Agilent Technologies SureCycler 8800 Safety guide

Agilent Technologies
SureCycler 8800
Setup and User’s Guide
Version A, March 2011

2 Agilent SureCycler 8800 Setup and User’s Guide
Notices
© Agilent Technologies, Inc. 2011
No part of this manual may be reproduced in
any form or by any means (including elec-
tronic storage and retrieval or translation
into a foreign language) without prior agree-
ment and written consent from Agilent
Technologies, Inc. as governed by United
States and international copyright laws.
Manual Part Number
G8800-90000
Edition
Version A, March 2011
Printed in USA
Agilent Technologies, Inc.
5301 Stevens Creek Rd
Santa Clara, CA 95051 USA
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Safety Notices
CAUTION
A CAUTION notice denotes a haz-
ard. It calls attention to an operat-
ing procedure, practice, or the like
that, if not correctly performed or
adhered to, could result in damage
to the product or loss of important
data. Do not proceed beyond a
CAUTION notice until the indicated
conditions are fully understood and
met.
WARNING
A WARNING notice denotes a
hazard. It calls attention to an
operating procedure, practice, or
the like that, if not correctly per-
formed or adhered to, could result
in personal injury or death. Do not
proceed beyond a WARNING
notice until the indicated condi-
tions are fully understood and
met.
Technical Support
For technical support, contact Agilent at
[email protected]. Complete con-
tact information for Technical Support is
listed on page 14.

Agilent SureCycler 8800 Setup and User’s Guide 3
In this Guide...
This document describes how to program and use the
Agilent SureCycler 8800.
1Before You Begin
This chapter contains information for you to read and
understand before you start.
2Installation
This chapter contains installation instructions for setting up
the cycler instrument.
3Getting Started
This chapter contains instructions to load samples, get
started with the software, set up user accounts and access
instruments remotely via a network.
4PCR Programs
This chapter contains instructions to work with PCR
programs, incubations and reports. Troubleshooting
suggestions are also provided.
5Maintenance and Updates
This chapter contains instructions for maintaining the
instrument and uploading software updates.

4 Agilent SureCycler 8800 Setup and User’s Guide

Agilent SureCycler 8800 Setup and User’s Guide 5
Contents
1 Before You Begin 9
Materials Provided 10
Safety Precautions 10
Indicator LED Light 13
Overview 13
SureCycler 8800 Technical Support 14
2 Installation 15
Installation 16
Step 1. Select a location for the instrument 16
Step 2. Unpack the cycler 16
Step 3. Install the thermal block on the instrument base 16
Step 4. Connect the instrument to a power supply 17
Step 5. Connect optional devices 17
Step 6. Turn on the instrument 17
Step 7. Connect the cycler to a network (optional) 17
Thermal Block Exchange 18
To remove the thermal block 18
To install the thermal block 18
3 Getting Started 19
Sample Preparation and Loading 20
To prepare samples 20
To load samples 20
Agilent Plasticware and Consumables 21
Starting Up the Software 22
Touchscreen Operation of the Software 22

6 Agilent SureCycler 8800 Setup and User’s Guide
Contents
Home Screen 22
User Accounts 24
Access Levels 24
Logging In to User Accounts 24
Managing User Accounts 26
Network Settings and Remote Access 29
To view or edit the cycler’s IP address and name 29
To access the cycler from another cycler 30
To access the cycler from a PC 31
Cycler Settings 32
Hot Top Setting 32
Cycler name 33
Time and date 33
4 PCR Programs 35
Creating New PCR Programs 36
To manually create programs 36
To create a PCR program using the PCR Wizard 39
Tips for Creating PCR Programs for the 384-well SureCycler 8800 42
Program Steps in the Commands List 43
Hot Start 43
Cycle Wizard 44
Start Cycle 45
Temperature Step 46
End Cycle 47
Gradient Step 47
Touchdown 49
Storage/Pause Step 50
Using a Preloaded PCR Program 51
To access the preloaded programs 52
To edit a preloaded program 52

Contents
Agilent SureCycler 8800 Setup and User’s Guide 7
Editing PCR Programs 53
To edit program step parameters 53
To copy a PCR step 54
To add or delete a PCR step 54
To delete a PCR program 54
Running a PCR Program 55
To run a PCR program 55
To stop or pause a program 55
Running an Incubation 56
To set up and run an incubation 56
Viewing Reports 57
To view reports 57
To delete a report 57
Troubleshooting 58
If PCR yield is low when running small reaction volumes with the Standard
ramp rate 58
If no actual temperature is displayed during the run 58
If the program does not start 58
If condensation is found in tubes during a run 59
If the sealed microplate loses sample volume 59
If USB devices including memory stick and keyboard not recognized 59
If cycler does not turn on 59
If screen is blank and unlit 60
If screen is lit but shows no information or has missing characters 60
60
5 Maintenance and Updates 61
Maintenance 62
Cleaning 62
Replacing a fuse 62
Software Updates 63

8 Agilent SureCycler 8800 Setup and User’s Guide
Contents

9
SureCycler 8800
Setup and User’s Guide
Agilent Technologies
1
Before You Begin
Materials Provided 10
Safety Precautions 10
Indicator LED Light 13
Overview 13
SureCycler 8800 Technical Support 14
This chapter contains information for you to read and understand before
you start.
For installation instructions, see “Installation” on page 16.

1 Before You Begin
Materials Provided
10 Agilent SureCycler 8800 Setup and User’s Guide
Materials Provided
*The thermal block units are sold separately as part numbers G8810A (96-well block)
and G8820A (384-well block).
Safety Precautions
Electrical
Standard electrical safety precautions should be applied, including the
following:
•Always put the instrument in a location where, if needed, the power
supply can be immediately disconnected.
•Proper voltage must be supplied before you turn on the instrument for
the first time.
•The device must be connected to a grounded socket.
•Do not touch any switches or outlets with wet hands.
•Turn off the instrument before you disconnect the power cord.
•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.
Tab le 1 Materials Provided
Part Quantity
SureCycler 8800 instrument base 1
Thermal block unit (96-well or 384-well)* 1
Power cord 1
Functional test certificate 1
Quick Start installation poster 1
CD with Setup and User’s Guide PDF 1

Before You Begin 1
Safety Precautions
Agilent SureCycler 8800 Setup and User’s Guide 11
•Do not service the electrical components unless you are qualified to
do so.
Fluids and Reagents
•Fill reaction vessels outside the cycler so that no fluids penetrate the
instrument.
•Never cycle or incubate explosive, flammable and reactive substances in
the instrument.
•You must observe the relevant safety regulations when handling
pathogenic material, radioactive substances or other substances
hazardous to health.
•Do not submerge the instrument in any liquid.
Danger of Burns
•Do not touch the thermal block, inner side of heated lid and reaction
vessels. These areas quickly attain temperatures of greater than 50°C.
Keep the heated lid closed until temperatures of 30°C or lower are
reached.
•Do not use any materials (plates, sealings, foils, mats) which are not
sufficiently temperature- stable (up to 120°C).
Operating Environment
•The ventilation slots of the device must remain free to vent at all times.
Leave at least 10 cm of space around the instrument.
•Keep the ambient temperature between 20°C and 30°C with humidity
levels between 20% and 80% non- condensing.
•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 to80%, non- condensing
•Electrical supply 100- 240 V, 50/60 Hz, 11 A

1 Before You Begin
Safety Precautions
12 Agilent SureCycler 8800 Setup and User’s Guide
•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. Wear a grounded wrist strap and take other
antistatic precautions prior to making contact with the device in high
static environments. ESD STM5.1- 1998 Class 3B.
Safety Symbols
The electrical/safety symbols described below may be displayed on the
instrument.
Power on
Power off
Caution
Caution, hot surfaces

Before You Begin 1
Indicator LED Light
Agilent SureCycler 8800 Setup and User’s Guide 13
Indicator LED Light
On the front of the instrument (top right corner) is a status indicator
LED. summarizes the status codes for this LED light.
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. The software interface, operated through the
color touchscreen, features an intelligent Program Wizard that can create
PCR protocols automatically from primer and template information.
Tab le 2 Appearance of the status indicator LED
Appearance Instrument Status
Off The cycler is idle.
Blinking green The cycler is running a program or incubation.
Solid green The cycler is paused.
Blinking red The cycler has detected an error. Check the display for an
error message containing further details.

1 Before You Begin
SureCycler 8800 Technical Support
14 Agilent SureCycler 8800 Setup and User’s Guide
SureCycler 8800 Technical Support
Email
USA and Canada: [email protected]
Europe: [email protected]
Japan: [e-mail]
All other countries: [email protected]
World Wide Web
www.genomics.agilent.com
Tele phon e
USA and Canada
[phone]
Europe
Japan
0120-477-111
All other countries
Go to www.genomics.agilent.com and click on the Contact Us link.
Austria 01 25125 6800
Benelux 02 404 92 22
Denmark 45 70 13 00 30
Finland 010 802 220
France 0810 446 446
Germany 0800 603 1000
Italy 800 012575
Netherlands 020 547 2600
Spain 901 11 68 90
Sweden 08 506 4 8960
Switzerland 0848 8035 60
UK/Ireland 0845 712 5292

15
SureCycler 8800
Setup and User’s Guide
Agilent Technologies
2
Installation
Installation 16
Step 1. Select a location for the instrument 16
Step 2. Unpack the cycler 16
Step 3. Install the thermal block on the instrument base 16
Step 4. Connect the instrument to a power supply 17
Step 5. Connect optional devices 17
Step 6. Turn on the instrument 17
Step 7. Connect the cycler to a network (optional) 17
Thermal Block Exchange 18
To remove the thermal block 18
To install the thermal block 18
This chapter contains installation instructions for setting up the cycler
instrument.

2 Installation
Installation
16 Agilent SureCycler 8800 Setup and User’s Guide
Installation
Step 1. Select a location for the instrument
•Locate a solid, flat clean surface for the instrument. Make sure:
•The instrument can stand completely stable.
•The rear air slots will not be covered.
•The unit always has at least 10 cm (approximately 4 inches) to the
next wall or neighboring instrument.
•The temperature (normal ambient) is between 20°C and 30°C with
humidity levels between 20% and 80% non- condensing.
•The atmosphere is not explosive.
Step 2. Unpack the cycler
1Open the shipping containers and unpack the contents.
Detailed unpacking instructions are provided on the installation
poster (packed inside the same box as the instrument base).
Step 3. Install the thermal block on the instrument base
1Using both hands, grasp the thermal block unit on the left and right
sides and place it on top of the instrument base.
2Firmly press down on both sides of the thermal block unit until it locks
into place. Ensure both the left and right sides of the thermal block
unit are locked in place by pressing down on both sides.
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.

Installation 2
Step 4. Connect the instrument to a power supply
Agilent SureCycler 8800 Setup and User’s Guide 17
Step 4. Connect the instrument to a power supply
The instrument must be connected to a grounded AC outlet.
1Plug the instrument’s power cord into the power connector at the rear
of the instrument.
2Connect the other side of the cable to the outlet.
Step 5. Connect optional devices
If desired, you can connect an optional USB device (such as a keyboard
mouse or memory stick) to the instrument via the USB ports on the front
of the instrument.
1Plug the USB cable of the device into either USB port on the
instrument.
Step 6. Turn on the instrument
1Press the power button located near the bottom left corner on the front
of the instrument.
You can turn off the instrument any time. You do not need to close
the software before you turn off the instrument.
Step 7. Connect the cycler to a network (optional)
1Plug one end of an ethernet cable into the ethernet port on the back of
the instrument.
2Plug the other end of the cable into a network port.

2 Installation
Thermal Block Exchange
18 Agilent SureCycler 8800 Setup and User’s Guide
Thermal Block Exchange
Two interchangeable thermal block units are available with the SureCycler
8800: the 96- well block and the 384- well block.
To remove the thermal block
1Power off the instrument and disconnect the power supply.
2Lift the lid off the thermal block by pressing firmly on the gray button
on the top of the instrument.
3Using both hands, grasp the thermal block unit on the left and right
sides while using your thumbs to press down on the buttons in the
upper left and right corners.
4With the buttons firmly pressed, lift the thermal block unit up and off
the instrument base.
Use care when lifting the thermal block unit to avoid letting the lid
fall closed on your hands. Keeping the unit tilted slightly away from
you may help prevent the lid from falling closed.
To install the thermal block
1Using both hands, grasp the thermal block unit on the left and right
sides and place it on top of the instrument base.
2Firmly press down on both sides of the thermal block unit until it locks
into place. Ensure both the left and right sides of the thermal block
unit are locked in place by pressing down on both sides.
The thermal block unit will only lock into place if it is placed on the
instrument base in the proper orientation.
3Reconnect the power supply when finished.

19
SureCycler 8800
Setup and User’s Guide
Agilent Technologies
3
Getting Started
Sample Preparation and Loading 20
To prepare samples 20
To load samples 20
Agilent Plasticware and Consumables 21
Starting Up the Software 22
Touchscreen Operation of the Software 22
Home Screen 22
User Accounts 24
Access Levels 24
Logging In to User Accounts 24
Managing User Accounts 26
Network Settings and Remote Access 29
To view or edit the cycler’s IP address and name 29
To access the cycler from another cycler 30
To access the cycler from a PC 31
Cycler Settings 32
Hot Top Setting 32
Cycler name 33
Time and date 33
This chapter contains instructions to load samples, get started with the
software, set up user accounts and access instruments remotely via a
network.

3GettingStarted
Sample Preparation and Loading
20 Agilent SureCycler 8800 Setup and User’s Guide
Sample Preparation and Loading
WARNING
To prevent damage to the block and the heated lid, use only
temperature- stable sample tubes and plates. Unsuitable tubes and plates
can become damaged during cycling. See “Agilent Plasticware and
Consumables” on page 21 for a list of recommended plasticware.
To prepare samples
Keep the following guidelines in mind when preparing samples in reaction
plates and tubes:
•Place caps on tubes before loading samples into the thermal block.
•For best results, just before loadingthe samples into the thermal block,
spin them briefly in a centrifuge.
•If using sealing film to cover a reaction plate, use a compression mat
during cycling to ensure the film stays firmly adhered to the plate. See
“Agilent Plasticware and Consumables” on page 21 for ordering
information on a compression mat.
To load samples
The instrument can be loaded with individual PCR tubes or strip tubes or,
depending upon the thermal block installed, one 96- well PCR plate or one
384- well PCR plate.
1Lift the lid of the thermal block by pressing firmly on the button on the
top of the instrument to unlatch the lid.
2Put your plate or tubes on the block and check that they are correctly
positioned.
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.
3Close the lid until it latches into place.
Danger of Burns: The thermal block, sample tubes and plates may reach
temperatures as high as 100°C. Keep hands away until temperature is 30°C or less.