Gel Doc XR+ and ChemiDoc XRS+ Systems with Image Lab 2.0 sw User Guide Ver 5.1 Rev G

Notice No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage or retrieval system, without permission in writing from Bio-Rad Laboratories, Inc. Bio-Rad reserves the right to modify its products and services at any time. This user guide is subject to change without notice. Although prepared to ensure accuracy, Bio-Rad assumes no liability for errors or omissions, or for any damage resulting from the application or use of this information.

Credits 1. Image Lab software is based in part on the work of the Qwt project (http://qwt.sf.net). 2. Image Lab software is based in part on the work of the CImg project (http://cimg.sourceforge.net/). See license for details at www.cecill.info/licences/Licence_CeCILL-C_V1-en.html 3. Image Lab software is based in part on the work of the Independent JPEG Group (www.ijg.org/) Alexa Fluor, Coomassie Fluor, Qdot, and SYPRO are trademarks of Invitrogen Corporation. Coomassie is a trademark of BASF Aktiengesellschaft. Cy2 and Cy3 are trademarks of GE Healthcare. DyLight and Krypton are trademarks of Thermo Fisher Scientific Inc. Excel, PowerPoint, and Windows XP, and Windows 7 are trademarks of Microsoft Corporation. iWork, Macintosh, Mac OS, and Numbers are trademarks of Apple Inc. GelGreen and GelRed are trademarks of Biotium, Inc. Intel Core and Pentium are trademarks of Intel Corporation. Mitsubishi is a trademark of Mitsubishi Companies. PulseNet International is a trademark of Centers for Disease Control and Prevention. Slo-Blo is a trademark of Littelfuse. CHEF (U.S. Patent Number 5,549,796, issued to Stanford University) is exclusively licensed to Bio-Rad Laboratories, Inc. Precision Plus Protein standards are sold under license from Life Technologies Corporation, Carlsbad, CA, for use only by the buyer of the product. The buyer is not authorized to sell or resell this product or its components. SYBR is a trademark of Life Technologies, Inc. Bio-Rad Laboratories, Inc. is licensed by Life Technologies, Inc. to sell reagents containing SYBR Green I for use in real-time PCR, for research purposes only. Bio-Rad Laboratories, Inc. is licensed by Invitrogen Corporation to sell SYPRO products for research use only under U.S. Patent Number 5,616,502. Copyright ©2014 Bio-Rad Laboratories, Inc.

Table of Contents Safety and Regulatory Compliance...11 Important Safety Information... 11 Warranty... 12 General Precautions... 12 Regulatory Notices... 13 Instrument Safety Warnings... 13 Notice... 14 Power Safety Information... 15 Voltage Setting Information... 15 Fuses... 15

Chapter 1 Introduction...17 Gel Doc XR+ Imaging System... 17 ChemiDoc XRS+ Imaging System... 18 System Components... 18 CCD Camera and Lenses... 18 Universal Hood... 19 Image Lab Software... 19 Emission Filters... 20 Optional Accessories... 20 Printer... 20 Conversion Screens... 20

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Chapter 2 Gel Doc XR+ Imager... 21 Gel Doc XR+ Imager Workflow... 21 Gel Doc XR+ Applications... 22 Gel Doc XR+ Technical Specifications... 23

Chapter 3 ChemiDoc XRS+ Imager... 25 ChemiDoc XRS+ Imager Workflow... 25 ChemiDoc XRS+ Applications... 26 ChemiDoc XRS+ Technical Specifications... 27

Chapter 4 Setting Up the Instrument with Image Lab Software . . . 29 System Requirements... 29 Image Lab Security Edition... 29 Computer Specifications... 29 Installing Image Lab Software... 30 Installing the Drivers on a Windows XP Computer... 36 Installing the Drivers on a Windows 7 Computer... 39 Setting Up Image Lab Security Edition... 39 Activating and Deactivating Security Edition... 39 Enabling and Disabling Image Lab Secure Mode... 46 Setting Security Preferences... 50 Renaming Security Groups... 53 Using Groups on a Local Domain... 53 Changing Security Preferences... 54

Chapter 5 Image Lab Software Overview... 55 Interface Overview... 57 Main Window... 57 Main Toolbar... 58 Results Data... 58 Display Toolbox... 58 Start Page... 59 Analysis Tool Box... 59 Status Bar... 61 Menu Commands... 62 iv

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Chapter 6 Acquiring Images... 69 The Protocol Setup Window... 70 Creating a Protocol... 71 Setting Up a New Protocol... 72 Step 1. Gel Imaging for Single-Channel Protocols... 73 Step 2. Detect Lanes and Bands... 78 Step 3. Analyze Molecular Weight... 79 Step 4. Specify Output... 82 Review Protocol Settings... 83 Creating a Multichannel Image from Single Images... 84 Editing a Saved Protocol... 85 Positioning the Gel... 87 Running a Protocol... 88 Running Signal Accumulation Mode (SAM) Protocols... 89 Saving Signal Accumulation Mode (SAM) Images... 90 Setting Up a Custom Application... 91 Regression Methods... 93 Application Tables... 94

Chapter 7 Viewing Images... 97 Displaying Gel Images... 98 Display Gel Options... 98 Zoom Tools... 99 Fit in Window... 100 Image Transform... 100 Image Colors... 102 3-D Projection... 103 Image Info... 104 Displaying Data... 104 Analysis Table Options... 105 Lane and Band Table Measurement Definitions... 107 Volume Measurement Definitions... 108 Lane Profile... 109 Standard Curve... 112 Report... 113 User Guide

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Chapter 8 Analyzing Images... 115 Using Auto Analysis... 115 Analysis Tool Box Tools... 117 Image Tools... 118 Correcting a Slanted Gel... 119 Cropping a Gel Image... 119 Inverting Data... 120 Merging Images... 120 Lane and Bands Tools... 121 Detecting Lanes... 122 Using the All Lanes and Single Lane Tools... 122 Copying Lanes... 125 Detecting Bands... 126 Editing the Detected Bands... 129 Molecular Weight (MW) Analysis Tools... 131 Quantity Tools... 135 Annotation Tools... 141 Add Annotations... 142 Alignment... 142 Text Properties... 143 Color... 143 Rotate... 143 Volume Tools... 144

Chapter 9 Generating Reports... 151 Report... 151 Report Settings... 152 Print Report... 155 Print Report to a PDF File... 155 Adjust the Printer Settings... 156

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Chapter 10 Exporting Results... 157 Exporting Gel Images... 157 Exporting Gel Images for Publication... 158 Exporting Gel Images for Analysis... 160 Exporting Gel Images to PulseNet International... 160 Exporting Lane and Band Tables to Excel... 161 Exporting Volume Tables to File... 161 Screenshot Tool Export... 161 Analysis Table Export... 161

Chapter 11 System Calibration... 163 Recalibrating Your Imager... 164

Chapter 12 Image Lab Logs... 167 Image Lab Logs... 167 Viewing the Instrument Log... 168 Viewing the System Log... 169 Viewing the Document Log... 170 Displaying Log Data... 171 Displaying Data Columns in Logs... 171 Filtering Data in Logs... 172 Collapsing or Expanding Data Rows... 174 Exporting Logs... 175 Printing Logs... 176

Chapter 13 Using the Security Edition... 179 21 CFR Part 11... 179 Standard Mode versus Secure Mode... 180 User Names, Groups, and Roles... 180 Role Restrictions... 182 Starting Image Lab Security Edition... 183 Electronic Records... 183 Unsecured Documents... 184 Secure Documents... 184

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Modifying Secure Documents... 185 Signing Documents... 186 Document Logs... 187 Viewing the Document Log... 188

Appendix A Maintenance... 189 UV Transilluminator Lamp and Starter Replacement... 189 Epi-Illumination Lamp Replacement... 191 Fuse Replacement... 192

Appendix B Troubleshooting... 193 Appendix C Setting Up Users and Groups... 195 Setting Up Image Lab Users and Groups... 195 User Accounts... 195 User Authentication and Group Membership... 195 Finding the name of your authentication domain... 197 Configuring Users and Groups on a Local Computer... 198 Configuring Users and Groups on a Network Domain... 202 Password Security... 206 Password Policy Setting Examples... 208 Account Lockout Policy Setting Examples... 208 Auditing Windows Event Logs... 208 Miscellaneous Security Measures... 209

Appendix D Accessories... 211 Calibrating Accessories... 211 Installing Optional Accessories... 211 UV/White Light Conversion Screen... 211 XcitaBlue™ Conversion Screen... 212 Gel Alignment Template Kit... 214 White Light Transilluminator... 215 Orange Fluorescence Reference Plate... 216 Ordering Information... 218 viii

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Appendix E Using Bio-Rad’s Stain-Free Technology... 223 Stain-Free Workflow... 224 Electrophoresis with Stain-Free Gels... 225 Imaging Gels... 225 Imaging Blots... 226

Appendix F Mitsubishi P93/P95 Thermal Printer... 227 Setting up a Thermal Printer on Windows... 227 Setting up a Thermal Printer on a Mac... 228

Appendix G Regression Calculation Methods... 229 Glossary... 231

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Gel Doc XR+ and ChemiDoc XRS+ with Image Lab Software

Safety and Regulatory Compliance Important Safety Information Please read these instructions before attempting to operate the Gel Doc™ XR+ or ChemiDoc™ XRS+ imaging system. This instrument is suitable for research use only. It must be used, therefore, only by specialized personnel who know the health risks associated with the reagents that are normally used with this instrument. Use of the Gel Doc XR+ or ChemiDoc XRS+ imaging system involves UV illumination. Proper precautions must be taken to avoid eye and skin exposure to the UV radiation. This instrument is meant for use only by trained personnel who know the health risks associated with the UV radiation normally used with this instrument. The acrylic shield provides some UV protection. However, it does not guarantee complete protection, and it is designed to shield only the person working in front of the imager. WARNING! Use of the acrylic screen does not guarantee the user protection from UV radiation. The use of protective eyeglasses, mask, and/or gloves is strongly recommended.

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Warranty The Gel Doc XR+ or ChemiDoc XRS+ imaging system is warranted against defects in materials and workmanship for one year. If any defect occurs in the instrument during this warranty period, Bio-Rad Laboratories, Inc. will repair or replace the defective parts at its discretion without charge. The following defects, however, are specifically excluded: 

Defects caused by improper operation

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Repair or modification done by anyone other than Bio-Rad Laboratories, Inc. or the company’s authorized agent

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Use of spare parts supplied by anyone other than Bio-Rad Laboratories, Inc.

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Damage caused by accident or misuse

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Damage caused by disaster

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Corrosion caused by improper solvents or samples

General Precautions

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Read the user guide carefully.

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The instrument must be used only for the intended purpose of gel documentation in research laboratories.

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The instrument must be connected to a grounded power source line and protected by a circuit breaker.

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Do not pour liquids directly on or inside the instrument.

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Switch off all lights on the instrument immediately after use.

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Clean the transilluminator sample area after use.

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Regulatory Notices

Regulatory Notices The Gel Doc XR+ or ChemiDoc XRS+ imaging system is designed and certified to meet EN 61010, the internationally accepted electrical safety standard, EMC regulations, and TUV requirements. Certified products are safe to use when operated in accordance with this user guide. Do not modify or alter this instrument in any way. Modification or alteration of this instrument will: 

Void the manufacturer’s warranty

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Void the regulatory certifications

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Create a potential safety hazard

WARNING! Bio-Rad Laboratories, Inc. is not responsible for any injury or damage caused by use of this instrument for purposes other than those for which it is intended or by modifications of the instrument not performed by Bio-Rad Laboratories, Inc., or an authorized agent.

Instrument Safety Warnings Notes, cautions, and warnings are used to highlight certain operating procedures and recommendations. The table below describes how each is used in this document. Table 1. Notes, Cautions, and Warnings Icon

Meaning

Note:

Note: A note indicates a special procedure, an exception to normal operation, or something else of specific interest to the reader. Notes are preceded by the word Note. Caution: A caution precedes an operational step that could damage the instrument or destroy data unless the operator takes certain precautions. Cautions located in the main text are preceded by the word Caution and are accompanied by the caution symbol in the left margin.

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Table 1. Notes, Cautions, and Warnings, continued Icon

Meaning Caution: With the exception of cleaning or replacing light bulbs, refer all servicing to qualified Bio-Rad personnel or their agents. If you experience technical difficulties with the instrument, contact Bio-Rad to schedule service. The instrument should not be modified or altered in any way. Alteration voids the manufacturer’s warranty and might create a potential safety hazard for the user. Caution: If the case interlock is defeated, there is a possibility of UV-B radiation hazard due to UV-B light exposure. Exercise caution when servicing the instrument. Caution: Bio-Rad is not responsible for any injury or damage caused by the use of this instrument for purposes other than that for which it is intended, or by the modification of this instrument when not performed by qualified Bio-Rad personnel or their agents. Caution: Disconnect the AC power cord before removing the instrument

cover. Warning: A warning precedes an operating procedure that could cause injury to the operator if not followed correctly. Warnings located in the main text are preceded by the word Warning and are accompanied by the warning symbol in the left margin. Warning: This instrument must be connected to an appropriate AC voltage outlet that is properly grounded.

Notice TheGel Doc XR+ or ChemiDoc XRS+ imager is intended for laboratory use only. This device is meant for use by specialized personnel who know the health risks associated with reagents normally used in electrophoresis. The UV light source is computer controlled, and proper interlocks are implemented to avoid users’ accidental exposure to UV radiation. Bio-Rad Laboratories, Inc. is not responsible for any injury or damage caused by use of this instrument for purposes other than those for which it is intended, or for instrument modifications not performed by Bio-Rad Laboratories, Inc. or an authorized agent.

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Power Safety Information

Power Safety Information Voltage Setting Information The universal hood of the Gel Doc XR+ or ChemiDoc XRS+ imager has a power supply that automatically chooses the correct voltage for your country or region.

Fuses The universal hood of the Gel Doc XR+ or ChemiDoc XRS+ imager has two userserviceable fuses, F1 and F2, which are located on the bottom rear panel and are a part of the power entry module. See Fuse Replacement on page 192 for information about replacing the fuses.

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1 Introduction Gel Doc™ XR+ and ChemiDoc™ XRS+ gel documentation systems offer high performance and ease of use. They both contain a charge coupled device (CCD) camera to capture images in real time and allow you to accurately position your sample and generate optimized image data. The Gel Doc XR+ and ChemiDoc XRS+ systems use the same lighttight enclosure (the universal hood), which contains built-in UV and white light illumination, but different CCD cameras. Both systems feature dynamic flat fielding technology for superior image uniformity and accurate quantitation. Bio-Rad® Image Lab™ software controls image capture and optimization for your selected applications, analyzes results, and produces reports based on your specified output, all in a single workflow.

Gel Doc XR+ Imaging System Gel Doc XR+ imaging system is a high-resolution gel documentation system that allows fast, easy quantitation of gels and blots. Position your sample inside the imager and follow the onscreen steps to run a protocol with only one click. You can customize your applications within an existing protocol or create a new protocol using many options presented by the Image Lab software. Features include: 

Detection of dynamic ranges that cover >3 orders of magnitude

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Dynamic flat fielding specific to fluorescent and colorimetric applications

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Introduction 

Smart, application-based protocol setup using Image Lab software, which assists you by presenting appropriate filter and illumination sources for each application

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Ability to upgrade to the ChemiDoc XRS+ system

ChemiDoc XRS+ Imaging System In addition to the gel documentation applications of Gel Doc XR+ system, the ChemiDoc XRS+ imaging system offers sensitive chemiluminescent detection. The system includes a supersensitive 16-bit CCD camera that is deeply cooled for the long imaging times required for faint sample detection and for accurate quantification of image data. Features include: 

Suitability for imaging applications that require excellent sensitivity (chemiluminescent western blots)

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Smart, application-based protocol setup using Image Lab software, which assists you by presenting appropriate filter and illumination sources for each application

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Dynamic range >4 orders of magnitude

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Flexibility to image chemiluminescent, fluorescent, and colorimetric samples with dynamic flat fielding specific to each application

System Components CCD Camera and Lenses Either the Gel Doc XR+ or the ChemiDoc XRS+ camera is placed on top of a lighttight enclosure (the universal hood) for capturing images. The camera comes with a motorized zoom lens (MZL) that allows remote adjustment of the lens control functions (zoom, focus, and iris).

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System Components

A patent-pending software algorithm controls the MZL, giving the user automatic image focus once an initial calibration is performed during system installation. See the Technical Specifications table, included in the chapter which discusses your camera, for complete specifications of each system. A +1 diopter lens is factory installed to allow the entire sample stage to be visible. This lens should always remain on the MZL assembly.

Universal Hood The universal hood is designed to capture fluorescent and chemiluminescent images without using a photographic darkroom. The enclosure has built-in white light epi-illumination and UV transillumination. For easy sample loading, the UV transilluminator is located in the drawer of the universal hood and can be accessed from the front of the enclosure. When not imaging, the lights in the darkroom enclosure turn off automatically. The universal hood has touchpad buttons to perform various functions; however, Image Lab software controls all of these functions remotely, removing any requirement for manual control of the lens and lights. Running a protocol overrides any touchpad input.

Image Lab Software Each system ships with a full version of Image Lab software. In addition to controlling the imager systems, image capture, and optimization, Image Lab software can be used to annotate and document images, analyze molecular weights (or base pairs, when imaging nucleic acid gels), and to determine accurate quantitation and purity of samples. You can print all or a subset of your data in a report. Alternatively, you can export your data to other software, such as Microsoft Office programs, for further analysis or presentation options. See Chapters 5 to 11 for detailed instructions on the software.

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Introduction

Emission Filters The universal hood can hold two different emission filters for fluorescent applications. No filter is required to image chemiluminescent samples. A standard filter (catalog #170-8081) is used for colorimetric (white light) applications and is included in the installation kit.

Optional Accessories Bio-Rad Laboratories, Inc. offers a selection of optional filters and illumination sources. See Appendix D, Accessories, for ordering information and a complete listing of accessory filters, UV light sources, optional parts, and replacement parts.

Printer For your convenience, Bio-Rad offers an optional USB printer for use with the Gel Doc XR+ and ChemiDoc XRS+ systems: the Mitsubishi thermal printer, (catalog #170-8089).

Conversion Screens White Light Conversion Screen The white light conversion screen (catalog #170-8001) is a phosphor screen that produces white light transillumination when placed on top of the UV transilluminator.

White Light Transilluminator An optional white light transilluminator (catalog #170-7950) can also be used with either system. The white light transilluminator plugs inside the universal hood and is controllable by the touchpad or the computer software.

XcitaBlue Conversion Screen The optional XcitaBlue™ screen kit (catalog #170-8182) is a UV to blue light conversion screen, which allows you to visualize DNA samples while protecting them from UV damage.

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