S1000 Thermal Cycler Instruction Manual Rev A

Copyright ©2007 Bio-Rad Laboratories, Inc. Reproduction in any form, either print or electronic, is prohibited without written permission of Bio-Rad Laboratories, Inc. Chill-Out, iProof, iTaq, and the helix logo are trademarks belonging to Bio-Rad Laboratories, Inc. Other brands or product names are trademarks of their respective holders.

LICENSE NOTICE TO PURCHASER Purchase of this instrument, Serial No. ____________, conveys a limited non-transferable immunity from suit for the purchaser’s own internal research and development and for use in applied fields other than Human In Vitro Diagnostics under one or more of U.S. Patents Nos. 5,656,493, 5,333,675, 5,475,610 (claims 1, 44, 158, 160-163 and 167 only), and 6,703,236 (claims 1-7 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.

S1000 Thermal Cycler Manual |

Safety and Regulatory Compliance The S1000™ thermal cycler heats and cools quickly during operation. We strongly recommend that you follow the safety specifications listed in this section and throughout this 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 1 to review the meaning of each safety warning label: Table 1: Meaning of safety warning label. 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 warnings labels display on the instrument, and refer directly to the safe use of this S1000 thermal cycler: Table 2: Instrument safety warning labels. Icon

Meaning Warning about risk of harm to body or equipment. Operating the S1000 thermal cycler instrument 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 because you might 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 temperate before opening the lid and removing samples. Always allow maximum clearance to avoid accidental skin burns.

Table 2: Instrument safety warning labels. Icon

Meaning 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.

Safety Use Specifications and Compliance This instrument has been tested and found to be in compliance with all applicable requirements of the following safety and electromagnetic standards: Table 3: Safe use specifications Safe use requirements

Specifications

Input power

100–240 VAC, 50–60 Hz.

Rated

250 V, 10 A.

Fuses Temperature

Indoor use

Ambient temperature of 5oC to 31oC. Relative humidity maximum of 80% noncondensing.

Altitude

Up to 2,000 meters above sea level.

Overvoltage Categories

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: • UL Std No. 61010A-1 Electrical Equipment for Measurement, Control, and Laboratory Use, Part 1: General Requirements • UL Std No. 61010A-2-010 Electrical Equipment for Measurement, Control, and Laboratory Use, Part 1: General Requirements • CAN/CSA C22.2 No. 1010.1-92 - Safety Requirements for Electrical Equipment for Measurement, Control, and Laboratory Use, Part 1: General Requirements (includes Amendment 1) • CAN/CSA C22.2 No. 1010.1B-97 - Amendment 2 CAN/CSA C22.2 No. 1010.192 - Safety Requirements for Electrical Equipment for Measurement, Control, and Laboratory Use, Part 1: General Requirements • CAN/CSA C22.2 No. 1010.2.010A-97 - Safety Requirements for Electrical Equipment for Measurement, Control, and Laboratory Use, Part 2-010: Particular Requirements for Laboratory Equipment for the Heating of Materials, Amendment No. 1 • EC 61010-1 Safety Requirements for Electrical Equipment for Measurement, Control, and Laboratory Use, Part 2-010: Particular Requirements for Laboratory Equipment for the Heating of Materials

ELECTROMAGNETIC COMPATIBILITY (EMC) • F.C.C Title 47 Part 15B as a Class A digital device.

• EN61326 Class A Electrical Equipment for measurement, control, and laboratory use - EMC Requirements.

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 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. • Use only Bio-Rad USB cable (Catalog No. 184-8000) with your 1000 Series cyclers.

S1000 Thermal Cycler Manual | Safety and Regulatory Compliance

Table of Contents Chapter 1. Introduction... 1 The Bio-Rad 1000 Series Platform... 1 S1000 Thermal Cycler Performance and Features... 2 Bio-Rad Resources and References... 3 Writing Conventions Used in This Manual... 4

Chapter 2. Get Started... 5 Setting Up the S1000 Thermal Cycler... 5 Thermal Cycler Overview... 7 Front View without Reaction Module 7 Top View with Reaction Module 7 Back View with Reaction Module 8 Interchangeable Reaction Modules... 9 Inserting and Removing a Reaction Module 10 Opening and Closing the Adjustable Lid... 12 Opening the Lid 12 Closing the Lid and Setting Lid Force 13 Control Panel Keys and Main Menu... 13 Control Panel Keys 15 The Main Menu 16 The File Tree... 16

Chapter 3. Create and Edit Protocols... 19 Creating a Protocol File with the NEW Option... 19 Adding INC, EXT, RATE, and BEEP Parameters... 28 Adding an Increment (INC) to a Temperature Step 28 Extending (EXT) the Hold Time in a Temperature Step 30 Changing the Ramp Rate (RATE) in a Temperature Step 31 Adding a Beep (BEEP) to a Temperature Step 32 Setting Temperature Control Mode... 33 Choosing Lid Temperature... 33 Changing an Existing Protocol with the EDIT Option... 34

Chapter 4. Run Existing Protocols... 41 Running a Protocol With the RUN Option... 41 Monitoring a Run with the SCREEN Key... 46 Pausing and Resuming a Run with the PAUSE Key... 48 Skipping a Step... 49 Stopping a Run With the CANCEL Key... 50 Incubating Samples With the INCUBATE Key... 50

S1000 Thermal Cycler Manual | Table of Contents

Chapter 5. Optimizing PCR With the S1000 Thermal Cycler... 53 Optimizing for Faster Protocols... 53 Optimizing Temperature Steps With a Gradient... 55 Optimizing Runs With Small Sample Volumes... 56 Transferring Protocols From Another Thermal Cycler... 57 Troubleshooting PCR... 57 Microplate, Tube, Sealer and Cap Supplies... 58

Chapter 6. Protocol Files and Folders... 61 Protocol File Contents... 61 Protocol Steps 61 Options for Temperature and Gradient Steps 64 Managing protocols With the FILES Option... 65 Copying, Moving, Deleting, and Renaming Protocol Files... 65 Copying a File With the COPY Function 66 Moving a File With the MOVE function 67 Deleting a File With the DELETE Function 68 Renaming a File With the RENAME Function 69 Protecting Files in a Folder With the SECURE Function... 71 Creating, Deleting, and Renaming Folders... 72 Creating a New Folder With the NEW Function 72 Deleting a Folder with the DELETE Function 73 Renaming a Folder With the RENAME Function 74 Viewing Protocol Files With the VIEW Option... 75

Chapter 7. Advanced Tools and Functions... 79 The TOOLS Options... 79 View the LAST RUN Tool 80 Test the Instrument With the SELFTEST Tool 81 Check the Firmware Version With the VERSION Tool 82 Name the Thermal Cycler with the NAME Tool 82 Change Default Parameters With the DEFAULTS Tool 83 View a Temperature Gradient with the GRADCALC Tool 84 Changing Screen View with the CONTRAST Tool 86 Change Settings With the PORT Tool 87 Control an S1000 Thermal Cycler With the C1000 Thermal Cycler... 88 Connecting Directly to a C1000 via the S1000 USB B Port 88 Connecting Indirectly to a C1000 Thermal Cycler via the S1000 USB A Port 89 Operating the S1000 Thermal Cycler While Under C1000 Thermal Cycler Control 90 Automated Control for Robotic Systems... 90

Chapter 8. Maintenance & Troubleshooting... 91 Cleaning and Maintaining the S1000 Thermal Cycler... 91 Cleaning the S1000 thermal cycler Base 91 Cleaning the Reaction Modules 92 Maintaining Sufficient Air Flow... 93 Testing for Sufficient Airflow 93 Fixing Insufficient Airflow 94 Replacing Fuses 94 Troubleshooting... 95 Restarting After a Power Failure 95 Warning and Error Messages 95 ... 99

Appendix A: Preinstalled Protocols... 101 Standard Protocols... 101 Touchdown Protocol... 102 iTaq Polymerase Protocols... 102 iProof Polymerase Protocols... 103 IScript Polymerase Protocol... 104 Nested Primer Protocols... 104

Appendix B: Operating Specifications... 107 Instrument Operating Specifications... 107 Gradient Specifications... 108

Appendix C: Catalog Numbers... 109 Components of the 1000-series... 109 Accessories for the 1000-series... 111

S1000 Thermal Cycler Manual | Table of Contents

S1000 Thermal Cycler Manual

1

Introduction Congratulations on purchasing the S1000™ thermal cycler, a member of the Bio-Rad 1000 series thermal cycling platform. It combines powerful thermal performance with unsurpassed flexibility and expansion potential making it ideal for both large and small laboratories. This chapter provides an introduction to the S1000 thermal cycler and more, including: • The 1000 series platform of thermal cyclers (below). • S1000 thermal cycler features and performance (page 2). • Bio-Rad’s PCR resources and support (page 3). • Writing conventions for this manual (page 4).

The Bio-Rad 1000 Series Platform The 1000 series line of PCR instrumentation is a flexible and modular platform designed to offer best in-class performance and advanced features in an easy-to-use, reliable package. With the 1000 series platform, you can get results faster by seamlessly integrating your workflows with functions such as PC compatibility, optimization, programming options, online support, and USB connectivity.

Table 4: 1000 Series Catalog Numbers Product

Catalog Number

Item Description

C1000 Thermal Cycler

184-1000

C1000 thermal cycler, chassis only

C1000 Fast 96-well System

185-1096

C1000 chassis + Fast 96-well Rxn Module

C1000 48/48 System

185-1048

C1000 chassis + Dual 48/48 Rxn Module

C1000 384-well System

185-1384

C1000 chassis + 384-well Rxn Module

S1000 Fast 96-well System

185-2096

S1000 chassis + Fast 96-well Rxn Module

S1000 48/48 System

185-2048

S1000 chassis + Dual 48/48 Rxn Module

S1000 384-well System

185-2384

S1000 chassis + 384-well Rxn Module

S1000 Thermal Cycler

184-2000

S1000 thermal cycler, chassis only

96-well Fast Reaction Module

184-0096

96-well Fast Rxn Module for 1000 Series

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S1000 Thermal Cycler Manual | Introduction

Table 4: 1000 Series Catalog Numbers Product

Catalog Number

Item Description

48/48-well Fast Reaction Module

184-0048

Dual 48/48 Rxn Module for 1000 Series

384-well Reaction Module

184-0384

384-well Rxn Module for 1000 Series

CFX96 Real-Time System

185-5096

C1000 chassis + CFX96 Rxn Module

CFX384 Real-Time System

185-5384

C1000 chassis + CFX384 Rxn Module

CFX Manager Software

184-5000

PC Software for use with Real Time PCR

CFX Software, Security Edition

184-5001

Single User License real time software

S1000 Thermal Cycler Performance and Features The S1000 thermal cycler features superb thermal performance with the flexibility to expand throughput. It can perform standard polymerase chain reactions (PCR), cycle sequencing, or other techniques that require controlled temperature incubation. The S1000 operates as a stand-alone thermal cycler with the following features: • Reduced Protocol Run Times: The S1000 offers fast thermodynamics for shorter run times and expedited results. • Reliable Results with Precise Thermal Control: Sample block uniformity of +0.4oC at 90oC after 10 seconds with an accuracy of +0.2oC; adjustable lid temperature to further control reaction temperature and prevent evaporation. • Thermal Gradients: Optimize reaction performance using temperature gradients across sample blocks. • Flexible Vessel Format with Interchangeable Reaction Modules: Simply change reaction modules when you need 48, 96, or 384-well blocks with the same thermal cycler base. Uniform and repeatable microplate sealing with adjustable lid force. • Pre-installed, Customizable Protocols for Use as Templates: Speed protocol writing by customizing pre-loaded protocols. • Ready for High-Throughput: Use remote commands to control up to 32 thermal cyclers for automated robotic systems.

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Bio-Rad Resources and References

Bio-Rad Resources and References Bio-Rad Laboratories provides many resources for scientists. The following websites contain useful information about running PCR experiments: • Gene Expression Gateway (bio-rad.com/genomics/) This site provides rich technical resources on a wide variety of methods and applications related to PCR and real-time PCR. This site also features tools, citations, technical support, and troubleshooting resources. • Life Science Research web site (discover.bio-rad.com) This site includes links to technical notes, manuals, product information, and technical support. press the following links to download or request a copy of this manual or other Bio-Rad Laboratories literature: • press the PDF icon to download a portable document format copy and open it using Adobe Acrobat Reader software (www.adobe.com). • press the folder icon and order a printed copy. • press the FAX icon to request a FAX copy. • Phone your local Bio-Rad Laboratories office to request a printed copy. In the United States and Canada, call 1-800-424-6723 (toll-free phone), and select the Literature option. Use the following resources to locate what you need: Table 5. Bio-Rad resources. Resource

How to contact

Local Bio-Rad Laboratories representatives

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

Technical notes and literature

Go to the Gene Expression Gateway (bio-rad.com/ genomics/) and locate the Search box in the upper, right corner of the web page. Type a search term in the box to find links to products, technical notes, and manuals.

Technical specialists

Bio-Rad Laboratories provides quality technical support. We staff our Technical Support department with experienced scientists to provide our customers with practical and expert solutions. To find technical support on the web, go to the Gene Expression Gateway (bio-rad.com/genomics). To find local technical support, 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.

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S1000 Thermal Cycler Manual | Introduction

Writing Conventions Used in This Manual This manual uses the writing conventions shown in Table 6 to quickly provide relevant information. Table 6. Writing conventions Convention

Meaning

TIP:

Provides helpful instructions

NOTE:

Provides important information

WARNING!

Explains crucial information about a topic that may lead to injury, instrument damage, data loss

Screen message

Indicates the one or more words on the screen the user should select.

NAME of control panel Indicates a key on the thermal cycler control panel. For key example, these keys have the following names: • The ENTER key

• The RIGHT ARROW key

4

Select X

Select X by using the arrow keys. For example, “select New” means “Use the arrow keys or to highlight the New option on the screen”

Select X > Y

From menu X, select Y. For example, “Select Main > RUN” means “Select the RUN option in the main menu”

Press X

Press X key on the control panel. For example, “press ENTER” means “Press the ENTER key on the control panel”

S1000 Thermal Cycler Manual

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Get Started The S1000™ thermal cycler is easy to set up and run: insert the reaction module, plug in the thermal cycler base, then begin a PCR experiment. This chapter describes how to set up and operate the S1000 thermal cycler. Refer to the following sections for detailed instructions: • Setting up the S1000 thermal cycler (below) • Introducing the S1000 thermal cycler base and interchangeable reaction modules (page 7) • Choosing and inserting a reaction module (page 9) • Operating the lid of the reaction module (page 12) • Operating the control panel (page 13) • Selecting files and folders from the file tree (page 16)

Setting Up the S1000 Thermal Cycler This section provides an overview of the steps needed to safely unpack and set up the S1000 thermal cycler. Follow these instructions to prepare to run the thermal cycler: 1. Unpack the S1000 thermal cycler base and reaction module The S1000 thermal cycler base package includes the thermal cycler base, a power cord, quick guide, and this manual. Keep all packaging to safely move this instrument. Place the thermal cycler base in the desired location. NOTE: A thermal cycler requires sufficient cool air flow to run precisely. To check for sufficient air flow before running the instrument, see page 91. 2. Insert a reaction module The reaction module fits into the thermal cycler bay and locks in place for operation. For detailed instructions about loading the reaction module, see page 10. 3. Plug in the power cord and turn on the thermal cycler Use the supplied power cord to plug the thermal cycler base into an electrical outlet. Use the power switch on the back of the base to turn on the power. NOTE: Before operating the thermal cycler, be sure to read the safety warnings and operating requirements listed in the “Safety and Regulatory Requirements”.

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S1000 Thermal Cycler Manual | Get Started

As the instrument boots up, the thermal cycler runs a self-test to verify proper functions, and then displays the main menu. Use the main menu to begin operating the thermal cycler. The main menu provides access to all thermal cycler operations and indicates cycler status. If the thermal cycler is named, the name displays in the top of the main menu. For information about naming the thermal cycler, see page 82. For example, the main menu shows the options listed below, the status message Blocks are idle, and the thermal cycler name MENDEL: Thermal cycler name Main menu options

Status message For more information about the options listed in the main menu, see page 16. This thermal cycler, and associated accessories, are covered by a standard Bio-Rad warranty. Contact your local Bio-Rad Laboratories office for the details of the warranty. For more information about contacting your local Bio-Rad Laboratories office, see page 3.

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Thermal Cycler Overview

Thermal Cycler Overview When complete, the S1000 thermal cycler includes a base and reaction module. The following sections describe important parts of the thermal cycler and reaction modules: • Front view of the base without a reaction module (below) • Top view of the base with reaction module (page 7) • Back view base with reaction module (page 8)

Front View without Reaction Module This front view of the thermal cycler base shows a control panel and reaction module. The following image shows major features of the thermal cycler base, including the control panel, LCD screen and air vents.

Top View with Reaction Module This top view shows the reaction module docked in the bay of the thermal cycler base. The following shows major features of the reaction module, and thermal cycler base. For more information about reaction modules, see page 9.

Heated lid Heated lid

Reaction module

Module locking bar

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S1000 Thermal Cycler Manual | Get Started

Back View with Reaction Module The following shows the major components on the back of the thermal cycler with a reaction module, including the power switch, data ports, and reaction module.

Back of reaction module

Locking bar

Power switch Power input

Back panel of base

Data ports Cooling vents The back panel includes data ports that transfer data to and from the thermal cycler. • USB B port for connecting the S1000 thermal cycler to a C1000 thermal cycler. • USB A ports for connecting to another S1000 thermal cycler that is connected to a C1000 thermal cycler or to a USB hub (page 88). • Test port (used for service testing only). USB B port USB A ports Power switch Power input Fuses

8

Cooling vents

Test port

Interchangeable Reaction Modules

Interchangeable Reaction Modules The S1000 thermal cycler can run any of the 1000 series reaction modules. The reaction modules include fully adjustable heated lids that are capable of reliably running with a broad range of plastics. Table 7: 1000 series reaction module size and limits Number of wells

Number of blocks

Recommended sample volume (upper limit)

Dual-48

2

10-50 uL (50 uL limit)

96

1

10-50 uL (50 uL limit)

384

1

3-30 uL (30 uL limit)

CFX 96 Real-Time

1

10-50 uL (50 uL limit)

CFX 384 Real-Time 1

3-30 uL (30 uL limit)

All reaction modules are compatible with a large variety of PCR reaction vessels, in addition to the tested microplates, tubes, caps, and sealing tape listed on page 58. All reaction modules include the features shown in the following image: • Heated inner lid: Set the lid temperature for each protocol. The lid also applies the force that seals reaction vessels. • Lid force knob: Adjust the knob to obtain appropriate lid force to seal the reaction vessel. • LED: Turns on to show which block is selected and/or in use. • Locking lever: Secures the reaction module to the base during operation. • Sample Thermal block: Holds sample vessels and controls the temperature throughout the run. Lid locking lever Reaction module lid

Inner lid with heated pressure plate

Thermal block (96-well Fast) LED

9