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Table of Contents
Related Manuals for Agilent Technologies SureCycler 8800
Summary of Contents for Agilent Technologies SureCycler 8800
- Page 1 SureCycler 8800 Setup and User’s Guide Version A, March 2011 Agilent Technologies...
- Page 2 FAR 12.211 (Technical Data) and 12.212 (Computer Software) and, for the Department of Defense, DFARS 252.227-7015 (Technical Data - Commercial Items) and DFARS 227.7202-3 (Rights in Commercial Computer Software or Com- puter Software Documentation). Agilent SureCycler 8800 Setup and User’s Guide...
- Page 3 PCR Programs This chapter contains instructions to work with PCR programs, incubations and reports. Troubleshooting suggestions are also provided. Maintenance and Updates This chapter contains instructions for maintaining the instrument and uploading software updates. Agilent SureCycler 8800 Setup and User’s Guide...
- Page 4 Agilent SureCycler 8800 Setup and User’s Guide...
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Page 5: Table Of Contents
To remove the thermal block To install the thermal block Getting Started Sample Preparation and Loading To prepare samples To load samples Agilent Plasticware and Consumables Starting Up the Software Touchscreen Operation of the Software Agilent SureCycler 8800 Setup and User’s Guide... - Page 6 PCR Programs Creating New PCR Programs To manually create programs To create a PCR program using the PCR Wizard Tips for Creating PCR Programs for the 384-well SureCycler 8800 Program Steps in the Commands List Hot Start Cycle Wizard Start Cycle...
- Page 7 If cycler does not turn on If screen is blank and unlit If screen is lit but shows no information or has missing characters Maintenance and Updates Maintenance Cleaning Replacing a fuse Software Updates Agilent SureCycler 8800 Setup and User’s Guide...
- Page 8 Contents Agilent SureCycler 8800 Setup and User’s Guide...
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Page 9: Before You Begin
Setup and User’s Guide Before You Begin Materials Provided Safety Precautions Indicator LED Light Overview SureCycler 8800 Technical Support This chapter contains information for you to read and understand before you start. For installation instructions, see “Installation” on page 16. -
Page 10: Materials Provided
• Unplug the instrument before you clean any major liquid spills and before you service any of the electrical or internal components or swap out the thermal block. • Do not operate the instrument from a power outlet that has no ground connection. Agilent SureCycler 8800 Setup and User’s Guide... - Page 11 • Do not operate the instrument in a hazardous or potentially explosive environment. Equipment Ratings • Pollution degree 2 • Installation category 2 • Altitude 2000 m • Humidity 20 to 80%, non- condensing • Electrical supply 100- 240 V, 50/60 Hz, 11 A Agilent SureCycler 8800 Setup and User’s Guide...
- Page 12 • Temperature 20°C to 30°C • For Indoor Use Only Electrostatic Discharge The SureCycler 8800 is static sensitive. Electrostatic discharges greater than 8000 volts may interfere with the normal operation of the USB ports on the instrument. Handling precautions are required when working in high static environments.
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Page 13: Indicator Led Light
The cycler has detected an error. Check the display for an error message containing further details. Overview The SureCycler 8800 is a thermal cycler designed to perform polymerase chain reaction (PCR) and related methods for amplification of DNA templates. The cycler can run even the most complex thermal cycling techniques, including time and temperature increments, touchdown PCR and temperature gradients. -
Page 14: Surecycler 8800 Technical Support
Spain 901 11 68 90 Sweden 08 506 4 8960 Switzerland 0848 8035 60 UK/Ireland 0845 712 5292 Japan 0120-477-111 All other countries Go to www.genomics.agilent.com and click on the Contact Us link. Agilent SureCycler 8800 Setup and User’s Guide... -
Page 15: Installation
SureCycler 8800 Setup and User’s Guide Installation Installation Step 1. Select a location for the instrument Step 2. Unpack the cycler Step 3. Install the thermal block on the instrument base Step 4. Connect the instrument to a power supply Step 5. -
Page 16: Installation
The thermal block unit will only lock into place if it is placed on the instrument base in the proper orientation. For instructions on swapping out the thermal block, see “Thermal Block Exchange” on page 18. Agilent SureCycler 8800 Setup and User’s Guide... -
Page 17: Step 4. Connect The Instrument To A Power Supply
Step 7. Connect the cycler to a network (optional) 1 Plug one end of an ethernet cable into the ethernet port on the back of the instrument. 2 Plug the other end of the cable into a network port. Agilent SureCycler 8800 Setup and User’s Guide... -
Page 18: Thermal Block Exchange
The thermal block unit will only lock into place if it is placed on the instrument base in the proper orientation. 3 Reconnect the power supply when finished. Agilent SureCycler 8800 Setup and User’s Guide... -
Page 19: Getting Started
SureCycler 8800 Setup and User’s Guide Getting Started Sample Preparation and Loading To prepare samples To load samples Agilent Plasticware and Consumables Starting Up the Software Touchscreen Operation of the Software Home Screen User Accounts Access Levels Logging In to User Accounts... - Page 20 On the 96- well block, seat the tubes in the round holes on the thermal block. On the 384- well block, seat the tubes in the larger round holes. 3 Close the lid until it latches into place. Agilent SureCycler 8800 Setup and User’s Guide...
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Page 21: Agilent Plasticware And Consumables
96-well plate, 25-pack 410188 384-well plates, 50-pack 410186 Adhesive sealing films, 100-pack 410187 Compression mats, 10-pack Strip tubes, 200 μl, 80 strips of 12 410082 410086 Strip tube caps, 80 strips of 12 Agilent SureCycler 8800 Setup and User’s Guide... -
Page 22: Starting Up The Software
Use this button to connect to multiple instruments via a network. Incubate Starts a single temperature incubation for a predefined period or for an indefinite hold. Reports Opens the report directory allowing you to browse for stored report files. Agilent SureCycler 8800 Setup and User’s Guide... - Page 23 Getting Started Home Screen Table 3 Home Screen Button Descriptions (continued) Button Description Login Opens the Login screen. Settings Use this button to adjust cycler settings, upgrade software and manage user accounts. Agilent SureCycler 8800 Setup and User’s Guide...
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Page 24: User Accounts
Logging In to User Accounts To log in as Guest • No password is required to login as Guest. By default, the Guest account is automatically logged into the system each time the instrument is turned on. Agilent SureCycler 8800 Setup and User’s Guide... - Page 25 This logs you into the system and gives you reading and writing rights as specified for your user level. An administrator can reset user passwords if needed. See “To edit user accounts” on page 28. Agilent SureCycler 8800 Setup and User’s Guide...
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Page 26: Managing User Accounts
To add new user accounts 1 From the Home screen, press Settings. 2 Press User Management. (You must be logged in to an Administrator account to access the User Management features.) Agilent SureCycler 8800 Setup and User’s Guide... - Page 27 Administrator will give the user administrator rights. 7 Press OK to save the user account. After successful setup, a confirmation message appears and the new user name is added to the User Management list. Agilent SureCycler 8800 Setup and User’s Guide...
- Page 28 3 Select the user name to remove. 4 Press Remove to remove the user name from the user list. All user permissions for that account are deleted. All programs and GLP reports associated with that user are deleted. Agilent SureCycler 8800 Setup and User’s Guide...
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Page 29: Network Settings And Remote Access
OK to save your changes. Once logged in, you have control of the cycler from the PC using the web- based SureCycler 8800 software. Note that some of the screens of the web- based software differ slightly from the version of the software installed on the instrument. -
Page 30: To Access The Cycler From Another Cycler
6 Enter a valid User Name and Password to take over control of the instrument remotely and press Log In. You are now operating the software for the remotely connected instrument. Agilent SureCycler 8800 Setup and User’s Guide... -
Page 31: To Access The Cycler From A Pc
1 From the PC, open an internet browser application (Microsoft Internet Explorer is recommended). 2 In the URL field, enter the IP address for the cycler. The SureCycler 8800 software will open on the PC. 3 Login to the connected cycler with an appropriate User Name and Password. -
Page 32: Cycler Settings
The dashboard (which is displayed on several of the software screens) displays an icon to denote when the hot top has been disabled. Below is an image of the dashboard that includes this icon. Agilent SureCycler 8800 Setup and User’s Guide... -
Page 33: Cycler Name
The time and date can be edited by an administrator using the following steps: 1 From the Home screen, press Settings. 2 Press System Setting. 3 To change the date, select the correct date using the calendar under System Date. Agilent SureCycler 8800 Setup and User’s Guide... - Page 34 Getting Started Time and date 4 To change the time, press the up/down arrows to adjust the hour, minutes or seconds listed under System Time. 5 Confirm your changes by pressing Apply. Agilent SureCycler 8800 Setup and User’s Guide...
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Page 35: Pcr Programs
Creating New PCR Programs To manually create programs To create a PCR program using the PCR Wizard Tips for Creating PCR Programs for the 384-well SureCycler 8800 Program Steps in the Commands List Using a Preloaded PCR Program Editing PCR Programs... -
Page 36: Creating New Pcr Programs
Figure 1 shows an example of a programming screen in which a Hot Start command has been added to the program. Figure 1 The programming screen of the SureCycler 8800 software. Agilent SureCycler 8800 Setup and User’s Guide... - Page 37 5 for each program step to be added to the program. You can change the order of commands in the Command Window at any time using the up/down arrow buttons (shown below). Agilent SureCycler 8800 Setup and User’s Guide...
- Page 38 Once the correct folder name is in the Save to User Folder field, press Save to save the program. e A dialog window will open indicating that the file was successfully saved. Press OK in this window to return to the programming screen. Agilent SureCycler 8800 Setup and User’s Guide...
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Page 39: To Create A Pcr Program Using The Pcr Wizard
See “Editing PCR Programs” on page 53 for further instruction. Agilent SureCycler 8800 Setup and User’s Guide... - Page 40 • Specify the source of template DNA from the list and then press Next. The source options are: •cDNA •Genomic DNA •Vector DNA The DNA source information is used to determine the duration of the hot start or initial denaturation step and the elongation step. Agilent SureCycler 8800 Setup and User’s Guide...
- Page 41 Program Window. A new screen will open showing the settings for that command, such as temperature and duration. See the section “Program Steps in the Commands List” on page 43 for more information on the parameters for each command. Agilent SureCycler 8800 Setup and User’s Guide...
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Page 42: Tips For Creating Pcr Programs For The 384-Well Surecycler 8800
PCR Programs Tips for Creating PCR Programs for the 384-well SureCycler 8800 Tips for Creating PCR Programs for the 384-well SureCycler 8800 When performing PCR on the 384- well block, reducing the duration of the denaturation step during cycling may improve product yield for certain enzymes. -
Page 43: Program Steps In The Commands List
Hot Start Enter the temperature for the Hot Start step. Temperature: Hold for Enter the duration of the step. Please consult the polymerase manufacturer’s literature for recommendations on hot start conditions. Agilent SureCycler 8800 Setup and User’s Guide... -
Page 44: Cycle Wizard
Use 3rd step. Enter the elongation temperature in °C (left field) and elongation time in hours : minutes : seconds (right field). Cycles Enter the number of cycles. Agilent SureCycler 8800 Setup and User’s Guide... -
Page 45: Start Cycle
If desired, enter a user- selected name for the cycle. (Optional) To have a valid program, the steps of a cycle need to be contained between a Start Cycle N O T E and an End Cycle command. Agilent SureCycler 8800 Setup and User’s Guide... -
Page 46: Temperature Step
Agilent’s Herculase II DNA Polymerase and PfuUltra II DNA Polymerase. Step Type Select the type of step from the drop- down. The options are denaturation, annealing and elongation. Agilent SureCycler 8800 Setup and User’s Guide... -
Page 47: End Cycle
(rather than a single temperature across the entire block) for a specified length of time. The Gradient Step is useful for optimizing the annealing temperature for your particular primer/template system. Agilent SureCycler 8800 Setup and User’s Guide... - Page 48 The Gradient Step will then automatically be converted to a standard Temperature Step in which the temperature of the thermal block is uniform. Agilent SureCycler 8800 Setup and User’s Guide...
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Page 49: Touchdown
Enter the maximum annealing temperature. The first cycle of the PCR Temperature program will use this annealing temperature. Min Annealing Enter the minimum annealing temperature. The last cycle of the PCR Temperature program will use this annealing temperature. Agilent SureCycler 8800 Setup and User’s Guide... -
Page 50: Storage/Pause Step
Select this radio button if you prefer to maintain the temperature for a set duration of time. Enter the duration in the accompanying field. Infinite Select this radio button to hold the specified store temperature for an unlimited period of time. Agilent SureCycler 8800 Setup and User’s Guide... -
Page 51: Using A Preloaded Pcr Program
The available preloaded programs are listed in Table Table 5 Description of the preloaded PCR programs for the 96-well SureCycler 8800 PCR Program File Name PCR Enzyme or Kit Denaturation Annealing Elongation Herculase II Fusion 1kb target.pcr... -
Page 52: To Access The Preloaded Programs
4 In the programming screen, press Save to save the file under a new name and/or directory location. 5 Edit the program as desired using the instructions provided in “Editing PCR Programs” on page 53. Agilent SureCycler 8800 Setup and User’s Guide... -
Page 53: Editing Pcr Programs
The USB drive on the front of the instrument allow you to back up your saved PCR programs to a USB stick or transfer them to another SureCycler 8800 instrument. To edit program step parameters 1 Press the Programs button on the Home screen. -
Page 54: To Copy A Pcr Step
Guest directory is displayed listing all existing PCR program files. 2 Press the program to be deleted to select it. 3 Press Delete to remove the program from the folder. Agilent SureCycler 8800 Setup and User’s Guide... -
Page 55: Running A Pcr Program
• Press the Pause button (shown below) to pause the run. The Pause button is only available when a program is actively running. When a program is paused, this button becomes a Play button. Press Play to restart the program. Agilent SureCycler 8800 Setup and User’s Guide... -
Page 56: Running An Incubation
Hold For option and enter the desired duration time in hours : minutes : seconds. • If you want the instrument to hold the incubation temperature indefinitely, select the Infinite option. 4 Press OK to begin the incubation. Agilent SureCycler 8800 Setup and User’s Guide... -
Page 57: Viewing Reports
When finished viewing, press the Back button to return to the Browse Reports screen. To delete a report • Select the report on the Browse Reports screen and then press Delete. Agilent SureCycler 8800 Setup and User’s Guide... -
Page 58: Troubleshooting
Check that the unit is installed correctly and reboot the cycler. If the program does not start The thermal block unit may not be correctly seated on the instrument. ✔ Check that the unit is installed correctly and reboot the cycler. Agilent SureCycler 8800 Setup and User’s Guide... -
Page 59: If Condensation Is Found In Tubes During A Run
Reboot the cycler. If cycler does not turn on ✔ Check that the power is on at supply and the power cord is connected. ✔ Check fuses at rear of instrument above power inlet. Agilent SureCycler 8800 Setup and User’s Guide... -
Page 60: If Screen Is Blank And Unlit
Check fuses at rear of instrument above power inlet. If screen is lit but shows no information or has missing characters ✔ Reboot the cycler. ✔ If the problem persists, call Technical Support. See “SureCycler 8800 Technical Support” on page 14. Agilent SureCycler 8800 Setup and User’s Guide... -
Page 61: Maintenance And Updates
SureCycler 8800 Setup and User’s Guide Maintenance and Updates Maintenance Cleaning Replacing a fuse Software Updates This chapter contains instructions for maintaining the instrument and uploading software updates. Agilent Technologies... -
Page 62: Maintenance
Maintenance Maintenance Cleaning The SureCycler 8800 is designed to require a minimum amount of maintenance by the user. • Use water or isopropyl alcohol to clean the instrument. • Do not let organic solvents or aggressive solutions come in contact with the instrument. -
Page 63: Software Updates
Maintenance and Updates Software Updates Software Updates When a new version of the SureCycler 8800 software is released, you can download the new version from the Agilent website and then upload it to your SureCycler 8800 using the following instructions. - Page 64 Maintenance and Updates Software Updates Agilent SureCycler 8800 Setup and User’s Guide...
- Page 66 In This Book This document describes how to program and use the Agilent SureCycler 8800. © Agilent Technologies, Inc. 2011 Version A, March 2011 *G8800-90000* G8800-90000 Agilent Technologies...