Related Manuals for Applied Biosystems StepOne
Summary of Contents for Applied Biosystems StepOne
- Page 1 Installation, Networking, and Maintenance Guide Applied Biosystems StepOne ™ and StepOnePlus ™ Real-Time PCR Systems Installation, Networking, and Maintenance...
- Page 3 Installation, Networking, and Maintenance Guide Get Started Applied Biosystems StepOne ™ and StepOnePlus ™ Real-Time PCR Systems Set Up the Instrument Installation, Networking, and Maintenance Guide Install the Colocated Layout Install the Standalone Layout Connect the System to a Network...
- Page 4 © Copyright 2007, Applied Biosystems. All rights reserved. Information in this document is subject to change without notice. Applied Biosystems assumes no responsibility for any errors that may appear in this document. APPLIED BIOSYSTEMS DISCLAIMS ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT, EXPRESSED OR IMPLIED, INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE.
-
Page 5: Table Of Contents
Get Started........1 ™ ™ About the StepOne and StepOnePlus Systems ......2 Before You Begin . - Page 6 ™ Install the StepOne Software ........31 Connect the System Components .
- Page 7 ™ Update the StepOne Software ........125 Appendix A How to Troubleshoot the Installation .
- Page 8 ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
-
Page 9: Preface
Preface Purpose of This Guide ™ About the System The guides listed below are shipped with the Applied Biosystems StepOne ™ ™ ™ Documentation StepOnePlus Real-Time PCR Systems (StepOne and StepOnePlus systems). Guide Purpose and Audience ™ ™ Applied Biosystems StepOne... - Page 10 For example: Select File Open. User Attention Two user attention words appear in Applied Biosystems user documentation. Each word Words implies a particular level of observation or action as described below: – Provides information that may be of interest or help but is not critical to the use of Note: the product.
-
Page 11: How To Obtain More Information
• Review the table of contents. • Search for a specific topic. • Search an alphabetized index. Send Us Your Applied Biosystems welcomes your comments and suggestions for improving its user Comments documents. You can e-mail your comments to: techpubs@appliedbiosystems.com... -
Page 12: How To Obtain Support
Applied Biosystems Technical Support and Sales facilities. Applied Biosystems Customer Care Center Contact the Applied Biosystems Customer Care Center when directed by this guide, or to schedule maintenance for your instrument (such as, annual planned maintenance or temperature verification/calibration). To contact the Applied Biosystems Customer Care Center call 1-800-762-4001, Option 1 (U.S.A. -
Page 13: Safety Conventions Used In This Document
Safety Conventions Used in This Document Safety Alert Words Four safety alert words appear in Applied Biosystems user documentation at points in the document where you need to be aware of relevant hazards. Each alert word—IMPORTANT, CAUTION, WARNING, DANGER—implies a particular level of observation or action, as defined below. -
Page 14: Symbols On The Instruments
Safety Symbols The following safety symbols may be displayed on Applied Biosystems instruments. Each symbol may appear by itself or with text that explains the relevant hazard (see “Safety Labels on Instruments”... -
Page 15: Safety Labels On Instruments
Preface Safety Labels on Instruments Safety Labels on Instruments The following CAUTION, WARNING, and DANGER statements may be displayed on Applied Biosystems instruments in combination with the safety symbols described in the preceding section. English Francais CAUTION Hazardous chemicals. Read the ATTENTION Produits chimiques dangeureux. -
Page 16: General Instrument Safety
General Instrument Safety PHYSICAL INJURY HAZARD. Using the instrument in a manner not specified by Applied Biosystems may result in personal injury or damage to the instrument. Moving and Lifting PHYSICAL INJURY HAZARD. The instrument is to be moved and the Instrument positioned only by the personnel or vendor specified in the applicable site preparation guide. -
Page 17: Chemical Safety
Each time you receive a new MSDS packaged with a hazardous chemical, be sure to replace the appropriate MSDS in your files. ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide... - Page 18 Preface Chemical Safety Obtaining The MSDS for any chemical supplied by Applied Biosystems is available to you free MSDSs 24 hours a day. To obtain MSDSs: 1. Go to docs.appliedbiosystems.com/msdssearch.html 2. In the Search field of the MSDS Search page: Type the chemical name, part number, or other information that you expect to appear in the MSDS of interest.
-
Page 19: Chemical Waste Safety
• Ensure that the instrument waste is stored, transferred, transported, and disposed of according to all local, state/provincial, and/or national regulations. Radioactive or biohazardous materials may require special handling, and IMPORTANT! disposal limitations may apply. xvii ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide... -
Page 20: Electrical Safety
LED Safety To ensure safe LED operation: • The system must be maintained by an Applied Biosystems Technical Representative. • All instrument panels must be in place on the instrument while the instrument is operating. When all panels are installed, there is no detectable radiation present. If any... -
Page 21: Biological Hazard Safety
• Use equipment that comfortably supports you in neutral working positions and allows adequate accessibility to the keyboard, monitor, and mouse. • Position the keyboard, mouse, and monitor to promote relaxed body and head postures. ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide... -
Page 22: Safety And Electromagnetic Compatibility (Emc) Standards
This instrument has been tested to and complies with standard AS/NZS 2064, “Limits and Standards Methods Measurement of Electromagnetic Disturbance Characteristics of Industrial, Scientific, and Medical (ISM) Radio-frequency Equipment.” ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide... -
Page 23: Get Started
For more information about any of the topics discussed in this guide, access the ™ Help from within the Applied Biosystems StepOne Real-Time PCR System Software by pressing F1, or clicking in the toolbar, or selecting Help StepOne Software Help. ™ ™ Applied Biosystems StepOne... -
Page 24: About The Stepone And Steponeplus Systems
• Four-color system ™ • VeriFlex sample blocks ™ ™ The Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems use fluorescent-based polymerase chain reaction (PCR) reagents to provide: • Quantitative detection of target nucleic acid sequences (targets) using real-time analysis. - Page 25 • After the PCR ™ Regardless of the run type, a data collection point or read on the StepOne ™ StepOnePlus instrument consists of three phases: 1. Excitation – The instrument illuminates all wells of the reaction plate within the instrument, exciting the fluorophores in each reaction.
- Page 26 Chapter 1 Get Started ™ ™ About the StepOne and StepOnePlus Systems ™ Filters and StepOnePlus System Filters and Dyes Supported Dyes ™ The StepOnePlus instrument features a four-color filter set that supports the following ™ ™ ® ™ ®...
-
Page 27: Before You Begin
™ ™ You can use this guide to reinstall the StepOne or StepOnePlus system IMPORTANT! following transportation, but you must have the necessary installation reagents. See “Check the Shipped Materials”... - Page 28 (or later XP service pack) ‡ A computer that meets the minimum requirement provides optimal software performance and is supported by Applied Biosystems. § Necessary only if you plan to connect the computer to the instrument or to a local area network.
-
Page 29: Select Protective Hardware And Software
Select Protective Hardware and Software Before installing the system, obtain any of the following optional hardware and/or software. Electrical Applied Biosystems recommends several protective devices to prevent loss of data and to Protective protect the system from damage resulting from electrical hazards. Devices Power Line Regulator Applied Biosystems recommends the use of a 1.5-kVA power line regulator in areas... - Page 30 Chapter 1 Get Started Select Protective Hardware and Software Third-Party Applied Biosystems recommends the use of several types of commercial software to Software ensure optimal performance of the system and software, including: • File compression software for archiving data generated by the system •...
-
Page 31: Select An Installation Layout
In the colocated layout, the instrument is directly connected to the computer by the Layout yellow StepOne system cable. In this configuration, you can set up, run, and analyze experiments from the colocated computer. The following figure shows an instrument in a colocated layout. - Page 32 The following steps summarize the experiment workflow for a standalone system: ™ 1. Create the experiment on the standalone computer using the StepOne software. 2. Transfer the experiment to the standalone instrument on a USB drive.
-
Page 33: Plan The Installation
Experiment Perform the RNase P Experiment (Optional) Install the system to a Network (Chapter Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide CONFIDENTIAL — For AB Internal Use Only. Do Not Distribute. - Page 34 Chapter 1 Get Started Plan the Installation Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide CONFIDENTIAL — For AB Internal Use Only. Do Not Distribute.
-
Page 35: Set Up The Instrument
For more information about any of the topics discussed in this guide, access the ™ Help from within the Applied Biosystems StepOne Real-Time PCR System Software by pressing F1, or clicking in the toolbar, or selecting Help StepOne Software Help. Notes ™ ™... -
Page 36: About The Installation
Chapter 2 Set Up the Instrument About the Installation About the Installation ™ ™ This chapter explains how to install the Applied Biosystems StepOne /StepOnePlus Real-Time PCR Instrument for both colocated and standalone layouts. Installation Chapter Get Started Workflow Unpack and Set Up the Instrument 1. -
Page 37: Unpack The Instrument
™ • Prepare the installation site as described in the Applied Biosystems StepOne ™ StepOnePlus Real-Time PCR Systems Site Preparation Guide. - Page 38 • Coordinate your intentions with your assistant before lifting and carrying. Do not carry the instrument by the instrument drawer. Carrying the instrument by the drawer can damage the instrument optics. Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
-
Page 39: Check The Shipped Materials
® • Dell laptop computer with a PCMCIA Network Card IMPORTANT! If you did not order a computer from Applied Biosystems, provide one that meets the requirements listed in “Minimum Computer Requirements” on page Packing Kit ™... - Page 40 RNase P Fast 96-Well Instrument Verification Plate 4351979 ™ StepOne System Chemistry Installation Kit Component ® TaqMan RNase P Fast 48-Well Instrument Verification Plate 4371439 Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
- Page 41 Experiments ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems 4379740 Reagent Guide ™ CD, Applied Biosystems StepOne Real-Time PCR System Software 4382355 ® Primer Express Software v3.0 4361938 Miscellaneous items (mouse pad, registration card, and others) — Notes ™...
-
Page 42: Set Up The Instrument
Instrument 2. (Optional) Install electrical protective devices to the power cord. Applied Biosystems recommends that you install at least one of the electrical protective devices (power line regulator, uninterruptible power supply, and/or surge protector) to prevent loss of data and to protect the instrument from damage resulting from electrical hazards. - Page 43 (such as ; : " < > * + = \ | ? , ). Touch Done to save the settings, then touch OK when prompted. Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
- Page 44 Touch Done to save the settings, then touch OK when prompted. 2c/2d 3. Touch , then touch Yes in the Confirmation Screen to enter standby mode. Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
-
Page 45: Complete The Installation
If you want to install the… Go to… instrument and the computer to the same location, connected by the Chapter 3, “Install yellow StepOne system cable. the Colocated Layout,” page instrument and the computer to different locations. - Page 46 Chapter 2 Set Up the Instrument Complete the Installation Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
-
Page 47: Install The Colocated Layout
For more information about any of the topics discussed in this guide, access the Note: ™ Help from within the Applied Biosystems StepOne Real-Time PCR System Software by pressing F1, or clicking in the toolbar, or selecting Help StepOne Software Help. Notes ™ ™ Applied Biosystems StepOne... -
Page 48: About The Colocated Installation
StepOnePlus Real-Time PCR System for colocated operation. When to Perform In this layout, the yellow StepOne system cable connects the instrument to the colocated a Colocated computer. Install the system in the colocated layout when both the computer and the Installation instrument will be placed together in the same location. -
Page 49: Install The Computer
If you ordered a computer from Applied Biosystems, you need only to IMPORTANT! unpack the computer as explained on page 28. Computers shipped by Applied Biosystems are ready for use with the instrument and already contain the ™ StepOne software. ™... -
Page 50: Set Up The Computer
• Instead of lifting the computer/monitor from the packing box, tilt the box on its side, then slide the contents out of the box. 2. Make the following connections: Connect Do Not Connect Power Mouse Keyboard Monitor Ethernet Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide... - Page 51 If you are installing your system in a colocated setup, do not connect the Note: StepOne system cable to the Ethernet port of the PCMCIA card. If you have already installed the instrument connection through the card, unplug and connect the StepOne system cable to the appropriate port.
- Page 52 • If you are using a computer that you provided, log on to the operating system as a member of the Administrators user group. • If you are using a computer from Applied Biosystems, enter Administrator in the User field, then click Login. Leave the Password field blank.
-
Page 53: Install The Stepone Software
Software” and go to “Perform the RNase P Experiment” on page ™ Computers supplied by Applied Biosystems already contain the StepOne software, and are ready for use with the instrument. Prepare the 1. Change the screen saver and power options settings: Operating Right-click the desktop, then select Properties. - Page 54 Select a time zone from the dropdown menu, then select Automatically adjust clock for daylight saving changes if necessary. Click OK. Computers on a network synchronize their date/time settings with the server. Note: Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
- Page 55 After you install the system, you can change ™ the computer name without disrupting the function of the StepOne software. 5. In the Systems Settings Change dialog box, click Yes to restart the computer.
- Page 56 IMPORTANT! ™ Software administrator to install the StepOne software. ™ If you encounter errors during the installation of the StepOne software, reinstall Note: ™ the software as described in “Uninstall the StepOne Software” on page 128.
-
Page 57: Connect The System Components
Windows operating system using a user account that belongs to the Administrators user group. 4. In the desktop, double-click StepOne Software v2.0 (or select Start All Programs Applied Biosystems StepOne Software StepOne Software v2.0). ™... - Page 58 5 on page Power off the instrument, then after 30 sec power on the instrument. When the instrument displays the main screen, click Retry. If the problem persists, contact Applied Biosystems as explained in “How to Obtain Support” on page Notes ™...
- Page 59 (Optional) Disable During normal operation, the Windows operating system displays Local Area ™ the Local Area Connection messages when the StepOne software and instrument communicate. You Connection can disable these messages by changing the network connection settings for the Ethernet Messages network interface adapter as explained below.
-
Page 60: Perform The Rnase P Experiment
• Powder-free gloves • Safety glasses • Centrifuge with reaction plate adapter When to Perform Applied Biosystems recommends performing an RNase P experiment: the RNase P • After installing the system. Experiment • After moving the instrument to another location. - Page 61 Chapter 3 Install the Colocated Layout Perform the RNase P Experiment ™ After the run, the StepOne software: 1. Generates a standard curve from the averaged threshold cycle (C ) values of the replicate groups of standards. 2. Calculates the concentration of the two unknown populations using the standard curve.
-
Page 62: Set Up The Experiment
Prepare the TaqMan RNase P Fast Instrument Verification Plate for the run. Prepare the IMPORTANT! Do not use an RNase P plate for another Applied Biosystems instrument ™ RNase P Plate to verify the performance of the StepOne system. RNase P plates for other instruments ™... -
Page 63: Run The Experiment
2. Place the RNase P plate in the sample block(s) so that the A1 position is at the back- left corner of the sample block(s). ™ ™ StepOnePlus System StepOne System 3. Close the instrument drawer carefully. Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide... - Page 64 Chapter 3 Install the Colocated Layout Perform the RNase P Experiment ™ Start the Run 1. If the StepOne software automatically opened the RNase P Run dialog box, go to step 2. Otherwise, display the wizard as follows: Select Instrument Instrument Maintenance Manager.
-
Page 65: Analyze The Experiment
Review the data to confirm the results of the experiment. ™ Confirm the Note: After the StepOne software completes the RNase P run, it automatically Results of the analyzes the run and displays the results in the Analysis screen. Analysis 1. - Page 66 If the status of the RNase P Run is “Failed” after performing steps 2 through 4, repeat the RNase P experiment using a different RNase P plate. If the problem persists, contact Applied Biosystems as explained in “How to Obtain Support” on page Outlier Notes ™...
- Page 67 Confirm that the R2 value is greater than or equal to 0.990. If the R2 value is less than 0.990, repeat the RNase P experiment using a different RNase P plate. If the problem persists, contact Applied Biosystems as explained in “How to Obtain Support” on page 6.
- Page 68 Power off the instrument only when it will not be used for an extended period. Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
-
Page 69: After The Installation
• Performance optimizing software Note: For more information, see “Select Protective Hardware and Software” on page ™ To confirm that third-party software does not interfere with the StepOne software: ™ 1. Install the software to the computer that contains the StepOne software. - Page 70 Chapter 3 Install the Colocated Layout After the Installation Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
-
Page 71: Install The Standalone Layout
For more information about any of the topics discussed in this guide, access the Note: ™ Help from within the Applied Biosystems StepOne Real-Time PCR System Software by pressing F1, or clicking in the toolbar, or selecting Help StepOne Software Help. Notes ™ ™ Applied Biosystems StepOne... -
Page 72: About The Standalone Installation
This chapter explains how to install the system for standalone operation. ™ When to Perform In this layout, the instrument is not connected to the computer running the StepOne a Standalone software. Instead, a USB drive ( ) is used to transfer data between the system Installation components. -
Page 73: Set Up The Computer
If you ordered a computer from Applied Biosystems, you need only to IMPORTANT! unpack the computer as explained on page 52. Computers shipped by Applied Biosystems are ready for use with the instrument and already contain the ™ StepOne software. ™... -
Page 74: Install The Computer
Keyboard Monitor Ethernet 3. If you ordered a laptop computer from Applied Biosystems, install the PCMCIA Network Card as described in the documentation accompanying the card. After installing the PCMCIA network card, wait several minutes to allow the computer to enable the device. The computer may require time to initialize the drivers and register the network card with the operating system before it is available for use. - Page 75 Chapter 4 Install the Standalone Layout Set Up the Computer 4. If you ordered a tower computer from Applied Biosystems, set the voltage appropriately for your region as described in the computer installation guide. 5. (Optional) Install electrical protective devices to the computer.
-
Page 76: Install The Stepone Software
“Install the StepOne Software” and go to “After the Installation” on page 71. Computers supplied by Applied Biosystems already contain the ™ StepOne software, and are ready for use with the instrument. Prepare the 1. Change the screen saver and power options settings: Operating Right-click the desktop, then select Properties. - Page 77 Select a time zone from the dropdown menu, then select Automatically adjust clock for daylight saving changes if necessary. Click OK. Computers on a network synchronize their date/time settings with the server. Note: Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
- Page 78 After you install the system, you can change ™ the computer name without disrupting the function of the StepOne software. 5. In the Systems Settings Change dialog box, click Yes to restart the computer.
- Page 79 ™ ™ StepOne administrator to install the StepOne software. Software ™ Note: If you encounter errors during the installation of the StepOne software, uninstall ™ the software as explained in “Uninstall the StepOne Software” on page 128. ™ 1. Insert the Applied Biosystems StepOne Real-Time PCR System Software CD into the CD drive of the computer and wait for the installer to start.
-
Page 80: Prepare The Stepone ™ Software For Standalone Use
If the version number is less than the version on the software box, close the ™ ™ StepOne software, then load the Applied Biosystems StepOne Real-Time PCR System Software CD into the computer to update the software. 3. When the Instrument Connection Failed dialog box appears, click Continue without connection. - Page 81 1. In the Main Screen, select Tools Preferences. Preferences 2. In the Preferences dialog box, select the Startup tab. 3. Deselect Connect to default instrument. 4. Click OK. Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
-
Page 82: Perform The Rnase P Experiment
Required • Powder-free gloves • Safety glasses • Centrifuge with plate adapter When to Perform Applied Biosystems recommends performing an RNase P experiment: the RNase P • After installing the system. Experiment • After moving the instrument to another location. - Page 83 Chapter 4 Install the Standalone Layout Perform the RNase P Experiment ™ After the run, the StepOne software: 1. Generates a standard curve from the averaged threshold cycle (C ) values of the replicate groups of standards. 2. Calculates the concentration of the two unknown populations using the standard curve.
-
Page 84: Set Up The Experiment
Prepare the TaqMan RNase P Fast Instrument Verification Plate for the run. Prepare the IMPORTANT! Do not use an RNase P plate for another Applied Biosystems instrument ™ RNase P Plate to verify the performance of the StepOne system. RNase P plates for other instruments ™... -
Page 85: Run The Experiment
2. Place the RNase P plate in the sample block(s) so that the A1 position is at the back- left corner of the sample block(s). ™ ™ StepOnePlus System StepOne System 3. Close the instrument drawer carefully. Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide... - Page 86 Perform the RNase P Experiment ™ Start the Run 1. Touch the StepOne instrument touchscreen to awaken it, then touch 2. In the Main Menu, touch Tools Menu, then touch RNase P Wizard. 3. In the Welcome screen, touch Continue, then touch four times to bypass the instructions screens.
-
Page 87: Analyze The Rnase P Experiment
• Safety glasses • USB Drive (from the system packing kit) Unload the Instrument ™ Unload the RNase P plate from the StepOne instrument. Remove the PHYSICAL INJURY HAZARD. During instrument operation, the temperature of the sample block(s) can exceed 100 ° C. If the instrument has been used RNase P Plate recently, keep your hands away until the sample block(s) reaches room temperature. -
Page 88: Transfer The Experiment
USB Drive 2. In the RNase P Wizard, touch ™ If the StepOne instrument cannot find the USB drive, touch OK, wait for 30 sec, then touch Collect Results again. 3. When prompted that the data has been transferred successfully, touch OK, then touch 4. - Page 89 Transfer the Data 1. Connect the USB drive to one of the USB ports on the computer. to the Computer ™ 2. In the StepOne software, select Instrument Instrument Maintenance Manager. 3. In the Instrument Maintenance Manager, click RNase P.
-
Page 90: Analyze The Experiment
The numbers on the X-axis of the plot correspond to the wells of the Note: reaction plate. Beginning with well A1, the wells are numbered from left-to- right, and top-to-bottom. Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide... - Page 91 If the status of the RNase P Run is “Failed” after performing steps 2 through 4, repeat the RNase P experiment using a different RNase P plate. If the problem persists, contact Applied Biosystems as explained in “How to Obtain Support” on page Outlier Notes ™...
- Page 92 Confirm that the R2 value is greater than or equal to 0.990. If the R2 value is less than 0.990, repeat the RNase P experiment using a different RNase P plate. If the problem persists, contact Applied Biosystems as explained in “How to Obtain Support” on page 6.
-
Page 93: After The Installation
• Performance optimizing software For more information, see “Select Protective Hardware and Software” on page Note: ™ To confirm that third-party software does not interfere with the StepOne software: ™ 1. Install the software to the computer that contains the StepOne software. - Page 94 Chapter 4 Install the Standalone Layout After the Installation Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
-
Page 95: Connect The System To A Network
StepOnePlus Real-Time PCR Instrument into all possible network architectures. Because your network may contain advanced features (such as a firewall or network domains), Applied Biosystems recommends that you to consult a ™ network administrator before connecting the Applied Biosystems StepOne ™... -
Page 96: Overview
Chapter 5 Connect the System to a Network Overview Overview ™ ™ After installing the Applied Biosystems StepOne or StepOnePlus Real-Time PCR System, you can connect the instrument to a local area network to enhance its functionality. This chapter describes how to: •... - Page 97 Network server Networked Networked Networked colocated colocated computer instrument instrument Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
- Page 98 Note: Applied Biosystems does not support colocated layouts in which the Computer Port does not directly connect the instrument to the colocated computer. The connection for a local area network.
- Page 99 Overview Networking • Consult a Network Administrator Guidelines and Applied Biosystems recommends that you consult a network administrator before Best Practices connecting the system to your laboratory network. • Confirm the Instrument Connections Confirm that the instrument is connected to the network by the blue LAN Port (...
-
Page 100: Connect The Instrument To A Network
The MAC address for the instrument appears in the rights side of the About Instrument screen. 3. When finished, touch Done. 4. In the Settings Menu, touch to return to the Main Menu. Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide... - Page 101 • Ethernet port for your network Do not connect the Ethernet cable to the yellow Computer Port IMPORTANT! ); this port is reserved for the colocated computer connection. Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
-
Page 102: Set Up A Computer For Remote Monitoring
• If the network requires a static IP address, obtain the IP address, subnet mask, and gateway address for the computer Connect the Applied Biosystems recommends that you arrange for a network IMPORTANT! Computer to the administrator to connect your computer to the network. The following procedure does not Network provide adequate detail for all network architectures. - Page 103 9. Restart the computer. The computer is now visible to other computers on the network. Note: ™ Install the 1. If you have not already done so, install the StepOne software to the networked ™ StepOne computer (see “Install the Software” pages 34 or 57).
-
Page 104: Monitor The Instrument
• Applied Biosystems does not recommend that an instrument be monitored by more than one computer simultaneously. • Unless you are sure that your instrument and computer exist on the same subnet, Applied Biosystems recommends that you use the IP address of the instrument to add it for remote monitoring. - Page 105 You will lose the software connection to the colocated instrument if you: • Change the instrument that is connected directly to your computer • Use the colocated instrument touchscreen to change the instrument name or IP address ™ To reestablish the colocated connection, restart the StepOne software. Notes ™ ™...
- Page 106 4. Click Browse, then navigate to and select the folder to which you want to send the experiment, then click Select. 5. Click Download Experiment, then click OK when prompted Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
- Page 107 Chapter 5 Connect the System to a Network Monitor the Instrument ™ Enable or Change The notification settings allow you to configure the StepOne software to alert you via Notification email when the instrument begins and completes a run, or if an error occurs during a run.
- Page 108 Chapter 5 Connect the System to a Network Monitor the Instrument Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
-
Page 109: Maintain The System
For more information about any of the topics discussed in this guide, access the Note: ™ Help from within the Applied Biosystems StepOne Real-Time PCR System Software by pressing F1, or clicking in the toolbar, or selecting Help StepOne Software Help. Notes ™ ™ Applied Biosystems StepOne... -
Page 110: Regular Maintenance
Connection The spatial, background, and dye calibrations must be performed while the system is in a Required for colocated layout. To set up the system for maintenance, connect the yellow StepOne Maintenance system cable between the: • Yellow Ethernet port ( ) of the instrument, and ™... - Page 111 The temperature verification service can be performed by Applied Biosystems when the instrument is shipped for an annual service, or by an Applied Biosystems service engineer at an additional cost. “How to Obtain Support” on page x to contact Applied Biosystems for pricing and further information.
-
Page 112: Perform A Spatial Calibration
IMPORTANT! Wear powder-free gloves when you handle calibration plates. 1. If you have not already done so, use the StepOne system cable to connect the: • Yellow Ethernet port ( ) of the instrument to the ™... - Page 113 Open the instrument drawer. Place the calibration plate in the sample block(s) so that the A1 position is at the back-left corner. Close the instrument drawer carefully. Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
- Page 114 Chapter 6 Maintain the System Regular Maintenance ™ Perform the 1. In the main screen of the StepOne software, select Instrument Instrument Calibration Maintenance Manager. 2. In the navigation pane of the Instrument Maintenance Manager, click Spatial. 3. In the Instrument Maintenance Manager, click Start Calibration.
- Page 115 – The instrument passed the calibration. Go to step • Failed – The instrument failed the calibration. Contact Applied Biosystems as described in “How to Obtain Support” on page 2. Click Finish. 3. When prompted to save the calibration, click Yes.
-
Page 116: Perform A Background Calibration
Background Plate” on page • Powder-free gloves • Safety glasses • Centrifuge with reaction plate adapter • StepOne system cable, yellow (from the system packing kit) Calibration • Make sure the centrifuge you use is clean. Before centrifuging, wipe down the Guidelines bucket using a tissue. - Page 117 Wear powder-free gloves when you handle the background plate. IMPORTANT! 1. If you have not already done so, use the StepOne system cable to connect the: • Yellow Ethernet port ( ) of the instrument to the ™...
- Page 118 Place the background plate in the sample block(s) so that the A1 position is at the back-left corner. Close the instrument drawer carefully. ™ Perform the 1. In the main screen of the StepOne software, select Instrument Calibration Instrument Maintenance Manager. 2. In the navigation pane of the Instrument Maintenance Manager, click Background.
- Page 119 –20 to –25 ° C, you can reuse it three times after you open it. 3. Close the instrument drawer carefully. Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
- Page 120 “Background Calibration Failure” on page 132. 4. If all spectra are acceptable, click Finish. 5. When prompted to save the background calibration, click Yes. Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
- Page 121 3. Seal the reaction plate using an optical adhesive film or optical flat caps. 4. Use the reaction plate to perform the background calibration. Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
-
Page 122: Perform A Dye Calibration
The StepOne and StepOnePlus instrument supports the use of custom dyes (dyes not supplied by Applied Biosystems) that fluoresce within the spectral range it supports (500 to 650 nm). See “How to Calibrate a Custom Dye” on page 110 for more information. - Page 123 The system can be used to run assays designed with custom dyes (dyes not supplied by Applied Biosystems). However, before using custom dyes with the instrument, you must create and run a custom calibration plate. The purpose of the custom plate is similar to ™...
- Page 124 ™ When the StepOne software extracts the calibration data from a dye run, it evaluates the fluorescence signal generated by each well in terms of the collective spectra for the entire calibration plate.
- Page 125 Prepare for the Wear powder-free gloves when you handle the calibration plates. IMPORTANT! Calibration 1. If you have not already done so, use the StepOne system cable to connect the: • Yellow Ethernet port ( ) of the instrument to the ™...
- Page 126 Open the instrument drawer. Place calibration plate 1 in the sample block(s) so that the A1 position is at the back-left corner. Close the instrument drawer carefully. Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
- Page 127 Calibration recently, keep your hands away until the sample block(s) reaches room temperature. ™ 1. In the main menu of the StepOne software, select Instrument Instrument Maintenance Manager. 2. In the Instrument Maintenance Manager, click Dye in the navigation pane.
- Page 128 – The instrument passed the calibration. Go to step • Failed – The instrument failed the calibration. Troubleshoot the error as described in “Dye Calibration Failure” on page 134. Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
- Page 129 4. Inspect the raw data for the as described in step 5. If all spectra are acceptable, click Finish. 6. When prompted to save the dye calibration, click Yes. 2b/4 Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
- Page 130 ™ StepOne System Dye Spectra Filter 1 Filter 2 Filter 3 (~520 nm) (~550 nm) (~610 nm) SYBR Green DRAFT September 25, 2007 1:07 am, 4376782_Maintain_the_System.fm...
- Page 131 DRAFT September 25, 2007 1:07 am, 4376782_Maintain_the_System.fm ™ StepOnePlus System Dye Spectra Filter 1 Filter 2 Filter 3 Filter 4 (~520 nm) (~550 nm) (~580 nm) (~610 nm) SYBR Green TAMRA...
- Page 132 Vortex the calibration plate for 5 sec. Centrifuge calibration plate for 2 min at less than1500 rpm. The calibration plate must be well mixed and centrifuged. IMPORTANT! Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
- Page 133 Close the instrument drawer carefully. Run the Custom Spectral Calibration Plate ™ 1. In the main screen of the StepOne software, select Instrument Instrument Maintenance Manager. 2. In the Instrument Maintenance Manager: In the navigation pane, click Dye.
- Page 134 Note: Set the temperature to match the temperature at which you intend to collect data. For example, the temperature for all Applied Biosystems system dyes is 60 ° C reagents occurs during the 60 ° C extension ®...
-
Page 135: Archive And Back Up Data
• Conserve space on the hard drive and to optimize performance, if you remove old data after backing up. “Select Protective Hardware and Software” on page 7 for more information on backup storage devices. Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide... -
Page 136: Infrequent Maintenance
■ ™ Update the StepOne Software ........ -
Page 137: Decontaminate The Sample Block
Wells recently, keep your hands away until the sample block(s) reaches room temperature. Prepare the 1. If you have not already done so, use the StepOne system cable to connect the: Instrument • Yellow Ethernet port ( ) of the instrument to the ™... - Page 138 6. Close the instrument drawer, then plug in and power on the instrument. 7. Perform a background calibration to confirm that you have eliminated the contamination. Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
- Page 139 Use deionized water to rinse wells after they have been treated with IMPORTANT! bleach or EtOH solution. 10. If the contamination is still present, contact Applied Biosystems technical support. Notes ™ ™...
-
Page 140: Move The Instrument
Wait for the instrument to raise the sample block(s), then power off the instrument when prompted. 3. Disconnect the power cord from the back of the instrument. Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide... - Page 141 Moving your instrument can create subtle changes in the alignment of the IMPORTANT! ® instrument optics. Applied Biosystems recommends that you run a TaqMan RNase P Fast Instrument Verification Plate after you move the instrument to confirm the performance of the system.
-
Page 142: Replace The External Fuses
About the Fuses The instrument uses two 10 A fast-acting 250 VAC fuses to protect the system electronics from power surges. When replacing one fuse, Applied Biosystems recommends that you replace the companion fuse, regardless of its condition. Acceptable AC line voltage tolerances are 100, 120, 220, 230 ±10%; 240 VAC Note: +6%/–10%, 50/60 Hz ±... - Page 143 If the instrument detects a problem, it displays an error code for the related failed test. Repeat the procedure above without replacing the fuses to reseat the fuse holder. If the problem persists, contact Applied Biosystems as explained in “How to Obtain Support”...
-
Page 144: Ship The Instrument For Service
Chapter 6 Maintain the System Infrequent Maintenance Ship the Instrument for Service If the instrument requires the attention of an Applied Biosystems service representative, decontaminate the instrument and package it for transportation to Applied Biosystems. ™ Materials MicroAmp Optical Reaction Plate... - Page 145 Chapter 6 Maintain the System Infrequent Maintenance 6. Using the packaging material provided by Applied Biosystems, create a package to ship the instrument that includes the: ™ ™ • StepOne or StepOnePlus instrument • Certificate of Decontamination (from step 3b...
-
Page 146: Update The Windows Operating System
Applied Biosystems website. Future versions of the Windows operating system and ™ an Upgrade or updates to the current operating system can conflict with the StepOne software and Update render the software inoperable. 1. From the desktop, open D:\Applied Biosystems\StepOne Software v2.0, double- ™... -
Page 147: Update The Stepone Software
Infrequent Maintenance ™ Update the StepOne Software ™ If you want to update the StepOne Software, prepare your computer by exporting the application libraries and backing up your experiment files. Prepare for the 1. Back up the application libraries: Upgrade ™... - Page 148 Chapter 6 Maintain the System Infrequent Maintenance Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
-
Page 149: Appendix A How To Troubleshoot The Installation
For more information about any of the topics discussed in this guide, access the ™ Help from within the Applied Biosystems StepOne Real-Time PCR System Software by pressing F1, or clicking in the toolbar, or selecting Help StepOne Software Help. Notes ™ ™... -
Page 150: Stepone ™ Software Problems
Software Problems ™ StepOne Software Problems ™ If you encounter errors during the installation of the StepOne software, uninstall the software before reinstalling it. Uninstall the 1. Log onto the operating system as Administrator, or as a member of the ™... -
Page 151: Network Connection Problems
Support” on page using the same IP address and you must reassign it to resolve the conflict. Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide... - Page 152 If you still cannot ping the instrument after two attempts, consult your network administrator to determine the source of the failed network connection. Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
- Page 153 Start Help and Support in the computer desktop, then use the Microsoft Windows Help System search for the procedure appropriate for the operating system. Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
-
Page 154: Background Calibration Failure
Start Workflow Does the instrument Repeat the calibration. If the problem persists, complete the contact Applied Biosystems as explained in background run? “How to Obtain Support” on page One or more wells 1. Repeat the calibration using the of the background same background plate. - Page 155 4. View the Spectral plot for the peak(s). If the peak is: • Visible – The optics of your instrument may be contaminated. Contact Applied Biosystems as explained in “How to Obtain Support” on page • Absent – The sample block(s) are contaminated. Decontaminate the sample block(s) as explained in “Decontaminate the Sample Block(s)”...
-
Page 156: Dye Calibration Failure
Start Workflow Reattempt the calibration. If the Does the instrument problem persists, contact complete the dye Applied Biosystems as explained in calibration? “How to Obtain Support” on page One or more wells Review the spectra for produced spectra: irregularities as explained in Does the •... - Page 157 2. If the spectral calibration plate appears to be normal, discard the plate and run another. 3. If the problem persists, contact Applied Biosystems as explained in “How to Obtain Support” on page Note: If you are running a custom spectral...
- Page 158 Appendix A How to Troubleshoot the Installation Dye Calibration Failure Notes ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
-
Page 159: Glossary
Glossary ™ Advanced Setup In the StepOne software, a feature that allows you to set up your experiment according to your experiment design. Advanced Setup provides you with maximum flexibility in the design and setup of your experiment. assay information file (AIF). - Page 160 StepOnePlus systems, a PCR reaction mix that contains primers to amplify a target and a reagent to detect the amplified target. ® Assay ID Identifier assigned by Applied Biosystems to TaqMan Gene Expression Assays and ® TaqMan SNP Genotyping Assays.
- Page 161 (C custom dye Dye that is not supplied by Applied Biosystems. Custom dyes may be adapted for use in ™ ™ experiments on the...
- Page 162 The instrument transforms the ™ signal to electronic data, and the data are saved in the experiment file. In the StepOne software, a data collection point is indicated by an icon in the thermal profile: •...
- Page 163 StepOne or StepOnePlus systems, including setup, run, and analysis. The types of experiments you can perform ™ ™ using the StepOne and StepOnePlus systems: • Quantitation - standard curve • Quantitation - relative standard curve • Quantitation - comparative C (∆∆C...
- Page 164 (Tm) of the target or can identify nonspecific PCR amplification. ™ In the StepOne software, you can view the melt curve as normalized reporter (Rn) vs. temperature or as derivative reporter (− Rn′ ) vs. temperature. Also called dissociation curve.
- Page 165 Normalization to the passive reference signal allows for high data precision. ™ plate layout An illustration of the grid of wells and assigned content in the reaction plate. In StepOne ™ systems, the grid contains 6 rows and 8 columns. In StepOnePlus systems, the grid contains 8 rows and 12 columns.
- Page 166 Speed at which the temperature ramp occurs during the instrument run. Available ramp speeds include fast and standard. • For optimal results using the fast ramp speed, Applied Biosystems recommends ® using TaqMan Fast reagents in your PCR reactions.
- Page 167 Polymorphism Database of Nucleotide Sequence Variation (dbSNP) at the National Center for Biotechnology Information (NCBI). The refSNP ID can be used to search the Applied Biosystems Store for an Applied Biosystems SNP Genotyping Assay. Also called an rs number. regression...
- Page 168 StepOnePlus systems. ROX dye is used as the passive reference. rs number refSNP ™ run method Definition of the reaction volume and the thermal profile for the StepOne ™ StepOnePlus instrument run. sample The template that you are testing. Sample DNA (10✕) In the StepOne™...
- Page 169 ™ ™ standalone layout A system layout in which the StepOne or StepOnePlus instrument is not connected to a computer by the yellow cable. In this layout, you control the instrument only with the instrument touchscreen, and you use a USB drive or network connection to transfer data between the instrument and computer.
- Page 170 For example, the standard stock is used to prepare the first dilution point, the ™ first dilution point is used to prepare the second dilution point, and so on. In the StepOne software, the volumes needed to prepare a standard dilution series are calculated by the number of dilution points, the number of standard replicates, the starting quantity, the serial factor, and the standard concentration in the stock.
- Page 171 Glossary ™ system dye Dye supplied by Applied Biosystems and precalibrated on the StepOne ™ StepOnePlus system. Before you use system dyes in your experiments, make sure the system dye calibration is current in the Instrument Maintenance Manager. ™ System dyes on the StepOne system: ™...
- Page 172 Part of the run method that specifies the temperature, time, ramp, and data collection ™ ™ points for all steps and stages of the StepOne or StepOnePlus instrument run. threshold 1. In amplification plots, the level of fluorescence above the baseline and within the...
- Page 173 VeriFlex Technology blocks, creating up to six different zones for the 96 sample wells. After you enable the ™ VeriFlex blocks in the StepOne software, you can set a different temperature for one or more of the VeriFlex blocks. y-intercept In the standard curve, the value of y where the regression line crosses the y-axis.
- Page 174 Glossary ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide CONFIDENTIAL — For AB Internal Use Only. Do Not Distribute.
-
Page 175: Index
Information Development department CAUTION, description Technical Support chemical temperature verification service safety Applied Biosystems StepOne and StepOnePlus Real- waste safety xvii Time PCR System. See instrument or system. chemistry archiving files chemistry installation kit assay... - Page 176 – electromagnetic compatibility standards. calibration – See EMC standards plate, how to create EMC standards customer feedback, on Applied Biosystems encryption software documents endogenous control cycle threshold endpoint read cycling stage ergonomics, safety experiment download from instrument...
- Page 177 – dye calibration – dye calibration (custom) dye spectra – installation IPV4LL LAN Port load MAC address maintenance data ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
- Page 178 MSDSs plate layout description obtaining plates background plate multicomponent plot background plate, custom MicroAmp plates number of reuses RNase P plate spectral calibration plate ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
- Page 179 (computer) security software removing outliers from RNase P runs serial factor repetitive motion, safety series replicate group service pack, updates ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
- Page 180 ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
- Page 181 Windows operating system operating system upgrades, installation service pack updates, installing workflow install the instrument install the system workstation safety y-intercept zone zone boundary ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
- Page 182 Index ™ ™ Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems Installation, Networking, and Maintenance Guide...
- Page 184 Web site at www.appliedbiosystems.com. Applera is committed to providing the world’s leading technology and information for life scientists. Applera Corporation consists of the Applied Biosystems and Celera businesses. Headquarters 850 Lincoln Centre Drive Foster City, CA 94404 USA Phone: +1 650.638.5800...