Thermo Fisher Scientific Applied Biosystems StepOne™ Real-Time PCR System: StepOne™ System Updates Owner's manual

Brand: Thermo Fisher Scientific

Model: Applied Biosystems StepOne™ Real-Time PCR System: StepOne™ System Updates

Type: Owner's manual

DRAFT

January 26, 2007 10:58 am, 4382787A.fm

User Bulletin

Applied Biosystems StepOne™ Real-Time PCR System

January 2007

SUBJECT: StepOne

™

System Updates

In This Bulletin

Installation Updates. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Networking Updates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Maintenance Updates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Documentation Updates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Getting Started Guides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Installation Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

How to Obtain Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Overview

This bulletin contains important updated information for installing, maintaining, and

networking the Applied Biosystems StepOne

™

Real-Time PCR System. If you are

responsible for installing or maintaining the StepOne

™

system, read this bulletin

before using the instrument.

Visit the

StepOne

™

System Website

Applied Biosystems now offers a website devoted to the StepOne

™

system. For the

latest services and support information for the StepOne

™

instrument, go to:

info.appliedbiosystems.com/stepone

The website contains the latest software and documentation updates for the

StepOne

™

instrument and analysis software.

At the StepOne

™

system support page, you can:

• Submit a question directly to Technical Support

• Order Applied Biosystems user documents, MSDSs, certificates of analysis,

and other related documents

• Download documents in Adobe portable document format (PDF)

• Obtain information about customer training

• Download software updates and patches for the StepOne

™

instrument

Applied Biosystems StepOne

™

Real-Time

PCR System User Bulletin

2Applied Biosystems StepOne

™

Real-Time PCR System User Bulletin

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January 26, 2007 10:58 am, 4382787A.fm

StepOne

™

System Updates

Installation Updates

Read this section before installing the StepOne

™

instrument.

Additional

Guidelines and

Best Practices

Vibration and Instrument Placement

Avoid placing the StepOne

™

instrument on surfaces that are subject to constant or

intermittent vibration. Tabletop centrifuges, vortex mixers, and other laboratory

equipment can vibrate the instrument during a run and produce data collection errors.

Packing Material Removal

When removing the packing material from the sample block, you must power on the

StepOne

™

instrument to lower the instrument drawer. The drawer is in the “raised”

position during transportation and it will not open until the instrument is powered on.

Instrument Boot Time

When you power on the instrument for the first time, the instrument may require

more than five minutes to boot. Proceed with the installation when the touchscreen

displays the main screen, indicating that the StepOne

™

instrument has completed the

boot.

Note:

If you are updating the StepOne

™

instrument firmware, the instrument may

pause for up to 20 min before completing the boot.

PCMCIA Card Installation

If you ordered a laptop computer with your StepOne

™

instrument, wait several

minutes after installing the PCMCIA network card 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.

Note:

If you are installing your StepOne

™

system in a colocated setup, do not

connect the StepOne

™

system cable to the PCMCIA card Ethernet port. If you have

already installed the instrument connection through the card, unplug and connect the

StepOne

™

system cable to the appropriate port.

3Applied Biosystems StepOne

™

Real-Time PCR System User Bulletin

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Networking Updates

Read this section before connecting the StepOne

™

system to a network.

Additional

Guidelines and

Best Practices

Consult a Network Administrator

Applied Biosystems recommends that you consult a network administrator before

connecting the StepOne™ system to your laboratory network.

Confirm the Instrument Connections

Confirm that the StepOne

™

instrument is connected to the network by the blue LAN

Port ( ). If the StepOne

™

system is installed in a colocated layout, confirm that the

instrument is connected to the colocated computer by the yellow Computer Port ( ).

Limit Remote Monitoring to One Computer

Avoid using more than one computer simultaneously to remote monitor the instrument.

Although the StepOne

™

system supports remote monitoring from multiple computers,

each connection taxes the instrument microprocessor. Too many connections can

overburden the StepOne

™

instrument and result in instrument errors.

Note:

The effects of an overburdened

StepOne

™

instrument

are evident in the

Temperature Plot during a run. Symptoms can include

extended hold times or brief,

unexpected plateaus in the instrument temperature plot.

Note Restrictions to mDNS and Auto Discovery

The StepOne

™

instrument supports multicast domain name service (mDNS) but only

when the instrument and computer share a direct network connection and are within

the same subnet. Consequently, computers on the network that are separated from the

StepOne

™

instrument by a router, hub, or other network device may not be able to

access the instrument by its host name.

The StepOne

™

instrument also does not support auto discovery for mDNS. However,

the instrument does support name resolution, but the instrument name must be

unique within the subnet.

Note:

Confirm the uniqueness of the instrument name manually. The StepOne

™

instrument does not test the uniqueness of the instrument name when it is set.

Add Instruments Using Lower Case Letters

When you add the StepOne

™

instrument for remote monitoring, enter the instrument

name using lower case letters only.

4Applied Biosystems StepOne

™

Real-Time PCR System User Bulletin

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January 26, 2007 10:58 am, 4382787A.fm

StepOne

™

System Updates

Troubleshooting

Workflow

Use the following workflow to troubleshoot the network connection to the StepOne

™

system when setting up the instrument for remote monitoring.

Add and monitor the instrument using the

IP address of the LAN Port.

Is the instrument

connected to the

network by the blue

LAN Port? No

Ye s

Static IP

DHCP

Are the instrument and

computer located on

the same subnet?

Ye s

Connect the Ethernet

cable for the network

connection to the blue

LAN Port at rear of the

StepOne

™

instrument.

Determine the IP address and network

settings

of the instrument

LAN port

explained in step 1 on page 5

StepOne

™

software cannot add

instrument for remote monitoring

Start

Contact Applied Biosystems

as explained in

“How to Obtain

Support” on page 11

Can you add or monitor

the

instrument

using the

StepOne

™

software?

Can you “ping”

the instrument from

a computer on the

network? No

Ye s

Confirm the network connection by

pinging the instrument as explained in

“How to Ping the Instrument” on page 5.

Consult your network administrator to

determine the source of the failed

network connection.

Determine the subnet address for the

instrument

as explained in “How to

Determine the Subnet Address” on page 6

Is the LAN Port of the

instrument set up for

static IP or DHCP?

Confirm with your network administrator

that the static IP Address, Subnet Mask,

and Default Gateway settings are correct.

Correct the network settings as directed

by your network administrator.

Unplug the instrument from the network,

then ping the IP address. If you can ping

the address after removing the instrument

from the network, then another device is

using the same IP address and you must

reassign it to resolve the conflict.

When you add the instrument for remote

monitoring, enter the instrument name

using

lower case

letters only.

If you cannot use the instrument name to

add the instrument for remote monitoring,

try using the IP address of the instrument.

5Applied Biosystems StepOne

™

Real-Time PCR System User Bulletin

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Networking Updates

How to Ping the

Instrument

Note:

The procedure below is a revision of the “Confirm the Network Connection”

procedure found in the Applied Biosystems StepOne

™

Real-Time PCR System

Installation Guide.

You can confirm the connection between a network computer and StepOne

™

instrument

by “pinging” the instrument name or IP address from the computer. The ‘ping’ command

issued from the DOS command shell causes the computer to send a series of 32-byte data

packets to the instrument. If the network connection between the computer and the

StepOne

™

instrument is unobstructed, the instrument sends data packets in reply.

1. Determine the IP address of the StepOne

™

instrument:

a. Touch the StepOne

™

instrument touchscreen to awaken it, then touch .

b. In the Main Menu, touch Settings MenuAdmin Menu

Set IP Address.

c. Record the IP address in the IP Address field.

2. Ping the StepOne

™

instrument:

a. Power on the StepOne

™

instrument and wait for the instrument to boot.

b. In the computer desktop, select StartProgramsAccessories

Command Prompt.

c. In the Command Prompt window, enter

ping <IP address>

, then

press Enter.

Resolving an IP Address Conflict

If you suspect that the IP address used by either port of the StepOne

™

instrument

may conflict with another device on your network, you can use the following

procedure to test for the conflict.

1. Unplug the instrument from the network.

2. Ping the IP address of the instrument LAN port as explained above.

If you can ping the IP address, then another device on the network is already

using the address and you must reassign the IP address of the instrument to

resolve the conflict.

If the DOS

prompt displays… Then…

replies to the pings the computer can communicate with the IP address.

“request timed out” Wait a few minutes for the network to update the IP address of the

instrument, then ping the instrument again.

If you still cannot ping the StepOne

™

instrument after two attempts,

ping the IP address of the alternate port. Consult your network

administrator to determine the source of the failed network

connection.

6Applied Biosystems StepOne

™

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StepOne

™

System Updates

How to

Determine the

Subnet Address

1. Touch the StepOne

™

instrument touchscreen to awaken it, then touch .

2. In the Main Menu, touch Settings MenuAdmin MenuSet IP Address.

3. Record the IP address in the IP Address field. The first three numbers of the IP

address are the subnet address.

For example, the italicized numbers in the following IP address are the subnet

address: 192.168.100.140

If the subnet address for the StepOne

™

instrument is different than that of the

computer used for remote monitoring, then you cannot use the instrument name to

add the instrument for remote monitoring. The mDNS limitation explained in

“Additional Guidelines and Best Practices” on page 3 restricts the use of the

instrument name as an identifier to network devices on the same subnet.

Note:

To determine the subnet address of the computer that you want to use to

monitor the StepOne

™

instrument, select StartHelp and Support in the computer

desktop, then use the Microsoft Windows Help System search for the procedure

appropriate for the operating system.

Maintenance Updates

Read this section before maintaining the StepOne

™

instrument.

Guidelines for

Bleach Solution

Use

Applied Biosystems recommends the use of 10% bleach solution

for resolving fluorescent contamination on the StepOne

™

instrument sample block.

However, excessive use of the solution can corrode the block material.

To prevent degradation of the block, observe the following guidelines when using

bleach solution:

• Decontaminate the sample block using bleach solution as a last resort. Rinse the

sample block with bleach only after treatments of deionized water and 95%

ethanol fail to remove the contamination.

• Rinse the sample block thoroughly using deionized water after treating the block

with bleach solution. Thoroughly removing residual bleach from the metal

surfaces with water will minimize the long term effects of bleach.

7Applied Biosystems StepOne

™

Real-Time PCR System User Bulletin

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January 26, 2007 10:58 am, 4382787A.fm

Documentation Updates

This addendum to the StepOne

™

system documentation describes the latest updates

to the StepOne

™

software and StepOne

™

instrument touchscreen user interface.

Getting Started Guides

The updates below apply to the following StepOne

™

system getting started guides:

•Applied Biosystems StepOne

™

Real-Time PCR System Getting Started Guide for

Genotyping Experiments

•Applied Biosystems StepOne

™

Real-Time PCR System Getting Started Guide for

Relative Standard Curve and Comparative C

(

∆∆

) Experiments

• Applied Biosystems StepOne

™

Real-Time PCR System Getting Started Guide for

Standard Curve Experiments

Chapter 1:

Get Started

About Data Collection

The StepOne

™

system can collect real-time data for presence/absence experiments.

Advantages of TaqMan Reagents

With the design wizard, the presence/absence experiments use TaqMan

reagents in

the PCR reactions. If you want to perform a presence/absence experiment using other

reagents to detect amplification of the target sequence, set up an experiment using

advanced setup.

With the design wizard, the genotyping and presence/absence experiments use the

standard ramp speed in the instrument run. If you want to perform a genotyping or

presence/absence experiment using the Fast ramp speed, set up the experiment using

advanced setup.

IMPORTANT!

Applied Biosystems does not support the use of SYBR Green

TaqMan

Fast reagents for presence/absence or genotyping experiments.

Note:

The Reaction Setup screen is not available if you are using other reagents.

This note is to clarify the design wizard setup for quantitation experiments.

Chapter 2: Design

the Experiment

Set Up the Targets (Quantitative PCR Only)

When you use the Design Wizard to set up a quantitation experiment (standard curve,

relative standard curve, or comparative C

), you can set up only singleplex reactions

(amplification and detection of one target sequence). To set up a quantitation

experiment with multiplex reactions (amplification and detection of two target

sequences), set up the experiment using Advanced Setup.

Note:

For more information on Advanced Setup, access the Help from within the

StepOne

™

software by pressing F1, click in the toolbar, or selecting Help

StepOne Help.

8Applied Biosystems StepOne

™

Real-Time PCR System User Bulletin

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January 26, 2007 10:58 am, 4382787A.fm

StepOne

™

System Updates

Chapter 4: Run

the Experiment

About the Run Method Screen

The Run Method screen is not updated throughout the run; however, the Run Status

element of the Amplification, Temperature, and Run Method screens are updated

continuously.

Note:

The Run Method screen does not behave similarly to the standalone

monitoring that appears in the StepOne

™

instrument interface.

Colocated Data Transfer

The last line of the paragraph should read: “The StepOne

™

software automatically

transfers the experiment data from the StepOne instrument after the run.”

Load the Instrument

2. Place the reactions in the sample block:

• If using a reaction plate: Place the reaction plate in the sample block with

well A1 at the back-left corner.

• If using reaction tube strips: Place the tray containing the tube strips in the

sample block.

• If using reaction tubes: Place the tray containing the tubes in the sample

block.

IMPORTANT!

Load at least 4 tubes for optimal performance.

Chapter 5:

Analyze the

Experiment

View the Amplification Plot

The “background” is not a characteristic of the amplification curve as are the

baseline, exponential (geometric phase), linear, and plateau phases. Background

describes the noise that remains after the StepOne

™

software compensates for the

baseline, which is present throughout the amplification curve, not just in one region.

The other four phases describe distinct sections of the Amplification curve.

View the Multicomponent Plot

The Multicomponent Plot can display the data for multiple wells simultaneously.

View the Raw Data Plot

The legend of the Raw Data Plot displays the color coding for each row of the plate.

Appendix A

Export/Import Workflow

When importing setup data, it is easier to set up a new experiment using the data

exported from a similar experiment.

9Applied Biosystems StepOne

™

Real-Time PCR System User Bulletin

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January 26, 2007 10:58 am, 4382787A.fm

Documentation Updates

Glossary

baseline-corrected normalized reporter (∆Rn) / delta Rn (∆Rn)

For presence/absence experiments, the difference in the normalized reporter value

) between the pre-read and the post-read of the data calculated as follows:

∆

= R

n (Post Read)

– R

n (Pre Read)

IPC+

No longer used. See negative control - IPC wells.

threshold

[1] Level of fluorescence above the baseline and within the exponential growth

region of the amplification plot. The threshold can be determined automatically

(see automatic C

) or can be set manually (see manual C

). [2] Level of fluorescence

above which the StepOne

™

software assigns a positive call to a well.

Installation Guide

The updates below apply to the Applied Biosystems StepOne

™

Real-Time PCR

System Installation, Network, and Maintenance Installation Guide.

Chapter 1:

Get Started

Minimum Computer Requirements

If you did not purchase a computer with your StepOne™ system, supply one that

meets the following requirements:

Component Minimum Requirements

‡

‡ A computer that meets the minimum requirement provides optimal software performance

and is supported by Applied Biosystems.

Computer • Intel processor, 1.0 GHz

• 512 MB of RAM

• One 20-GB hard drive

• 20/48X IDE CD-ROM

• Ethernet network interface adapter (10BASE-T)

• UL-listed

•CE-marked

• FCC-labelled

§ Necessary only if you plan to connect the computer to the StepOne

™

instrument or to a local

area network.

Monitor • 1280 × 1024 pixel resolution

• 32-bit color

• UL-listed

Operating

System

Microsoft Windows

XP Professional Operating System, Service Pack 2

or higher

10 Applied Biosystems StepOne

™

Real-Time PCR System User Bulletin

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January 26, 2007 10:58 am, 4382787A.fm

StepOne

™

System Updates

Chapter 2: Set Up

the StepOne

™

Instrument

Define the Settings

Reverse the order of steps for changing the instrument date and time. Also, note that

the Touchscreen Calibration is no longer part of the installation.

Instrument Standby

When the power button ( ) is touched, the StepOne

™

instrument interface displays

a Confirmation Screen that prompts you to enter Standby mode. Touch Ye s to enter

standby mode.

Chapter 5:

Connect the

StepOne

™

System

to a Network

Define the LAN Port IP Settings

Step 2 should read: “In the Main Menu, touch Settings Menu, touch Admin Menu,

then touch Set IP Address.”

(Optional) Define the Computer Port IP Settings

The StepOne

™

instrument no longer permits changes to the IP settings of the

Computer Port. The IP address settings accessed from the Set IP Address command

of the Admin Menu are for the LAN Port.

Chapter 6:

Maintain the

StepOne

™

System

Decontaminate the Sample Block

Note the importance of rinsing the sample block using deionized water following

treatment with bleach solution as explained in “Guidelines for Bleach Solution Use”

on page 6 of this bulletin.

Appendix A: How

to Troubleshoot

the Installation

Network Connection Problems

Add the “Troubleshooting Workflow” on page 4 of this bulletin to the section to aid

in troubleshooting failed network connections when setting the StepOne

™

instrument

for remote monitoring.

Confirm the Network Connection

Replace with the procedures in “How to Ping the Instrument” on page 5 of this

bulletin.

11Applied Biosystems StepOne

™

Real-Time PCR System User Bulletin

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January 26, 2007 10:58 am, 4382787A.fm

How to Obtain Support

For the latest services and support information for all locations, go to

www.appliedbiosystems.com

, then click the link for

Support

At the Support page, you can:

• Search through frequently asked questions (FAQs)

• Submit a question directly to Technical Support

• Order Applied Biosystems user documents, MSDSs, certificates of analysis, and

Thermo Fisher Scientific Applied Biosystems StepOne™ Real-Time PCR System: StepOne™ System Updates Owner's manual

Brand: Thermo Fisher Scientific

Model: Applied Biosystems StepOne™ Real-Time PCR System: StepOne™ System Updates

Type: Owner's manual

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Thermo Fisher Scientific Applied Biosystems StepOne™ Real-Time PCR System: StepOne™ System Updates Owner's manual

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