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Summary of Contents for BIO RAD 170-6555
- Page 1 GLYCO DOC GEL IMAGING SYSTEM INSTRUCTION MANUAL Catalog Numbers 170-6555 170-6556 170-6557 170-6558 170-6559...
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Page 2: Table Of Contents
Table of Contents TABLE OF CONTENTS Safety Section 1.0 Installation and Startup ....................1 1.1 Unpacking........................2 1.2 Set-up the Computer and Imager...................2 1.2.1 Installing the Camera Circuit Board in a Computer..........2 1.2.2 Setting Up the System..................4 1.2.3 Installing the Glyco Doc Software ................6 1.3 Verify system Operation ....................7 1.3.1 Starting the Glyco Doc Software ................7 1.3.2 Acquire an Image using the Test Plate..............8... - Page 3 Table of Contents Figures 1. Glyco Doc Imaging System ......................1 2. Installing the Camera Board in the Computer ................3 3. Glyco Doc Imaging System Cable Connections ................4 4. Imager Power and Filter Indicators ....................5 5. Glyco Doc Icon ..........................7 6. Test Plate............................8 7.
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Page 4: Safety
Safety SAFETY Warning Disconnect the Glyco Doc Imager before servicing. Refer servicing to Bio-Rad service personnel. This Glyco Doc Imager is certified to meet the I.E.C. 1010* safety standard. Certified products are safe to use when operated in accordance with the instruction manual. This safety certification does not extend to other equipment or accessories not I.E.C. -
Page 5: Section 1.0 Installation And Startup
Installation and Startup 1.0 INSTALLATION AND STARTUP The Glyco Doc Imaging System simplifies analysis of small format carbohydrate electrophoresis gels. Its primary components are the Imager, the Glyco Doc analytical software, and a host computer. The Imager is suitable for both fluorescent and visible dye applications. The Glyco Doc analytical software features auto- matic acquisition and analysis of fluorescent labeled oligosaccharide and monosaccharide gels, as well as DNA and Protein gels and gels stained with visible dyes. -
Page 6: Unpacking
Installation and Startup 1.1 UNPACKING Carefully inspect the shipping cartons for any damage which may have occurred in shipping. Severe dam- age to a carton may indicate damage to its contents. If you suspect damage to the contents may have occurred, immediately file a claim with the carrier in accordance with their instructions before contacting Bio- Rad Laboratories. -
Page 7: Installing The Camera Board In The Computer
Installation and Startup To install the camera board, follow the procedure below. 1. Turn off your computer and unplug the power cord. This procedure assumes the computer was previously set up and used for other applications. 2. Turn off all connected peripheral devices. Connected devices include printers, monitors, etc. -
Page 8: Setting Up The System
Installation and Startup 7. Place the Camera board in the slot The connector on the Camera board must face the back of the computer. Insert the board, pressing firmly so that it slips into place. 8. Re-mount the screw removed in Step 6. This screw will hold the board in place. -
Page 9: Imager Power And Filter Indicators
Installation and Startup To set-up the Imager, you need a Phillips head screw driver. Refer to Figure 4. 1. Locate the Filter Lock Screw on the bottom of the Imager and turn it counter clockwise, two com- plete turns. The Filter Lock Screw is encircled by an orange marker on the bottom of the Imager. The Filter is locked in place for shipping. -
Page 10: Installing The Glyco Doc Software
Installation and Startup 1.2.3 Installing the Glyco Doc Software Note If your purchase included a computer, proceed to section 1.3. Your computer was shipped with the Glyco Doc software installed. To install the Glyco Doc software, you need the following items: •... -
Page 11: Verify System Operation
Installation and Startup 1.3 VERIFY SYSTEM OPERATION This section provides a general description of the use of the Glyco Doc system. 1.3.1 Starting the Glyco Doc Software When you power-up the computer, monitor, and Imager, a series of self-test and configuration status mes- sages is displayed, followed by the C:\>, which is the indication that the system is ready. -
Page 12: Acquire An Image Using The Test Plate
Installation and Startup 1.3.2 Acquire an Image using the Test Plate To verify system operation, start by acquiring an image of the Test Plate. Note If you did not purchase a computer with the Glyco Doc system: Before doing any imaging, you must first create a Bright Field file. Refer to the chapter on Maintenance for discussion of the purpose of the Bright Field and the process for creating a Bright Field file IMAGE AREA SETUP PATTERN... - Page 13 Installation and Startup To acquire an image using the text plate, follow the procedure below. 1. Turn on the Imager and set the Filter Switch to 500 nm. The Power On/Off and Filter Switches are located on the rear of the Imager. The Filter Switch should be set to Carbohydrate, which uses a 500 nm filter.
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Page 14: Image Analysis Using The Image Provided With Your System
Installation and Startup 1.4 IMAGE ANALYSIS USING THE IMAGE PROVIDED WITH YOUR SYSTEM The key steps to analyzing an image are: • Open the image file (Use the image file demo1.RAW) • Adjust the image display • Find bands • Perform a standard lane analysis •... -
Page 15: Image Display, Control, And Status Windows
Installation and Startup Bio-Rad Glyco Doc Analytical Software Files Image Bands Options Window Help Mouse x=200 Grey=5451 Zoom Image Histogram Quan AutoScale Range: 5376 to 18175 Contrast Brightness Figure 7. Image Display, Control, and Status Windows 5. Selectively insert and mark a band or remove a marker from a band of no interest: •... - Page 16 Installation and Startup 7. Analyze band data as presented in the Band Tables. The following tables are available: Band Location Description Band Location | Total Gray Total Gray Degree of Polymerization Peak Gray Base Pairs Percent Luminance of Selected Bands Molecular Weight Quantity 8.
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Page 17: Preparing For Gel Imaging
Installation and Startup 1.5 PREPARING FOR GEL IMAGING This section discusses the preparation of gels prior to imaging. The table below provides some examples of how gels must be prepared before they are placed in the Imager tray. Table 1. Preparing Gels for Imaging CARBOHYDRATE GELS DNA GELS (STAINED WITH... -
Page 18: Example Of A Standard Lane Analysis
Installation and Startup 1.6 EXAMPLE OF A STANDARD LANE ANALYSIS In the oligosaccharide sample image (demo1.raw) provided with your Glyco Doc system, there must be at least nine Band Markers in the oligosaccharide standard lane or the analysis will fail and the error dialog box is displayed. -
Page 19: Section 2.0 Software Reference
Software Reference 2.0 SOFTWARE REFERENCE This chapter discusses each of the software functions. The chapter is organized according to the software’s menu structure. 2.1 FILES MENU Each of the Files drop down menu’s selections is discussed below. Open... Displays the Open File window, which lists all the files available to Glyco Doc and their location on the com- puter’s hard disk. - Page 20 Software Reference Densitometer Reports A printout is generated for each lane, with the Densitometer positioned next to its corresponding lane. All quantitative and migration data for that lane is included. The Densitometer report can be scaled in two ways: Normalized to each Lane - This report scales the densitometer output so that the brightest peak in each lane corresponds to the top of the densitometer scale for that lane’s output.
- Page 21 Software Reference Image File To export an image from Glyco Doc, so that it can be incorporated into a report or document created in a different application. In the Save As window that is displayed, 1. Use the File Name field to change the displayed filename’s extension to .RAW, which is required of all Image files.
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Page 22: Image Menu
Software Reference 2.2 IMAGE MENU To obtain the best image from which both image and band data files are derived, the Image menu offers a number of setup controls and options. Acquire This selection initiates image acquisition. It requires you to specify the type of gel to be imaged: Carbohydrate, DNA, or Protein, before bringing up the SE1000 Camera Control window. -
Page 23: Typical Exposure Strategies
Software Reference The Exposure Time is influenced by how intensely the fluorophore is emitting light. This, in turn, is pro- portional to the concentration of the substance containing the fluorophore in the gel; greater intensity means shorter exposure. The Exposure time... setting should prevent overexposure of bands of inter- est;... - Page 24 Software Reference Acquire Options These selections must be made before you acquire the image. Select Image Rectangle After you acquire the first image of a gel, you may be able to improve the quality of subsequent images by drawing an Image Rectangle over your area of interest. (The sensitivity of the camera becomes greater as you reduce the extremes of intensity in the imaging area.) To mark a region using the Image Rectangle, 1.
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Page 25: Bands Menu
Software Reference 2.3 BANDS MENU Glyco Doc identifies bands by looking for sudden drop-offs in intensity. Glyco Doc then groups bands according to the following definitions: • Lane: Glyco Doc defines a Lane as all bands in the same column. •... - Page 26 Software Reference Insert Band This selection allows you to insert a band which may otherwise have been overlooked by the automatic band marking function. Selecting Insert Band causes the Outline cursor to be displayed. By pressing the left mouse button and dragging, you draw the band’s outline. When you release the left mouse button, the band’s marker appears and the band data is included in the band tables.
- Page 27 Software Reference Set Quantitive Standard Band... This allows you to select a band other than the standard. Display Standard Plot on Log Scale This allows you to plot Size versus Rf for Protein and DNA gels. Band Information This is the data available for analysis and displayed in the band tables. (For a complete discussion of the Band Tables, refer to that section later in this chapter.) To display a band’s information, double click on its marker, or click once and select Band Information..
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Page 28: Options Menu
Software Reference 2.4 OPTIONS MENU The Options menu provides a number of display selection, each of which is discussed below. Reverse Palette When selected, the displayed image is reversed, so that a negative image becomes positive and a positive image becomes negative. HiLite Saturated Pixels When selected, saturated pixels are displayed in yellow. -
Page 29: Window Menu
Software Reference 2.5 WINDOW MENU This menu allows you to specify what type of data you want to display. Band Table A band table is a resizable and scrollable window displaying data about each marked band. This selection is a toggle function for hiding or displaying band tables. The different band tables are available by clicking on the word “Mode”... - Page 30 Software Reference Rf (Relative mobility) are determined by setting the center point of one band to have an Rf = 1 and that of another band to have an Rf = 0. All bands between those two points are given a value between 1 and 0 based on a linear scale.
- Page 31 Software Reference Show Selected Lanes This mode displays the intensity levels within a lane or compares between two or more lanes. Include the first lane by clicking on the number found at the top of the lane. Include additional lanes by holding down the <Ctrl>...
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Page 32: Section 3.0 Theory Of Operations
Theory of Operation 3.0 THEORY OF OPERATIONS During exposure, the Imager’s CCD (Charge Coupled Device) detector collects photons emitted by the fluo- rophore in a prepared gel. The detector is a semiconductor grid of approximately 180,000 cells for collecting these photons. Each cell in the grid can collect up to 65,535 charge units per exposure. If a cell receives more than 65,535 charge units, the excess charge units spill into the surrounding grid squares (in a phe- nomena called “blooming”), and that area of the gel is considered saturated. -
Page 33: Section 4.0 Maintenance And Troubleshooting
Maintenance and Troubleshooting 4.0 MAINTENANCE AND TROUBLESHOOTING In this chapter, the following Imager hardware maintenance procedures are given: • Replacing the UV Light • Cleaning the Excitation Filter • Creating a New bright field A trouble-shooting chart for the Imager is provided in Section 4.5. For trouble-shooting computer problems, consult the appropriate computer vendor’s documentation. -
Page 34: Inside The Imager
Maintenance and Troubleshooting 8. Perform the previous steps in reverse to install the new tube and close-up the Imager. 9. Create a new Bright Field file. Refer to Section 4.4. EXCITATION FILTER EMISSION FILTER Figure 10. Inside the Imager... -
Page 35: Cleaning The Excitation Filter
Maintenance and Troubleshooting 4.2 CLEANING THE EXCITATION FILTER The Excitation Filter is located immediately above the gel holder and just below the UV lamp. It is a glass square approximately 3.75” and is a metallic brown color. Follow the procedure below to replace the Excitation Filter. -
Page 36: Preparing Gel Plates
Maintenance and Troubleshooting 4.3 PREPARING GEL PLATES The gel plates should be free of smudges, blotches, or any film on both sides. Clean off any pieces of acry- lamide, fingerprints or lint which will appear as artifacts in the image. If the glass needs to be cleaned, we recommend using Kimwipes EX-L Lens Cleaning Station, sold as Kimwipes No. - Page 37 Maintenance and Troubleshooting 2. From the Image menu’s Acquire Options, select Make New Bright Field File. Follow the on-screen instructions, directing you to insert the Bright Field Plate. After the Bright field image is acquired, remove the plate. 3. Save the Bright Field file. After selecting OK at the prompt to save, the file is stored as se1000.brt.
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Page 38: Imager Troubleshooting
Maintenance and Troubleshooting 4.5 IMAGER TROUBLESHOOTING Try all appropriate actions in the chart below for the imaging problem you are experiencing, before calling a Bio-Rad technical representative (Appendix D). Table 3 Imager Troubleshooting Indication Problem Action Image is solid black in normal Imager is turned off. -
Page 39: Software Troubleshooting
Maintenance and Troubleshooting Table 3 (continued) Imager Troubleshooting Indication Problem Action Too little or too much of the Incorrect Image Rectangle. Reselect the Image Rectangle gel is being acquired. using the Select Image Rectangle command in the Image menu’s Acquire Options. -
Page 40: Appendix A. Initialization File
Initialization File APPENDIX A. INITIALIZATION FILE The GLYCODOC.INI initialization file defines the default options an application automatically selects when it is first envoked. Because it is a text file, it can be easily edited by the user. The Glyco Doc Imaging initial- ization file specifies: •... -
Page 41: Colors
Initialization File A.3 COLORS Colors are designated by their Red, Green, and Blue contents. Some common colors are: • 255 0 0 • Green 0 255 0 • Blue 0 0 255 • Yellow 255 255 0 • Tourquise 0 255 255 •... -
Page 42: Band Descriptions
Initialization File A.4 BAND DESCRIPTIONS The value set in the Band Associations Dialog Box is the band association pixel distance. It determines whether or not two bands are associated. • BandLinkOverlap=6 Band description settings are used by the Band Descriptions pulldown item. •... -
Page 43: Last Exposure Time
Initialization File [Monosaccharides] • KeyBand=GlcNAc • RF0Band=GlcNAc • RF1Band=GalNAc • BandNames=GlcNAc 50.00,Galactose 50.00,Glucose 50.00,Fucose 50.00,Mannose 50.00,GalNAc 50.00 [Oligosaccharides] • KeyBand=G4 • RF0Band=G12 • RF1Band=G4 • DP=4 • Quantity=50.0 • QuantBand=G4 • BandNames=G2,G3,G4,G5,G6,G7,G8,G9,G10,G11,G12,G13,G14 [Lane Descriptions] • Monosaccharides= • Oligosaccharides= • StandardsNames=Monosaccharides,Oligosaccharides A.5 LAST EXPOSURE TIME This reflects the last user-entered exposure time. -
Page 44: Appendix B. Imager Specifications
Imager Specifications APPENDIX B. IMAGER SPECIFICATIONS Imaging Type: Fluorescence, Transmittance Detector Type: CCD array, 753 x 244 pixels Light Source: UV lamp filtered for maximum output at 368 nm Imaging Resolution: Vertical resolution of 320 µm Excitation: Wavelength maximum output at 368 nm Imaging Area: 10 x 10 cm cassette holder, 8 x 8 cm imaging area Imager Dimensions:... -
Page 45: Appendix C. Warranty And Ordering Information
Warranty and Ordering Information APPENDIX C. WARRANTY AND ORDERING INFORMATION The Glyco Doc Imaging System is warranted for 1 year against defects in materials and workmanship. If any defects should occur during this warranty period, Bio-Rad Laboratories will replace the defective parts without charge. -
Page 46: Test Plate
Prices and part numbers are subject to change. Call for current prices. Catalog Number Description 170-6555 Glyco Doc Imager, 100/240 V, includes Glyco Doc imager, Glyco Doc analytical software, and Glyco Doc imager interface card and cable. 170-6557 Glyco Doc Imaging System, 100/240 V, includes Glyco Doc imager, Dell 486 computer with 8 MB RAM, 1.08 GB internal hard drive, and 230 MB internal optical... -
Page 48: Declaration Of Conformity
? O 2 @ 6 K ? O 2 @ 6 K ? O 2 @ 6 K ? O 2 @ 6 K ? O 2 @ 6 K ? O 2 @ 6 K ? O 2 @ 6 K ? O 2 @ 6 K ? O 2 @ 6 K ? O 2 @ 6 K ? - Page 49 Bio-Rad Laboratories, Inc. Life Science Bio-Rad Laboratories Main Office, 2000 Alfred Nobel Drive, Hercules, California 94547, Ph. (510) 741-1000, Fx. (510) 741-5800 Also in: Reagents Park, Australia, Ph. 02-9914-2800, Fx. 02-9914-2888 Wien, Austria, Ph. (1) 877 89 01, Fx. (1) 876 56 29 Nazareth, Belgium, Ph. 09-385 55 11, Fx. 09-385 65 54 Group Mississauga, Canada, Ph.
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