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Related Manuals for Thermo Scientific Applied Biosystems GeneChip System 3000
Summary of Contents for Thermo Scientific Applied Biosystems GeneChip System 3000
- Page 1 GeneChip System 3000 Instrument Operation and Use Publication Number MAN0028330 Revision A.0 For Research Use Only. Not for use in diagnostic procedures.
- Page 2 Affymetrix, Inc. 3450 Central Expressway Santa Clara, CA 95051 The information in this guide is subject to change without notice. DISCLAIMER TO THE EXTENT ALLOWED BY LAW, LIFE TECHNOLOGIES AND/OR ITS AFFILIATE(S) WILL NOT BE LIABLE FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING YOUR USE OF IT.
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Page 3: Table Of Contents
Contents CHAPTER 1 Introduction ........7 Product overview . - Page 4 CHAPTER 3 System operation basics ......18 Before you begin ............18 Start and shut down the system .
- Page 5 Fluidics station troubleshooting and assistance ........42 Troubleshooting decision tree .
- Page 6 APPENDIX A Specifications and labeling information... . 70 Specifications ............70 GeneChip fluidics station 450 .
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Page 7: Chapter 1 Introduction
Introduction Product overview The GeneChip™ Instrument System is a fully integrated platform for conducting your research using GeneChip brand probe arrays. We offer three versions of this system: The GeneChip Scanner 3000 7G System, GeneChip Scanner 3000 7G Whole- Genome Association System and the GeneChip Scanner 3000 Targeted Genotyping System. -
Page 8: Alerts
Chapter 1 Introduction Alerts Array: A microarray is a glass substrate with oligonucleotide probes. A plastic cartridge surrounds and protects the array and forms the array cartridge. Array also typically refers to the array cartridge. Fluidics station or FS450: GeneChip Fluidics Station 450. -
Page 9: General Chemical Safety
Chapter 1 Introduction General chemical safety General chemical safety Minimize contact with chemicals. Wear appropriate personal protective equipment when handling chemicals (for example, safety glasses, gloves, or protective clothing). Minimize the inhalation of chemicals. Do not leave chemical containers open. Use only with adequate ventilation (a fume hood). -
Page 10: Fluid Safety
Chapter 1 Introduction Fluid safety Fluid safety Reagent Contains Warnings/Precautions Toxic if swallowed and in contact with skin; causes skin irritation, serious eye irritation; may cause respiratory irritation. Avoid breathing and avoid contact Hyb Buffer 1 Tetramethylammonium chloride with skin or eyes; if contact occurs wash immediately. If skin irritation or rash occurs, seek medical advice. -
Page 11: Customer Support
Chapter 1 Introduction Customer support WARNING! Contact your Thermo Fisher Field Service Engineer (FSE) for instrument disposal information. Customer support Affymetrix, Inc. 3450 Central Expressway Santa Clara, CA 95051 Phone: 408-731-5572 FAX: 408-731-5950 Customer Support Email: support@thermofisher.com Phone: 1-888-362-2447 Before contacting technical support for unresolved issues, see "Troubleshooting"... -
Page 12: Chapter 2 System Overview
System overview The GeneChip System 3000 (GCS 3000) consists of hardware and software components for processing microarrays based on assay parameters. The GeneChip Data Collection (GCDC) software manages assay workflows. Hardware Standard The GCS 3000 comes with these standard hardware components: hardware ... -
Page 13: Fluidics Station 450
Chapter 2 System overview Hardware Fluidics station 450 Figure 2 Fluidics Station 450 The Fluidics Station 450 (Figure 2) consists of four modules installed in a single housing. Each module holds a single array and performs the hybridization, washing, and staining functions for that array. Up to eight stations can communicate with one system workstation. -
Page 14: Software
Chapter 2 System overview Software Software GCDC GCDC is the user interface for the system. It provides control of the instruments, assay workflow, and the data collection processes. When array finishes scanning, the data is processed by GCDC using the library file parameters. Data files are stored in the storage location (local or network) defined when configuring GCDC. -
Page 15: Launcher Modules
Chapter 2 System overview GCDC workflow overview Launcher modules Fluidics: Controls the Fluidics Station 450. Scanner: GeneChip 3000 (GCS3000) with Autoloader scanner software. Array Registration: Used to register samples and attributes. Data Viewer: Used for viewing image data and workflow status. ... -
Page 16: Registration
Chapter 2 System overview GCDC workflow overview Registration Registering the samples and arrays In GCDC, the Sample file is the beginning of the data chain for a given experiment. The sample information is stored in a Sample file with an ARR extension. The arrays used in analysis and data files produced by analysis are linked to this Sample File. -
Page 17: Gcdc File Types
Chapter 2 System overview GCDC file types GCDC file types Different types of information are collected by GCDC in different types of files: Information about the sample and experiment are collected in "Sample files". Probe array data generated during scanning and processing are collected in Data files of various types. -
Page 18: Chapter 3 System Operation Basics
System operation basics Before you begin Read this entire User Guide and familiarize yourself with the instrument, software, and procedure. Start and shut down the system Starting the Turn on the computer workstation to launch its Windows 10 Operating System. workstation Log onto the system using the username and password Starting the... -
Page 19: Using The Barcode Reader
Chapter 3 System operation basics Using the barcode reader IMPORTANT! You should not restart or shutdown the instrument control software when fluidics or scans are in progress. Doing so will result in a loss of data. Using the barcode reader Use the barcode reader to: ... -
Page 20: Chapter 4 Genechip Fluidics Station Fs450
GeneChip Fluidics Station FS450 Before you begin Familiarize yourself with the GeneChip Data Collection (GCDC) software interface before operating the Fluidics Station 450 (see Chapter 2, System overview). Also refer to the GCDC User Guide (P/N MAN0026726). IMPORTANT! You must read and understand the contents of this manual before operating the Fluidics Station 450 (fluidics station). -
Page 21: When To Contact Support
Chapter 4 GeneChip Fluidics Station FS450 When to contact support The fluidics station requires two people to lift and handle it safely. Each person should firmly grasp the base of the instrument at the end opposite the other to lift. ... -
Page 22: Modules
Chapter 4 GeneChip Fluidics Station FS450 About the instrument Modules The fluidics station contains four modules. The software and computer workstation control each of the four modules independently of the others. Each module holds one array cartridge and up to three vials. ... - Page 23 Chapter 4 GeneChip Fluidics Station FS450 About the instrument Figure 6 Fluidics Station 450 and components 3. Needle Lever 1. & 2. Wash block 4. LCD screen and Cartridge Holder 6. Sample Needles 9. Module Door 5. Waste Bottle 8. Cartridge Lever 7.
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Page 24: Connections
Chapter 4 GeneChip Fluidics Station FS450 Using the fluidics station 450 Connections Communication connections are shown in Figure 7 Figure 7 Location of the serial ports and On/Off switch CommLink Out Connectors (To terminator or cable to next fluidics station) CommLink In Connector Power Cable On/Off Switch (Power Main) -
Page 25: Fluidics Station Operation
Chapter 4 GeneChip Fluidics Station FS450 Fluidics station operation Fluidics station operation The information in this section is general because the number and types of steps required to process an array vary, as does the specific design of the assay and the contents of its array. -
Page 26: Fluidics Control
Chapter 4 GeneChip Fluidics Station FS450 Fluidics control Figure 9 Sample vials on sample holder with needle lever down. Note the orientation of vial caps Needle Lever Vials Fluidics control 1. At the Launcher window, double-click on The Fluidics Control window appears. (Figure 10) Figure 10 Fluidics Control window GeneChip System 3000 Instrument Operation and Use... -
Page 27: Fluidics Control Window
Chapter 4 GeneChip Fluidics Station FS450 Fluidics control Fluidics Control window Menu bar: Use to access to Fluidics Control functions. Tool bar: Quick access buttons to frequently used functions. Master controls: (Figure 11) (Left pane) Use to select a single protocol to run on multiple stations and/or modules. -
Page 28: Status Window
Chapter 4 GeneChip Fluidics Station FS450 Fluidics control Figure 12 Station Controls Status window The Status window (lower pane) displays 11 columns of status, as shown in Figure Figure 13 Status window Station ID: Fluidics station in operation. Module: Current module in operation. -
Page 29: Running Protocols
Chapter 4 GeneChip Fluidics Station FS450 Running protocols Running protocols Fluidics Control offers different options for selecting and running protocols. Priming fills the fluidics station lines with wash buffers and/or deionized water. The GeneChip Fluidics Station must be primed before it can be used to run assay protocols. -
Page 30: Running A Fluidics Station Protocol
Chapter 4 GeneChip Fluidics Station FS450 Running protocols 8. Click the Run All button. 9. Monitor the prompts in the Status window (also shown in the module LCD window). The fluidics station is ready to use when priming is completed and Priming done, Ready appears in the module LCD window. - Page 31 Chapter 4 GeneChip Fluidics Station FS450 Running protocols Load Cartridge: Flip cartridge lever up to engage cartridge septa needles into the septa (Figure 16). LCD screen indicates when cartridge engagement is correct. Figure 16 Flip the cartridge lever up to engage the cartridge septa needles into the septa, as shown.
- Page 32 Chapter 4 GeneChip Fluidics Station FS450 Running protocols Figure 18 Needle lever and vials When vials are loaded, gently but firmly press down on needle lever to insert the needles into the vials. Run commences automatically, as shown in Figure 19 Figure Figure 19 Press down on the needle levers to start the protocol.
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Page 33: Shutting Down The Fluidics Station
Chapter 4 GeneChip Fluidics Station FS450 Running protocols Figure 20 The sample vials on the sample holder with the needle lever down. Note the orientation of the vial caps. 12. After the fluidics protocol completes, you are prompted to: Eject Cartridge: Flip cartridge lever down and remove and inspect cartridge. - Page 34 Chapter 4 GeneChip Fluidics Station FS450 Running protocols Figure 21 Modules to be shut down In the Station Control pane, you can: Select individual check boxes for each module. A green box denotes a selected module. Click Check/Uncheck All Stations to select/deselect all displayed stations and modules.
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Page 35: Fluidics Station Care And Maintenance
Chapter 4 GeneChip Fluidics Station FS450 Fluidics station care and maintenance Fluidics station care and maintenance IMPORTANT! To maintain the cleanliness of the fluidics station and obtain the highest quality image and data possible, perform a weekly bleach protocol (see Fluidics station bleach protocol). -
Page 36: Bleach Cycle
Chapter 4 GeneChip Fluidics Station FS450 Fluidics station bleach protocol Bleach cycle 1. Disengage cartridge holder for each module by pressing down on the cartridge lever. Remove any array cartridges. (Figure 22) Figure 22 Disengaged washblocks showing cartridge levers in the down position; remove any cartridges Remove cartridges (if any) Washblocks disengaged... - Page 37 Chapter 4 GeneChip Fluidics Station FS450 Fluidics station bleach protocol 5. Insert waste line into the waste bottle. (Figure 23) Figure 23 Immerse the tubes into the 0.525% sodium hypochlorite solution. The waste line remains in the waste bottle. 6. Immerse all three wash and water lines of the fluidics station into the 500-mL bottle of bleach solution (Figure 23).
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Page 38: Rinse Cycle
Chapter 4 GeneChip Fluidics Station FS450 Fluidics station bleach protocol Figure 24 Press down on the needle levers to start the bleach protocol The fluidics station begins the protocol. After approximately 30 minutes, the LCD prompts you when the bleach cycle is over and the rinse cycle is about to begin. 11. - Page 39 Chapter 4 GeneChip Fluidics Station FS450 Fluidics station bleach protocol Figure 25 Immerse the three wash and water lines in the DI water bottle. Note: The waste line remains in the waste bottle. 4. Press down on the needle levers to begin the rinse cycle. When the rinse is completed (approximately 1 hour), the fluidics station brings the temperature back to 25°C and drains the lines with air.
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Page 40: Peristaltic Tubing Maintenance
Chapter 4 GeneChip Fluidics Station FS450 Peristaltic tubing maintenance Peristaltic tubing maintenance You must periodically replace the peristaltic tubing because of wear, contamination, or to avoid salt buildup. Inspect the tubing on a weekly basis and use the following procedure when needed. CAUTION! Wear gloves when changing tubing. - Page 41 Chapter 4 GeneChip Fluidics Station FS450 Peristaltic tubing maintenance Figure 27 Releasing the peristaltic tubing White Clamps IMPORTANT! Do not remove the module. Do not attempt to replace tubing where the module has been removed from the fluidics station case–this can damage the motor driver circuitry. 3.
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Page 42: Fluidics Station Troubleshooting And Assistance
Chapter 4 GeneChip Fluidics Station FS450 Fluidics station troubleshooting and assistance Fluidics station troubleshooting and assistance If problems arise with the fluidics station, use the following tables to locate the description that matches the problem. If you cannot find a solution, call customer support for assistance. - Page 43 Chapter 4 GeneChip Fluidics Station FS450 Fluidics station troubleshooting and assistance Figure 29 Troubleshooting decision tree, page 2 GeneChip System 3000 Instrument Operation and Use...
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Page 44: Problems And Solutions
Chapter 4 GeneChip Fluidics Station FS450 Fluidics station troubleshooting and assistance Problems and The table below lists alert messages. To resolve these alerts, follow the recommended solutions resolution in the current Worklist screen on the alert pane. Error Message Problem Possible Cause Possible Solution Missing Fluid Error... - Page 45 Chapter 4 GeneChip Fluidics Station FS450 Fluidics station troubleshooting and assistance Error Message Problem Possible Cause Possible Solution Error While Draining Cartridge is not filling Defective septa in Follow the recommended resolution. You or draining properly. cartridge. may need to use a new cartridge. Error While Filling Add more sample solution to sample vial.
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Page 46: Error Message Meanings
Chapter 4 GeneChip Fluidics Station FS450 Fluidics station troubleshooting and assistance Error Message meanings The table below lists common error messages and meanings. To resolve these alerts, follow the recommended resolution in the current Worklist screen on the alert pane. Error Message Meaning Temperature Timeout... -
Page 47: Other Problems And Solutions
Chapter 4 GeneChip Fluidics Station FS450 Fluidics station troubleshooting and assistance Other problems The table below lists other problems and their solutions. Follow the recommended and solutions resolution in the current worklist screen on the Alert pane. Problem Possible Cause Possible Solution Air bubbles left in Air bubble in wash line... -
Page 48: When To Contact Support
Chapter 4 GeneChip Fluidics Station FS450 When to contact support When to contact support Under any of the following conditions, unplug the instrument from the power source and contact support: When the power cord is damaged or frayed. If any liquid has been spilled into the instrument. - Page 49 Chapter 4 GeneChip Fluidics Station FS450 Fluidics station LCD messages Message Meaning Draw 1st Stain Empty, draw sample to both sensors. Draw 2nd Stain Empty, draw sample to both sensors. Draw 3rd Stain Empty, draw sample to both sensors. EJECT CARTRIDGE Prompt for removal of cartridge.
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Page 50: Chapter 5 Genechip Scanner 3000 With Autoloader
GeneChip Scanner 3000 with AutoLoader Before you begin Familiarize yourself with the GCDC software interface (see Chapter 2, System overview) before operating the GeneChip Scanner 3000 (Scanner 3000). Also refer to the GeneChip Data Collection User Guide (P/N MAN0026726) IMPORTANT! You must read and understand the contents of this manual before operating the scanner. -
Page 51: Safe Operation
Chapter 5 GeneChip Scanner 3000 with AutoLoader Safe operation Safe operation WARNING! Do not remove the external case or skin or scanner cover of the AutoLoader. Use the scanner only as instructed in this manual. Do not attempt to service the instrument. Only qualified service engineers can open and service the scanner. -
Page 52: Location Of Safety Symbols
Chapter 5 GeneChip Scanner 3000 with AutoLoader Safe operation WARNING! Laser radiation when open. Avoid direct exposure to laser beam. The lasers can cause serious injury if the instrument is not operated in accordance with instructions in this user guide. IMPORTANT! Scanner is a Class 1 laser product when the laser is enclosed in the scanner case. - Page 53 Chapter 5 GeneChip Scanner 3000 with AutoLoader Safe operation Figure 32 Safety symbols - Back panel On Back Panel 12-0008 64-0177 Label personnel warning 64-0178 Label Heavy Object Figure 33 Safety symbols - Right panel On Right Panel 10-0196 Label 64-0034 UL Label Combo Label 64-0998 Caution Class 3b Laser GeneChip System 3000 Instrument Operation and Use...
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Page 54: Electrical Safety
Chapter 5 GeneChip Scanner 3000 with AutoLoader Safe operation Electrical safety The scanner is designed for input voltage from 100 to 240 VAC nominal, 50 to 60 Hz. Note: The scanner power supply auto-detects input voltage and configures itself. CAUTION! The power supply cord is used as the main disconnect device. -
Page 55: Connections
Chapter 5 GeneChip Scanner 3000 with AutoLoader Connections Connections IMPORTANT! Permit only an field service representative to service or change the instrument cable connections (see Figure 34 Figure 35). Workstation connections Figure 34 Workstation cable connections Monitor Internet connection Fluidics Scanner Power GeneChip System 3000 Instrument Operation and Use... -
Page 56: Scanner: Rear Connections
Chapter 5 GeneChip Scanner 3000 with AutoLoader Connections Scanner connections Figure 35 Scanner connections Cable Receptacle to Workstation Circuit Breaker (Reset button) Upper Drain Tube Lower Drain Tube Power Cable GeneChip System 3000 Instrument Operation and Use... -
Page 57: Scanner Indicator Lights And On/Off Button
Chapter 5 GeneChip Scanner 3000 with AutoLoader Scanner indicator lights and on/off button Scanner indicator lights and on/off button The front panel buttons and indicators as shown in Figure Figure 36 Scanner 3000 Indicator Lights 1. AutoLoader Indicator Light 2. Scanner Indicator Light 5. -
Page 58: Indicator Lights Summary Table
Chapter 5 GeneChip Scanner 3000 with AutoLoader Scanning arrays Indicator lights summary table Table 2 Light colors and meanings Condition Green Yellow Blue Blue Scanner Meaning Scanner Light Light Indicator Light Indicator Light Initial boot up Initial power up; embedded PC takes control Scanner boot up On Embedded PC takes control of scanner boot up Laser warm up... -
Page 59: Loading Arrays Into Carousel
Chapter 5 GeneChip Scanner 3000 with AutoLoader Scanning arrays 1. On back of array cartridge, clean excess fluid from around septa. (Figure 38) Figure 38 Applying Tough-Spots to array cartridge septa 2. Carefully apply one Tough-Spot over each of the two septa and press to ensure that the spots remain flat. - Page 60 Chapter 5 GeneChip Scanner 3000 with AutoLoader Scanning arrays 2. Load Carousel into AutoLoader and turn carousel until alignment pin seats into alignment hole. (Figure 40) Figure 40 Loading the carousel into the AutoLoader Alignment Hole Carousel Mounting Key Flat Alignment Pin Alignment Key in the Autoloader...
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Page 61: Starting The Scanner
Chapter 5 GeneChip Scanner 3000 with AutoLoader Scanning arrays Figure 41 Inserting and turning the carousel. The carousel must be seated and flush with the housing. Note: You may have to turn the carousel several times before it seats into the alignment pin and alignment key. - Page 62 Chapter 5 GeneChip Scanner 3000 with AutoLoader Scanning arrays Figure 42 Scan Options - Disable AutoLoader 2. Click OK. A dialog window appears prompting you to restart the scanner. (Figure 43) Figure 43 Scan Control - Restart Scanner 3. Click OK to acknowledge the message. 4.
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Page 63: Cleaning And Maintenance
Chapter 5 GeneChip Scanner 3000 with AutoLoader Cleaning and maintenance Cleaning and maintenance Keep the scanner clean and free of dust. Dust buildup can degrade performance. Wipe the exterior surfaces clean using a mild dish detergent solution in water. Do use ammonia-based cleaners or organic solvents, such as alcohol or acetone, to clean the system because they may damage the exterior surfaces. -
Page 64: Scanner Operation Issues Table
Chapter 5 GeneChip Scanner 3000 with AutoLoader Troubleshooting Scanner operation issues table Issue Explanation If communications are GCDC notes the failure and opens an alert that says “Cannot connect to scanner” or interrupted during a scan. For something similar. However, there are two issues to note. First, GCDC reports such a failure example, by a faulty cable only after a network time-out of about 30 seconds. -
Page 65: Scanner Error Messages
Chapter 5 GeneChip Scanner 3000 with AutoLoader Removing a lodged array cartridge manually Problem Possible Cause Corrective Action Scanner overheats Heater Failure Call technical support. TE failure TE hot fans vent blocked Call technical support. Autofocus routine fails to Salt buildup on array cartridge substrate Check for salt on chrome border. - Page 66 Chapter 5 GeneChip Scanner 3000 with AutoLoader Removing a lodged array cartridge manually Figure 44 Hole plug 5. Use a standard, flat (-) screwdriver and gently slide it down through the hole making sure not to damage the shaft and spring that are protruding into the hole. When the screwdriver stops, it should be in contact with the Scanner Y stage screw.
- Page 67 Chapter 5 GeneChip Scanner 3000 with AutoLoader Removing a lodged array cartridge manually Figure 45 Slot pin and pinch rollers Pinch rollers Slot Pin 8. Insert a 3/16-inch hex driver into the hole that is located on the front of the AutoLoader housing on the left.
- Page 68 Chapter 5 GeneChip Scanner 3000 with AutoLoader Removing a lodged array cartridge manually 10. Grab and hold the array with your fingers. Using your other hand slowly slide the slot pin (Step 7) back to the left. This should open up the pinch rollers. Pull the array out.
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Page 69: When To Contact Support
Chapter 5 GeneChip Scanner 3000 with AutoLoader When to contact support When to contact support Under any of the following conditions, unplug the instrument from the power source and Technical Support support: When the power cord is damaged or frayed. ... -
Page 70: Appendix A Specifications And Labeling Information
Specifications and labeling information Specifications GeneChip fluidics station 450 Table 3 Fluidics Station 450 Specifications Height 15.8 inches (40.2 cm) Width 28 inches (71.1 cm) Depth 16.1 inches (41 cm) Weight 80 pounds (36.3 kg) Voltage 100-240 VAC, 3 A; 300 watts Operating Temperature Range 15 to 30°C Operating Humidity Range 10 to 90% RH (non-condensing) -
Page 71: Hybridization Oven
Appendix A Specifications and labeling information Specifications Table 4 Scanner 3000 Specifications Weight without 70 pounds (31.8 kg) AutoLoader Weight with AutoLoader 105 pounds (47.6 kg) (fully loaded) 100-240 VAC, 50-60 Line (Mains) Voltage Current 4-2 Amps Excitation 532 nm (green) laser, wavelength 10 mW maximum Emission Filter... -
Page 72: Labeling Symbols
Appendix A Specifications and labeling information Labeling symbols Labeling symbols Symbol/Label Statement/Meaning Part/Catalog Number Read Safety Data Sheet Unique Device Identifier Lot Number Expiration Date (YYYY–MM) Note: Kit expires on the last day of the month. Temperature Limitation Contains Sufficient for <n> tests Hazards Irritant Consult Instructions for Use... -
Page 73: Appendix B Collecting Log Files
Collecting log files Using the log collector Log files are produced by different GCDC components. The logs provide a record of the tasks performed by different components, such as the migration tools and installer. These log files provide useful information for troubleshooting problems and may be requested by your support person. - Page 74 For support visit thermofisher.com/support or email techsupport@lifetech.com thermofisher.com 1 March 2023...
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