Bio-Rad S1000 User Manual

S1000™ Thermal Cycler

Instruction Manual

Catalog #184-2000
#185-2196
#185-2197
#185-2148
#185-2138

S1000 Thermal Cycler Manual

Copyright ©2009 Bio-Rad Laboratories, Inc. Reproduction in any form, either print or
electronic, is prohibited without written permission of Bio-Rad Laboratories, Inc.

Windows XP and Windows Vista are trademarks of Microsoft Corporation.

LICENSE NOTICE TO PURCHASER

This base unit, Serial No. ____________, in combination with its immediately attached Bio-Rad sample
block module(s), constitutes a thermal cycler whose purchase conveys a limited non-transferable
immunity from suit for the purchaser’s own internal research and development and for use in human in
vitro diagnostics and all other applied fields under U.S. Patent No. 5,475,610 (claims 1, 44, 158, 160-163
and 167 only) or corresponding claims in their non-U.S. counterparts, owned by Applera Corporation. No
right is conveyed expressly, by implication, or by estoppel under any other patent claim, such as claims
to apparatus, reagents, kits, or methods such as 5´ nuclease methods. Further information on purchasing
licenses may be obtained by contacting the Director of Licensing, Applied Biosystems, 850 Lincoln
Centre Drive, Foster City, California 94404, USA.

Bio-Rad’s thermal cyclers and real-time thermal cyclers are covered by one or more of the
following U.S. patents or their foreign counterparts owned by Eppendorf AG: U.S. Patent Nos.
6,767,512 and 7,074,367.

Hard-Shell PCR plates are covered by one or more of the following U.S. patents or their
foreign counterparts owned by Eppendorf AG: U.S. Patent Nos. 7,347,977, 6,340,589,
6,528,302.

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Bio-Rad Laboratories Resources

Table 1 lists Bio-Rad resources and how to locate what you need.

Table 1. Bio-Rad resources

Resource How to Contact

Local Bio-Rad Laboratories
representatives

Technical notes and literature Find technical information on the Bio-Rad Laboratories

Technical specialists Bio-Rad Laboratories provides quality technical support.

Find local information and contacts on the Bio-Rad
Laboratories website by selecting your country on the
home page (www.bio-rad.com). Find the nearest
international office listed on the back of this manual

website (www.bio-rad.com). Type a term in the Search box
and select Literature to find links to technical notes,
manuals, and other literature

We staff our Technical Support department with
experienced scientists to provide our customers with
practical and expert solutions

To find local technical support on the phone, contact your
nearest Bio-Rad Laboratories office. For technical support
in the United States and Canada, call 1-800-424-6723
(toll-free phone) and select the technical support option

S1000 Thermal Cycler Manual

Warranty

The S1000 thermal cycler and associated accessories are covered by a standard Bio-Rad
warranty. Contact your local Bio-Rad Laboratories office for details of the warranty.

Safety and Regulatory Compliance

The S1000 thermal cycler heats and cools very quickly during operation. We strongly
recommend that you follow the safety specifications listed in this section and throughout this
manual.

Use only Bio-Rad USB cable (catalog #184-8000) when using any 1000-series cycler.

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S1000 Thermal Cycler Manual

Safety Warning Labels

Warning labels posted on the instrument and in this manual warn you about sources of injury
or harm. Refer to Table 2 to review the meaning of each safety warning label.

Table 2. Instrument safety warning labels

Icon Meaning

CAUTION: Risk of danger! This symbol identifies components that pose a risk of

personal injury or damage to the instrument if improperly handled. Wherever this
symbol appears, consult the manual for further information before proceeding

CAUTION: Risk of electrical shock! This symbol identifies components that pose a
risk of electrical shock if improperly handled

CAUTION: Hot surface! This symbol identifies components that pose a risk of
personal injury due to excessive heat if improperly handled

Instrument Safety Warnings

The following warning labels display on the instrument and refer directly to the safe use of this
S1000 thermal cycler (Table 3).

Table 3. Instrument safety warning labels

Icon Meaning

Warning about risk of harm to body or equipment.

Operating the S1000 thermal cycler before reading this manual can constitute a
personal injury hazard. Only qualified laboratory personnel should operate this
instrument

Warning about risk of harm to body or equipment from electrical shock.

Do not attempt to repair or remove the outer case of this thermal cycler base, power
supply, heat pump, or other accessories. If you open these instruments, you put
yourself at risk for electrical shock and void your warranty. All repairs must be done
by an authorized repair service

Never remove the outer case of a thermal cycler base. This may cause you to
receive an electrical shock.

This thermal cycler uses neutral fusing, which means that live power could still be
exposed inside the instrument even when the fuse is blown or removed

Warning about risk of burning.
A thermal cycler generates enough heat to cause serious burns. Wear safety
goggles or other eye protection at all times during operation. Always allow the
sample block to return to idle temperature before opening the lid and removing
samples. Always allow maximum clearance to avoid accidental skin burns

Warning about risk of explosion.
The sample blocks can become hot enough during the course of normal operation
to cause liquids to boil and explode

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S1000 Thermal Cycler Manual

Safety and Regulatory Compliance

This instrument has been tested and found to be in compliance with all applicable
requirements of the following safety and electromagnetic standards (Table 4).

Table 4. Conditions for safe use

Usage Aspect Conditions for Safe Use

Rated input power 100–240 VAC, 50–60 Hz

Fuses 10 A, 250 V, 5 x 20 mm, fast blow (qty. 2)

Environment Indoor use only

Temperature

Relative humidity Up to 80% (noncondensing)

Altitude Up to 2,000 meters above sea level

Overvoltage category II

Pollution degree 2

SAFETY COMPLIANCE

This instrument has been tested and found to be in compliance with all applicable
requirements of the following safety and electromagnetic standards:

• IEC 61010-1:2001 Safety Requirements for Electrical Equipment for Measurement,
Control, and Laboratory Use, Part 1: General Requirements

• IEC 61010-2-010:2003 Safety Requirements for Electrical Equipment for
Measurement, Control, and Laboratory Use, Part 2-010: Particular Requirements for
Laboratory Equipment for the Heating of Materials

• CAN/CSA-C22.2 No. 61010-1-04 Safety Requirements for Electrical Equipment for
Measurement, Control, and Laboratory Use, Part 1: General Requirements

• CAN/CSA-C22.2 No. 61010-2-010-04 Safety Requirements for Electrical Equipment
for Measurement, Control, and Laboratory Use, Part 2-010: Particular Requirements
for Laboratory Equipment for the Heating of Materials

• EN 61010-1:2001 Safety Requirements for Electrical Equipment for Measurement,
Control, and Laboratory Use, Part 1: General Requirements

• EN 61010-2-010:2003 Safety Requirements for Electrical Equipment for
Measurement, Control, and Laboratory Use, Part 2-010: Particular Requirements for
Laboratory Equipment for the Heating of Materials

• UL 61010-1:2004 (R2008) Safety Requirements for Electrical Equipment for

Measurement, Control, and Laboratory use, Part 1: General Requirements

15-31

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C

ELECTROMAGNETIC COMPATIBILITY (EMC)

• IEC61326-1:2005 Electrical Equipment for Measurement, Control, and Laboratory
Use - EMC Requirements, Class A

• EN61326-1:2006 Electrical Equipment for Measurement, Control, and Laboratory
Use - EMC Requirements, Class A

• FCC Part 15, Subpart B, Sections 15.107 and 15.109 as a Class A digital device

FCC WARNINGS AND NOTES

• Warning. Changes or modifications to this unit, not expressly approved by the party

responsible for compliance, could void the user’s authority to operate the equipment

•Note. This equipment has been tested and found to comply with the limits for a Class A
digital device, pursuant to part 15 of the FCC Rules. These limits are designed to provide

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S1000 Thermal Cycler Manual

reasonable protection against harmful interference when the equipment is operated in a
commercial environment. This equipment generates, uses, and can radiate radio
frequency energy and, if not installed and used in accordance with the instruction
manual, may cause harmful interference to radio communications. Operation of this
equipment in a residential area is likely to cause harmful interference, in which case the
user will be required to correct the interference, at his own expense

• Note regarding FCC compliance. Although this design of instrument has been tested
and found to comply with Part 15, Subpart B of the FCC Rules for a Class A digital
device, please note that this compliance is voluntary, for the instrument qualifies as an
“exempted device” under 47 CFR 15.103(c), in regard to the cited FCC regulations in
effect at the time of manufacture

• Note regarding Canadian EMC compliance: Le present appareil numerique n’emet
pas de bruits radioelectrique depassant les limites applicables aux appareils numeriques
de class A prescrites dans le reglement sur le brouillage radioelectrique edicte par le
Ministere des Communications du Canada

•Cables. Shielded cables must be used with this unit to ensure compliance with the Class
A FCC limits

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S1000 Thermal Cycler Manual

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S1000 Thermal Cycler Manual

Table of Contents

Bio-Rad Laboratories Resources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ii

Warranty . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ii

Safety and Regulatory Compliance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ii

Chapter 1. Introduction to the S1000™ Thermal Cycler . . . . . . . . . . . . . . . 1

System Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Reaction Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Setting Up the S1000 Thermal Cycler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Operating the Reaction Module Lid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Main Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Chapter 2. Creating and Editing Protocols . . . . . . . . . . . . . . . . . . . . . . . . . 7

Creating a New Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Editing an Existing Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Sample Volume and Lid Temperature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Chapter 3. Running Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Preparing to Run a Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Monitoring the Protocol Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Canceling a Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Incubating Samples. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Chapter 4. Managing Protocol Files and Folders . . . . . . . . . . . . . . . . . . . 17

Managing Protocol Files and Folders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Chapter 5. Advanced Tools and Functions . . . . . . . . . . . . . . . . . . . . . . . . 21

TOOLS Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Controlling S1000 Thermal Cyclers with a C1000™ or C1000 Touch

TM

. . . . . . . . . 21

Chapter 6. Maintenance and Troubleshooting . . . . . . . . . . . . . . . . . . . . . 23

Cleaning and Maintaining the S1000 Thermal Cycler . . . . . . . . . . . . . . . . . . . . . . . 23

Maintaining Sufficient Airflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Replacing Fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

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S1000 Thermal Cycler Manual

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S1000 Thermal Cycler Manual

Module locking bar

Control panel

Air vents

Reaction module bay

1 Introduction to the S1000™

Thermal Cycler

Read this chapter for information on setting up the S1000 thermal cycler.

• System overview (page 1)

• Reaction modules (page 2)

• Setting up the S1000 thermal cycler (page 3)

• Operating the reaction module lid (page 4)

• Main menu (page 5)

System Overview

The S1000 thermal cycler base (Figure 1) includes:

• Reaction module bay — holds the inserted reaction module

• Reaction module locking bar — locks the inserted module in place

• Control panel — provides access to all the functions needed to create and run PCR
protocols

• Air vents — allow the thermal cycler to heat and cool quickly

Figure 1. Front view of the S1000 thermal cycler.

The back panel of the S1000 thermal cycler includes data ports (Figure 2).

• USB B port — connects the S1000 thermal cycler to a C1000
thermal cycler

• USB A ports — inactive

TM

or C1000 TouchTM

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S1000 Thermal Cycler Manual

Cooling vents

Power

Power

USB B port

USB A ports

Test port

input

Fuses

switch

Main menu

Screen

options

Numeric and
command keys

LCD

key

Navigation
keys

• Test port — for service testing only

Figure 2. Back panel of the S1000 thermal cycler.

The control panel on the S1000 thermal cycler provides access to all the functions needed to
run the thermal cycler and includes the following components:

• Liquid crystal display (LCD) — displays the main menu and other screens

• Command, numeric, and navigation keys — use these keys to enter commands,
numbers, or letters and to navigate various screens

The main screen is displayed after booting is complete. Figure 3 shows the components of the
control panel.

Figure 3. Components of the control panel on the S1000 thermal cycler.

Reaction Modules

The S1000 thermal cycler is compatible with any 1000-series reaction module. The reaction
modules come in four sizes: the 96-well fast, 96-deep well, dual 48/48-well, or 384-well
blocks. Each reaction module includes a fully adjustable heated lid that is capable of running
reliably with a broad range of reaction vessels.

Each reaction module contains cooling fins for fast heating and cooling and a fully adjustable,
heated lid.

• Heated inner lid — adjusts the lid temperature to prevent condensation and

• Sample/reaction block — holds reaction vessels, including tubes and microplates

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evaporation

S1000 Thermal Cycler Manual

Lid force knob

Lid lever

Status LED

Lid

Cooling fins

The top of a reaction module lid includes a lid lever, lid force knob, and status LED.

• Lid lever — opens and closes the lid

• Lid force knob — sets lid force and seals the reaction

• Status LED — turns on to indicate that the block is selected or running

Figure 4 shows the components of a 96-well fast reaction module.

Figure 4. Components of a reaction module.

Setting Up the S1000 Thermal Cycler

The S1000 thermal cycler package includes:

• S1000 thermal cycler base

• Power cord

• Consumables selection guide

• Instruction manual

• Quick guide for system installation

Reaction modules for use with the S1000 thermal cycler are shipped in separate packaging.

Remove all packaging materials and store them for future use. If any item is missing or
damaged, contact your local Bio-Rad office.

Place the S1000 thermal cycler base on a flat, dry surface with sufficient cool airflow to run
properly. The instrument can run in two modes: stand-alone or software-controlled. When
running the system under software-controlled mode, make sure during setup there is sufficient
space for a computer.

To insert a 96-well fast, 96-deep well, dual 48/48-well, or 384-well reaction module into
the reaction module bay of the thermal cycler base, follow these instructions:

1. With the locking bar in the down position and the lid lever of the reaction module pointing
to the front, lift the reaction module into the reaction module bay. Leave about 1-2 cm of
space in front of the module.

2. Pull the locking bar up to lock the reaction module in place. There is no space at the front
of the module when it is locked into the S1000 thermal cycler base.

3. Plug the supplied power cord into the appropriate electrical outlet.

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S1000 Thermal Cycler Manual

4. Turn on the thermal cycler using the power switch on the back panel of the thermal
cycler base.

NOTE: Before operating the thermal cycler, be sure to read the safety
specifications (Safety and Regulatory Compliance on page ii) and operating
requirements.

5. When the S1000 thermal cycler starts up, it goes through two screens: the black booting
and the self-test screens. Once the self-test is run to verify proper functions, the main
menu is displayed. Use the main menu to begin operating the thermal cycler.

To remove the reaction module from the thermal cycler base, follow these instructions:

1. Turn off the thermal cycler.

2. Unlock and release the reaction module by pushing the locking bar down.

3. Carefully lift the reaction module out of the bay.

WARNING! Cooling fins may be hot immediately after running a protocol or
incubation. Before lifting the reaction module, make sure that the cooling fins are
not hot.

4. After removing the reaction module from the S1000 thermal cycler, store it on a clean,
flat surface where it cannot get bumped, scraped, or dropped.

Operating the Reaction Module Lid

The inner lid of the reaction module applies heat and force to the reaction vessel lids (caps or
tape) to produce consistent and successful reactions. Heating the inner lid prevents
condensation, while applying force seals the reaction to prevent evaporation.

WARNING! After a run, the heated inner lid can remain hot. Use caution when
opening and closing the lid.

To open the lid, use the following steps:

1. Turn the lid force knob counterclockwise to release the inner lid.

2. To open the lid, lift the lid lever up.

3. Lift the lid lever completely until the reaction module stays open without assistance.

To close the lid, use the following steps:

1. Push the lid lever down, making sure that the front of the lid is secured beneath the
housing.

2. Adjust the lid force by turning the lid force knob.

• Turn the knob clockwise to increase the lid force

• Turn the knob counterclockwise to decrease the lid force

3. Increase the lid force until the heated lid touches the reaction vessel. Continue to
increase the lid force based on the following recommendations:

• If using tubes, increase the lid force by a quarter turn after the lid touches the

tubes

• If using plates, increase the lid force by a half turn after the lid touches the plate

NOTE: The position marks on the lid indicate quarter turns.

WARNING! If the lid is tightened past the recommended force, tightening the lid
further will result in the knob slipping and causing a clicking sound. This is
designed as a warning that the lid force is past the recommended setting and may

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