the chassis if required, 100mm is sufficient for PCR-300-S. -
Page 22: Operation
OPERATION 1. Release the heated lid by pressing the blue circular button located towards the front edge of the lid. The lid is sprung and should open to around 45 degrees with little assistance. To close the lid, lower the lid onto the block and press until you hear a click. 2. 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. 3. 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:... -
Page 23: General Software Features
General software features INTRODUCTION The Alpha Cycler software is aimed at being consistent with all the instruments in the Cole-Parmer range. The common themes of simplicity and performance are echoed in all Cole-Parmer thermal cyclers. The software will boot automatically when the system is switched on. The Alpha Cycler 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 six modules which are accessed from the Home Screen. The Home Screen has the following buttons and associated features. • Run a program allows the user to run an existing program, selecting from templates or programs saved on the unit. • New program allows the user to manually build a custom thermal cycling program. • Program wizard allows the user to automatically generate a protocol based on primer sequences, Tm’s and template size. • Edit program gives access to the File Manager and allows the user to search for programs and reports stored on the unit and to edit existing programs. • Block status allows the user to monitor the progress of the program running on one or more of the blocks. • Settings allows the user to define default states of the system e.g. temperatures for cycling steps, language and response to power outages etc. The Recent Programs panel displays the most recent protocols which have been run on the system. Note: The Recent Programs panel will allow users to quickly access and run common programs without the need to navigate the File Manager. -
Page 24: Basic Android Commands And Data/Text Input
BASIC ANDROID COMMANDS AND DATA/TEXT INPUT The Alpha Cycler system interface is Android based and as such responds and operates similarly to other Android devices. The standard Android navigation bar is located at the bottom of all Alpha Cycler screens: • Back: This will take you back to the previous page. Repeatedly press this button to go back multiple screens. • Home: This will take you back to the Home Screen for the Alpha Cycler. • Recent: This will allow you to toggle between recent pages you have open. End users can also close open pages by swiping the windows left or right, as you would normally with Android interfaces. Note: If you have opened multiple pages, for example you been in settings, started writing a protocol and had a protocol running, selecting the recent button allows you to easily toggle between these open pages. When users are required to input data, either an Android keyboard will open in the screen or a scrolling wheel may appear (the scrolling wheel is used more for defining values such as number of cycles and time). Example keyboard Example time wheel during step duration input... -
Page 25: Template Programs
TEMPLATE PROGRAMS To help with programming, a number of program templates are provided on the USB memory stick supplied with the system. These are available to copy and edit or can be run directly without changes. Details of the installed program templates are given below. Instrument and program defaults Parameter Gradient 50 to 60 deg. 3 Step Template RT PCR Template Heated Lid 110°C 110°C 110°C Heated lid before program Sample cooling... -
Page 26: Gradient
GRADIENT The gradient feature of the Alpha Cycler can be useful in optimising the annealing conditions for reactions. A gradient can be set around a temperature in any step of a program. The set temperature is the temperature in the middle columns and the range around the set point defines the gradient’s minimum and maximum temperatures, see diagram below. The maximum temperature gradient range which can be set is 29°C (depending on block type) and the minimum is 1°C; within the temperature range of 10°C and 100°C. Examples are given in the table below: Gradient Set temperature Lowest temperature Highest temperature (°C) -
Page 27: Creating User Profiles
Creating user profiles The Alpha Cycler system allows for individual user profiles to be created, simplifying file management and controlling access to certain programs. CREATING A NEW USER ACCOUNT • To create a new user account tap the LOGIN button located at the top of the Home Screen. • Select Create an account. • Complete the details: User name, Password and Re-enter password. • Tap on Create Account to save the profile. Note: Programs written by a logged in user will only be available to that user unless the user chooses to share these programs with everyone; see the programming section. TO LOG IN AS AN EXISTING USER • Select LOGIN from the top of the Home Screen. • Select Log in from the login screen. • Log in with your user-specific name and password. Tap on Log in. •... -
Page 28: Creating Usb Login
Creating USB Login The Alpha Cycler system allows for individual user profiles to be created, simplifying file management and controlling access to certain programs. CREATING A USB LOGIN • To create a USB LOGIN device click on the login button located at the top of the home screen. • LOGIN with existing account. • Return to the login screen • Insert a USB drive and click Authorize USB drive. Note: Any USB drive can be authorised as the users login device. When logging in via USB all specified user defaults will be carried forward and applied. Removing the USB drive will logout the user. • To log in with the authorised USB drive, simply insert the authorised / USB into the Alpha Cycler • When a program is started from a logged in user and the user then logs out the running program can only be interrupted or stopped by inputting the specific users login details. • Removing the USB drive will automatically log the user out. -
Page 29: Programming
Programming This section gives instructions for the two methods of programming the Alpha Cycler systems. The first method uses the Program Wizard to automatically generate a program based on a few user defined parameters. The second method is accessed through the New program button from the Home Screen and allows the user to control every element of the program. Note: When programming an Alpha Cycler protocols are built with a steps and stages structure. Individual steps can be created and a collection of those steps make up a stage. Stages have a number of cycles applied to them and all steps in a stage will cycle the specified number of times before progressing to the next stage. Protocols can have multiple stages comprising multiple temperature steps. USING THE PROGRAM WIZARD The Program wizard allows users to automatically generate a protocol based upon the following criteria: • Primer Sequence or Tm’s • Length of amplicon • Template source (bacterial, eukaryote or plasmid) • Special considerations Special considerations has a series of options which accommodate for the use of hot start Taq polymerases, adjusts the temperatures based upon the amplicons A/T and G/C bias and will allow for the user to add a touchdown PCR stage as a means of improving specificity. - Page 30 • If selecting the primer sequences, tap “I’d like the melting temperatures calculated for me from the primer sequences” to input the sequence of each primer. • Tap on the line Primer Sequence 1; a keyboard will appear on the screen. Type in the sequence of the first primer then tap on Next. • Type in the sequence of the second primer then tap on Done. Primer sequences can be uploaded direct from the root of a USB drive. To input your own primer Tm values, tap “I’d like to provide the melting temperatures myself”. • Tap on the line Primer 1 (°C); a keyboard will appear on the screen. Type in the melting temperature • of the first primer then tap on Done.
- Page 31 The next step is to input the length of the PCR product in kb. • Either tap the line next to Product length (Kb) to enter the size of the PCR product (in kb) or drag the slider to the right or left to select the size. Note: values of between 0-5kb are valid: all values below 0.5kb will be given an extension time of 30 seconds. Tap NEXT PAGE at the top right of the screen to progress to the next step. To go back, tap on • PREVIOUS PAGE. The next step is to select the source of the DNA. • Select one of the three options. Tap NEXT PAGE at the top right of the screen to progress to the next step. To go back, tap on •...
- Page 32 When finished, tap FINISH WIZARD at the top right of the screen. • Once you have completed the Program wizard, the final program will be displayed based upon the answers/data given in the previous steps. Note: all parameters of a Program wizard-generated program can be adjusted either before or after it is saved. Ensure that heated lid is set how you wish it to be and add any special stages such as a final extension or a store step at this point. • To save the program, tap SAVE at the top right of the screen. Select whether the program will be available to Everyone or Just me (current logged-in user) and • assign a name. • Tap Save.
-
Page 33: Manual Program Entry
MANUAL PROGRAM ENTRY The Alpha Cycler will also allow users to manually create a protocol by inputting the individual temperatures and hold durations for each step. Where a temperature or hold time is visible/required the user will be able to tap to select that step and either edit or input a time/temperature. • From the Home Screen select New program. The basic program will contain the defaults as set by the user in the Settings (see section on Settings). A. Toggle on and off the Heated Lid. B. Toggle on/off Preheat Lid. C. Toggle on/off Sample Cooling before the run begins. D. Add a new stage - adds a stage with one temperature step plus the option to add further temperature steps within the same stage. The stage can be cycled up to 99 times. Add a special step - including Touchdown, Final Extension and Final Store steps. - Page 34 To change the step temperature, tap on the default temperature value and enter the desired value followed by Done. To change the steps hold temperature, click on the hold temperature and a window will open, scroll the temperature in that window and select Change to update to the new hold temperature. To change step hold time, the same applies but to the duration not temperature. Note: Alpha Cycler Temperature steps carry an inherent hold time of 30 sec and temperature of 95˚C, 56˚C and 72˚C for a three step stage. Tap Add stage to complete adding the first stage and step.
-
Page 35: Editing Step Parameters
Continue by adding further steps and stages as required in the same way. Note: If a protocol has several stages it may appear to extend beyond the screen; simply swipe the screen to the left or the right to view the whole protocol. To adjust the number of cycles of a stage, tap on the cycle button at the bottom of each stage area; a scrolling selector will appear. Select the desired number of cycles followed by Change. As the program is written, the total duration of the protocol is displayed at the bottom of the programming screen. EDITING STEP PARAMETERS To edit the parameters of a step e.g. the temperature, hold time, ramp rate etc. tap on the grey shaded area of the step. The Change step parameters window (see below) will open. Make any changes to the parameters then tap on Change to accept. Note: The ramp rate (heating/cooling rate from the previous step to the current step) can be defined between 0.1 ºC/sec up to 3 ºC/sec or MAX. ADDING A GRADIENT STEP Select the step on which you wish to add a gradient and tap on the grey shaded area. The Change step parameters window will open. Toggle ON the parameter Gradient around step temperature. Next, define the range of temperature you wish to run the gradient over. Tap on Change to accept the changes. The gradient and range will then be displayed within the program. -
Page 36: Adding A Temperature Or Time Increment Or Decrement
Note: After running a gradient protocol to optimise a reaction, the program can be easily modified to set the annealing temperature to that of the column in which the optimal reaction occurred. Simply tap on the gradient step to edit it then select Convert to fixed temperature °C. A window showing the actual temperature in each column of the block is displayed. Select the column which gave the optimal reaction conditions to re-set the annealing temperature. ADDING A TEMPERATURE OR TIME INCREMENT OR DECREMENT Select the step on which you wish to add the increment or decrement and tap on the grey shaded area. The Change step parameters window will open. Toggle ON the parameter Temperature change per cycle or Time change per cycle as desired. Next, define the increment or decrement temperature or time. Tap on Change to accept the changes. Note: The maximum allowed temperature increment/decrement is between -10 °C and + 10°C/cycle and the maximum time increment/decrement -30 seconds and +30 seconds/cycle. This will also be dependent on the number of cycles in the stage and the limits of the thermal block. -
Page 37: Deleting A Step Or Stage
The temperature/time changes will be displayed with the program. DELETING A STEP OR STAGE To delete a step, tap in the area just below or above the step (not in the grey boxed area) so that the step is highlighted. Multiple steps may be selected. Next, tap on DELETE at the bottom of the screen. The step(s) will be deleted. To delete a complete stage, all steps within the stage must be deleted, this can be done by highlighting the temperature steps, press the screen underneath the temperature step box to highlight and then press DELETE. Note: At the top of the screen there is an UNDO button to undo the last series of commands if a mistake such as unintentionally deleting a step/stage is made. SAVING THE PROGRAM To complete writing a program and to store it to the cycler memory, tap SAVE on the top right corner of the program window. The Save program window will appear. - Page 38 Define who will have access to the program: • Everyone, meaning all users of the system will have access to this protocol, or • Just me, meaning only the current logged-in user will have access. Add a name for the program for future identification then tap on Save. Programs can also be password protected. Click on the box marked “Protect the program from further changes’ and assign a password. To alter the program the password must be known. Programs with password protection can not be interrupted/stopped mid cycle without applying the password. Note: The RUN AND SAVE button allows you to start the protocol from the programing screen without the need to first save and then go into the File Manager to run the protocol. Run and save can be useful for when you are modifying an existing protocol.
- Page 39 Special steps When writing a protocol there is an option to add a special step, these include: • Polymerase Activation • Touchdown • Final Extension • Final Store Tap on Add a special step and the Add a special step or stage window will open. Polymerase Activation allows for a one off temperature/time step to activate the polymerase, this step will not cycle. Touchdown stage allows users to generate a touchdown protocol which will change the temperature uniformly across the entire block each cycle between two set temperatures (high to low) over a defined number of cycles. Define the starting (maximum) annealing temperature and the end (minimum) annealing temperature. The temperature change per cycle will be equal to the difference in temperature between the maximum and minimum divided by the number of cycles -1.
- Page 40 Note: The software allows the user to either increment or decrement the time and/or temperature of a step within a cycling stage. These features are used with applications such as touchdown PCR where the annealing temperature is gradually decreased during the cycling process and long range PCR amplification, where due to the size of the product, long annealing/extension times are required and the extension time is increased by, for example, 15 to 20s per cycle during the final stages of the reaction. Final extension allows users to add a final temperature step at the end of normal cycling. Final store allows users to store the PCR reactions in the system at a set temperature until they are ready to be taken out for further analysis. The default temperature is 10°C as this is suitable for storing DNA for prolonged periods of time.
-
Page 41: Running A Program
Running a program There are two main options for running a program; either selecting the program from the Home Screen Recent Programs shortcut list or by searching through the system’s File Manager accessed through either Run a program or Edit program. RUNNING A PROGRAM FROM THE SHORTCUT LIST When a program has been run on the Alpha Cycler it will appear in the Recent Programs list. To re-run the same program, tap to select one of the programs from this list. The Pre-run screen will be displayed. The Pre-run Screen shows a graphical representation of the program allowing for a rapid check of the temperature parameters. Any of the parameters can be edited at this point. • Touch any stage or step to edit the program. Touch RUN AND SAVE to start the program. Note that this will over-write the existing program if • any edits have been made. • Touch Back to return to the previous screen. Note: With the PCR-300-D / PCR-300-Q you will be asked at this point on which block(s) the program is to be run. Any number of the available blocks can be selected. Select the required block(s) by tapping to display YES. -
Page 42: Running A Program From The Instrument Memory
Tapping on Run will send the program to the thermal cycler and it will begin automatically. Note: PCR-300-D only has left/right block option. RUNNING A PROGRAM FROM THE INSTRUMENT MEMORY If the program required is not present in the Recent programs list it must be located using the File Manager. From the Home Screen, tap on Run a program to open the File Manager. Select the required program by tapping to highlight it. Note: With the PCR-300-D / PCR-300-Q you will be asked on which block(s) the program is to be run. Any number of the available blocks can be selected. Select the required block(s) by tapping to display YES. Tapping on Run will send the program to the thermal cycler and it will begin automatically. Note: This route of selecting a program does not allow you to view the thermal profile before it is run. An alternative way of accessing the File Manager is to go through Edit program. Using this route you will be able to view the program in the Pre-run screen and make any changes before sending it to the thermal cycler. Once you are satisfied the program is correct, tap RUN AND SAVE to start the program as described above. - Page 43 CREATING A FAVOURITE PROGRAM. A program can become a favourite by pressing on the start icon in the Edit Programs menu or by pressing the three stacked boxes icon while writing a program and selecting favourite as images below. In Edit programs check the Star icon to Favourite a Program. In New Program press the three stacked boxes icon and check Favourite to assign it as such. NOTE: Favourite programs can then be visualised together on the home screen, see instrument setting section for how to display Favourites on the home screen.
- Page 44 There is also an option to display the countdown clock in full screen while the system is running. This feature is only available in the PCR-300-S and is accessed by clicking on the four arrow icon in the status bar. With the PCR-300-D / PCR-300-Q, status of each block is shown separately across the bottom of the screen. To view the running program in more detail, from the Home Screen tap on Block status. Note: With the PCR-300-D / PCR-300-Q, the status of all blocks will be displayed.
- Page 45 To view an individual block, tap on the full screen icon close to program name. This will expand the run screen of the selected block to fit the entire screen. Note: If a protocol has several stages which extend beyond the screen; simply slide the screen to the left or the right to view the protocol. When viewing an individual program there is the option to toggle between viewing the real time temperature of the block and the program display. To view the block temperature, tap on DISPLAY REAL-TIME TEMPERATURE at the top right of the screen. Note: see settings too toggle between displaying the average temperature across the block or the actual temperature recorded at the four temperature sensors. When Real Time Temperature is selected the user is shown the current temperature of the block as it progresses though the program. Approximately 5 minutes of temperature profile is shown on the display.
-
Page 46: Stopping A Program
STOPPING A PROGRAM When in the full screen display, tap STOP to stop the program. A prompt will ask you to confirm the stop. Note: For the PCR-300-D / PCR-300-Q all active blocks can be stopped together from the block status screen. To stop an individual program, first select the full screen display by tapping on the block area close to program name to open up the full screen. Alternatively, programs can be stopped from the Home Screen by tapping on the status bar. This will open up the run screen. -
Page 47: Pausing A Program
PAUSING A PROGRAM A program can be paused in the same way as stopping a program. After a program has been paused, it can be resumed by tapping on RESUME. Note: It is possible to access all modules of the software while the unit is running a program. Simply use the Return button or Home button at the bottom of the screen to access other areas of the software. Program finished When a program has completed, a Summary Report will be displayed on the screen. • Click on OK to close the report. Note: With the PCR-300-D / PCR-300-Q a report will be presented for each individual block as each program finishes. -
Page 48: Using The File Manager
Using the File Manager The File Manager is used to find and view programs and reports stored in the system memory or on an external device such as a USB memory stick. • To access the File Manager, tap on Edit program from the Home Screen. • Touch PROGRAMS or REPORTS to view all those saved under the current profile (shown in the top right of the screen). • To view the files belonging to different profiles, tap the Profiles icon (head and shoulders of a person) at the top right of the screen. • Select whether to view the files available to Everyone or just the currently logged-in user. Note: If a USB memory stick has been inserted into the USB port, A USB icon will also be visible at the top right of the screen. • To view files stored on the USB memory stick, tap on the USB icon. SEARCH FOR A FILE •... -
Page 49: Reports
REPORTS Reports of runs performed on the Alpha Cycler are stored in the unit memory and can be accessed any time. • To view the report lists, from the File Manager select REPORTS. • Select a program name. All reports for that program will be displayed in chronological order. • Tap on a report from the list and the individual Summary Report will be displayed. Tap OK to exit. Note: It is not possible to view the temperature log contained within the report on the Alpha Cycler itself, it must first be copied to a USB memory stick then viewed on a PC using Excel®. The file will be saved as a .csv file. See the directions given in the next section for copying files to a USB memory stick. -
Page 50: Deleting A Program Or Report From The File Manager
DELETING A PROGRAM OR REPORT FROM THE FILE MANAGER Programs and reports can be deleted from the File Manager. • Tap the command button ( ) at the top right of the screen. • Select the file(s) you wish to delete; selected files will be highlighted blue. Tap again to deselect. • Touch the delete icon (large X) at the top right of the screen. • A prompt will appear to confirm the delete; once confirmed the selected files will be deleted from the system’s memory. • If you choose not to delete a file, touch Cancel. • Touch the tick icon next to Done to return to the File Manager. -
Page 51: Copying And Transferring Programs And Reports
Copying and transferring Programs and reports COPYING A PROGRAM TO A USB MEMORY STICK To copy a program from the system’s memory to an external memory device such as a USB drive, first search for the desired program using the File Manager accessed through Edit program on the Home Screen. • Insert a USB memory stick into the port on the Alpha Cycler. A USB icon will appear at the top right of the screen. • Tap the Command button ( ) at the top right of the screen. • Select the file(s) you wish to copy; selected files will be highlighted blue. Tap again to deselect. • Touch the Copy icon at the top right of the screen. • A prompt will appear indicating that the selected files are ready for copy. • To copy the files to the USB memory stick, tap on the USB icon to select the destination then tap the Paste icon (clip board). TRANSFERRING A PROGRAM FROM A USB MEMORY STICK TO THE ALPHA CYCLER Transferring programs from one Alpha Cycler to another avoids the user having to re-write new programs for each additional instrument and is an easy way to share optimised protocols with other Alpha Cycler users. -
Page 52: Instrument Settings And Defaults
Instrument settings and defaults The Settings button on the Home Screen gives access to the instrument settings and allows you to set up your own preferences and defaults for writing programs. Tap the Settings button on the Home Screen to access the instrument Settings menu. Note: The system must be restarted for the system settings and defaults to be applied. If the settings are changed, always restart the system. Touch any of the headings on the left hand side to view and edit those settings. Once all the settings and defaults have been set as required, touch the Back button at the bottom of the screen to return to the Home Screen. PREFERENCES This allows you to select the preferred operation language. The options are: • English • French • Spanish • Italian • German... -
Page 53: Instrument Settings
INSTRUMENT SETTINGS These allow setting of temperature logs, auto restart and date and time. TEMPERATURE LOG When set to ON the temperature log will record the block temperatures for every run and save them as a Report. If temperature logs are not required, set to OFF. AUTO-RESTART This determines whether the unit will restart after a power failure. Setting Auto-restart to Always will allow the unit to re-start irrespective of the length of the power failure. Selecting Never will mean the system will not auto-restart after a power outage. In addition, the user can select a time in which, if the power comes back on in that window, then the system will resume. The options are shown below. Note: the time periods in the auto-restart allow the end user to select windows of power loss which they deem acceptable for the power to be disrupted during their protocols. Example: if the system is set to 10 minutes and the power is out for 8 minutes the system will resume, if the power is out for 12 minutes the system will not auto-restart. -
Page 54: Date And Time
DATE AND TIME This allows you to set the current date, time and format. Check the required boxes then tap the back button to return. PROGRAM DEFAULTS This section allows you to define a number of parameters as defaults which will be applied to all protocols created on the system. Note: Defaults are merely a starting point and are not fixed, if the default value is not appropriate for your reaction simply edit that value here or during programing. Use the heated lid Use this to set the heated lid temperature to approximately 10°C higher than the hottest block temperature in the program. • Touch ON/OFF to toggle between settings. • Touch the temperature button to set the required lid temperature (35°C to 115°C). - Page 55 Preheat lid before program starts Set to ON to pre-heat the lid to the set temperature before the thermal cycling program begins (recommended, especially if the first step involves a high block temperature). • Touch ON/OFF to toggle between settings. Cool the block whilst heating the lid Set to ON to cool the block to 4°C while the lid preheats. • Touch ON/OFF to toggle between settings. Include a polymerase activation This will automatically program an initial denaturation/polymerase activation step at the beginning of a program.
- Page 56 Administrator Level The Alpha Cycler software has an administrator level which allows the administrator to reset passwords for users and delete accounts which are no longer required. Default Admin Login Details User: admin Password: admin...
-
Page 57: Updating The Alpha Cycler Software
Updating the Alpha Cycler software The Alpha Cycler software can be updated by downloading the latest version from the Cole-Parmer website www.Cole-Parmer.com or by contacting your local distributor. You will need a USB memory stick on which to save the update. PROCEDURE • Save the update file to the root folder on the USB device. • Insert the USB device into the USB port on the Alpha Cycler. • On the Home Screen select the Update icon on the top right of the page, (icon of three stacked vertical dots). Select Check for updates. • • A dialogue box will open in which information about the upgrade will be provided and the user will be given the option to carry out the update or not. • If Yes is selected the installer will describe the process on screen. • The user will be asked to confirm the installation of the new Alpha Cycler App and a confirmation note will assure end users that existing files and data will not be over written. -
Page 58: Technical Support And Servicing
Technical support and servicing If you require further technical or application assistance please contact your local distributor (details can be found at http://www.Cole-Parmer.com/distributors) or Cole-Parmer at: E-mail: cptechsupport@antylia.com Phone: +44 (0)1785 810433 For servicing information please contact your local distributor (details can be found at http://www. Cole-Parmer.com/distributors) or: Service Department Antylia Scientific Ltd. Beacon Road Stone Staffordshire ST15 0SA E-mail: cpservice@antylia.com Phone: +44 (0)1785 810475 We are continually striving to improve our products and software. If you have any comments or suggestions on how we can do things better please send them to us at: cpenquiries@antylia.com REPLACING BLOCKS... -
Page 59: Additional Information
Additional information USER MAINTENANCE Before cleaning your unit, disconnect it from the power supply. The outer case of the Alpha Cycler 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. Before using any cleaning or decontamination method except those recommended here, the responsible person should check with Cole-Parmer that the proposed method will not damage the equipment. Max Strength 70% IPA 2% neutracon detergent FAULT FINDING Note that this equipment should only be dismantled by properly trained personnel. Removing the outer cover exposes potentially lethal mains voltages. There are no user serviceable parts within this equipment. Should you have any problems with your Alpha Cycler which cannot be easily remedied, you should contact your supplier and return the unit if necessary. Please include details of the fault observed and remember to return the unit in its original packing. Cole-Parmer Ltd. accepts no responsibility for damage to units which are not properly packed for shipping. If in doubt, contact your supplier, providing the serial... -
Page 60: Declaration Of Conformity
Declaration of Conformity This product meets the applicable CE Directives that interference will not occur in practise. Where and UKCA Legislation for radio frequency there is a possibility that injury, damage or loss might interference and may be expected not to occur if equipment malfunctions due to radio interfere with, or be affected by, other equipment with similar frequency interference, or for general advise before... - Page 61 Ordering Information Order No. Series Model Legacy SKU 93945-00 PCR-300 PCR-300-S384 AC1384 93945-02 PCR-300 PCR-300-S96 AC196 93945-20 PCR-300 PCR-300-D196 AC2196 93945-22 PCR-300 PCR-300-D96 AC296 93945-28 PCR-300 PCR-300-D384 AC2384 93945-04 PCR-300 PCR-300-Q196 AC4196 93945-06 PCR-300 PCR-300-Q296 AC4296 93945-08 PCR-300 PCR-300-Q384 AC4384 93945-10 PCR-300 PCR-300-Q396...
Need help?
Do you have a question about the Alpha Cycler Series and is the answer not in the manual?
Questions and answers