Affymetrix GeneChip Fluidics Station 450 User Manual
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Affymetrix GeneChip Fluidics Station 450 User Manual

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Affymetrix
GeneChip
Fluidics Station
®
®
450/250
User's Guide
P/N 08-0092 Rev. G
April, 2006

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Summary of Contents for Affymetrix GeneChip Fluidics Station 450

  • Page 1 Affymetrix GeneChip Fluidics Station ® ® 450/250 User’s Guide P/N 08-0092 Rev. G April, 2006...
  • Page 2 Affymetrix product only in accordance with the manual and written instructions provided by Affymetrix. You understand and agree that except as expressly set forth in the Affymetrix terms and conditions, that no right or license to any patent or other intellectual property owned or licensable by Affymetrix is conveyed or implied by this Affymetrix product.

  • Page 3: Table Of Contents

    Contents CHAPTER 1 The Fluidics Station 450/250 Introduction Instrument Components Accessory Items How the Fluidics Station Works CHAPTER 2 Using the Fluidics Station 450/250 Introduction Starting the Fluidics Station Handling the Probe Array Cartridge Setting Up an Experiment Defining the Experiment Priming the Fluidics Station Washing and Staining the Probe Array Customizing the Protocol...
  • Page 4 GeneChip Fluidics Station 450 User’s Guide ® APPENDIX B Using More Than One Fluidics Station Introduction APPENDIX C Specifications Introduction APPENDIX D Warranty Warranty APPENDIX E Parameters and Messages Introduction LCD Messages INDEX...

  • Page 5: The Fluidics Station 450/250

    Chapter The Fluidics Station 450/250...
  • Page 6 Chapter...

  • Page 7: Introduction

    Introduction This chapter introduces the Affymetrix GeneChip Fluidics Station 450/250 ® ® and its components, gives an overview of how the fluidics station works, and covers the safe use of the fluidics station. Note that the Fluidics Station 250 is identical to the 450 except that, instead of four modules, only two modules are present.
  • Page 8 GeneChip Fluidics Station 450 User’s Guide ® FS450 FEATURES Table 1.1 FS-450 Features Feature Description Benefit 3 position sampling • System will accept 1 to 3 vials. • Flexible loading and operation to • System can detect the meet script and user with individual vial presence/absence of vials in the requirements.
  • Page 9 Affymetrix Technical Support representative. • Do not use the fluidics station in ways not specified by Affymetrix. Doing so may impair the protections provided by the fluidics station. Do not place hands or fingers inside the cartridge holder. Under fault conditions, the area behind the cartridge holder can have temperatures that rise to 100°C or higher.
  • Page 10 GeneChip Fluidics Station 450 User’s Guide ® Caution Notices: CAUTION • You must have read and understood the contents of this manual before attempting to operate this fluidics station. CAUTION • The power supply cord is used as the main disconnect device.
  • Page 11 Wycombe Lane, Wooburn Green, High Wycombe HP10 0HH United Kingdom E-mail: supporteurope@affymetrix.com Tel: +44 (0) 1628 552550 Fax: +44 (0) 1628 552585 Affymetrix Japan, K. K. Mita NN Bldg 16 Floor, 4-1-23 Shiba, Minato-ku, Tokyo 108-0014 Japan Tel: (03) 5730-8200 Fax: (03) 5730-8201 www.affymetrix.com...

  • Page 12: Instrument Components

    Wash A and Wash B reagents. The modules are numbered 1 through 4 near the LCD window. The GeneChip Fluidics Station 450/250 includes the following components. Figure 1.1 on page 1.
  • Page 13 chapter 1 | The Fluidics Station 450/250 6. Needle Lever 7. LCD Window 3 & 4. Wash block and Cartridge Holder 8. Wash B Bottle 8. Wash A Bottle 9. DI Water Bottle 10. Waste Bottle 11. Sample Needles (extended) 2.

  • Page 14: Accessory Items

    GeneChip Fluidics Station 450 User’s Guide ® Accessory Items Affymetrix provides the following accessories for Fluidics Station 450/250. Table 1.2 FS-450 accessories list Part Number Description Quantity 340011 Assy, Terminator Plug 350001 Assy, cable, CPU, DBP9,3/F 350014 Cord Power 370013...

  • Page 15: How The Fluidics Station Works

    • expel the staining solution to the waste line; • fill the cartridge with wash solution for scanning; • clean the module tubing and needles for the next cartridge to be processed. 5. After washing and staining, the Affymetrix GeneChip Scanner 3000 ®...
  • Page 16 In addition to the preceding protocol, the fluidics station can perform variations of the steps described in the protocol and can run other protocols. For more information about the protocols that can be performed on the fluidics station, please contact your Affymetrix ® Technical Support representative.

  • Page 17: Using The Fluidics Station 450/250

    Chapter Using the Fluidics Station 450/250...
  • Page 18 Chapter...

  • Page 19: Introduction

    Introduction This section describes how to use the Affymetrix GeneChip Fluidics Station ® ® 450/250 with fluidics protocols. Starting the Fluidics Station Check to ensure that the fluidics station is connected to the power main through the power cord provided.

  • Page 20: Handling The Probe Array Cartridge

    GeneChip Fluidics Station 450Dx User’s Guide ® Lid Release Buttons CommLink Out (Note: these Connector buttons may (to terminator or be present or cable to next absent fluidics station) depending on the model of the fluidics station.) ON/OFF CommLink In Connector Switch (Power Main)

  • Page 21: Setting Up An Experiment

    chapter 2 | Using the Fluidics Station 450/250 substances, such as lotions or ink, can fluoresce. If the surface of the probe array chip is noticeably dirty, you should carefully clean the chip with a nonabrasive laboratory tissue. Figure 2.2 The GeneChip probe array cartridge ®...

  • Page 22: Priming The Fluidics Station

    Please consult the probe array package insert that came with the cartridge kit for the appropriate wash buffer solutions, or contact your Affymetrix Technical Support representative. Remove any loaded cartridges and observe for possible leaks since the system will not report errors during the Prime protocol.

  • Page 23: Washing And Staining The Probe Array

    chapter 2 | Using the Fluidics Station 450/250 Figure 2.3 Select the protocol from the drop-down list. Follow the instructions in the LCD window as the prime progresses. You must load standard 1.5mL vials in the sample holders of each module that is to be primed.
  • Page 24 GeneChip Fluidics Station 450Dx User’s Guide ® In the Protocol drop-down list, choose the protocol that matches the cartridge type (Figure 2.4). Figure 2.4 Select the protocol from the drop-down list. You can also choose a customized hybridization-wash or wash protocol here.
  • Page 25 chapter 2 | Using the Fluidics Station 450/250 If prompted to “ ,” remove the vials from the Remove Vials sample holder of the fluidics station. If prompted to “ Load Cartridge ,” open the cartridge holder by pressing down on the cartridge lever to open the cartridge loading door.
  • Page 26 GeneChip Fluidics Station 450Dx User’s Guide ® Figure 2.5 Inserting the cartridge into the cartridge holder - note orientation and probe array label...
  • Page 27 chapter 2 | Using the Fluidics Station 450/250 Flip the cartridge lever up to engage the cartridge septa needles into the septa. Proper engagement of the washblock with the cartridge is indicated by a change in the message on the LCD (Figure 2.6).
  • Page 28 GeneChip Fluidics Station 450Dx User’s Guide ® To minimize damage to the probe array, the door closure forces are controlled. If proper engagement does not occur, simply press on the washblock cartridge door to complete the action. DO NOT FORCE UP THE CARTRIDGE LEVER. If prompted to “...
  • Page 29 chapter 2 | Using the Fluidics Station 450/250 biotinylated antibody in sample holder 2. Place one vial containing the streptavidin phycoerythrin (SAPE) solution in sample holder 3. If you are staining certain eukaryotic targets, you will use SAPE in vials 1 and 3.
  • Page 30 GeneChip Fluidics Station 450Dx User’s Guide ® Needle Lever in Up Position Vials Figure 2.7 The samples vials on the sample holder with the needle lever up — note the orientation of the vial caps. When you place the vials into the holders, orient the vial caps toward you so that the vials seat snugly into their respective holders.
  • Page 31 chapter 2 | Using the Fluidics Station 450/250 Figure 2.8 Press down on the needle lever to begin the run.
  • Page 32 GeneChip Fluidics Station 450Dx User’s Guide ® Needle Lever Vials Figure 2.9 The vials on the sample holder with the needle lever down- note the orientation of the vial caps. As the staining run progresses, check to ensure that the cartridge is filling properly and that bubbles are not forming.
  • Page 33 chapter 2 | Using the Fluidics Station 450/250 If bubbles are present in the cartridge, return it to the cartridge holder. Engage the cartridge by flipping up the cartridge lever to the closed position. The fluidics station will drain the cartridge and then fill it with a fresh volume of the last wash buffer used.

  • Page 34: Customizing The Protocol

    You must modify a protocol with the new parameters before you can run it on the fluidics station. Protocol changes will not affect runs in progress. For more specific instructions, refer to the GCOS user’s guide or contact your Affymetrix Technical Support representative.

  • Page 35: Shutting Down

    To maintain the cleanliness of the fluidics station and obtain the highest quality image and data possible, Affymetrix recommends performing a weekly bleach protocol. Please refer to Instrument Care and Maintenance on page 35 for further details.
  • Page 36 GeneChip Fluidics Station 450Dx User’s Guide ® Choose Shutdown_450 for all modules from the drop-down Protocol list in the Fluidics Station dialog box. Click the button for all modules. After the Shutdown protocol is complete, flip the ON/OFF switch to position.

  • Page 37: Instrument Care And Maintenance

    Chapter Instrument Care and Maintenance...
  • Page 38 Chapter...

  • Page 39: Introduction

    Introduction This chapter provides instructions on caring for and maintaining the instrument, and on troubleshooting if problems arise. INSTRUMENT CARE • Use a surge protector on the power line to the fluidics station. • Always run a Shutdown protocol when the instrument will be off or unused overnight or longer.

  • Page 40: Fluidics Station Bleach Protocol

    You can find the current version of the protocol at www.affymetrix.com/support/technical/fluidics_scripts.affx. THE BLEACH CYCLE To avoid carryover, or cross contamination, from the bleach protocol, Affymetrix recommends the use of dedicated bottles for bleach and DI water. You can obtain additional bottles from Affymetrix. Table 3.1 Affymetrix recommended bottles...
  • Page 41 chapter 3 | Instrument Care and Maintenance Remove cartridges (if any) Washblocks disengaged with cartridge lever down Figure 3.1 Disengaged washblocks showing cartridge levers in the down position, remove any cartridges Prepare 500mL of 0.525% sodium hypochlorite solution using deionized water. For example: follow these directions to make 500mL of bleach.
  • Page 42 GeneChip Fluidics Station 450 User’s Guide ® The shelf life of this solution is 24 hours. After this period, you must prepare a fresh solution. Each fluidics station with four modules requires 500mL of the 0.525% sodium hypochlorite solution. Place on the fluidics station an empty one liter waste bottle, a 500 ml bottle of bleach and a one liter bottle of DI water as shown in Figure 3.2.
  • Page 43 Figure 3.2 The bleach cycle. Immerse the tubes into the 0.525% sodium hypochlorite solution. The waste line remains in the waste bottle. Open GCOS, Microarray Suite, or the current version of the Affymetrix Run → Fluidics... control software. Click from the menu. Alternatively, click the down arrow Protocol list on the toolbar.
  • Page 44 GeneChip Fluidics Station 450 User’s Guide ® Figure 3.3 The Fluidics Station protocol window: select all modules. Choose the current bleach protocol (in the current example, it is BLEACHv2_450) for each of the respective modules in the Protocol drop-down list. Select all four modules, 1 to 4, and click .
  • Page 45 chapter 3 | Instrument Care and Maintenance Figure 3.4 Press down on the needle levers to start the bleach protocol. The fluidics station will begin the protocol and begin to empty the lines and perform the cleaning cycles using bleach solution. After approximately 30 minutes, the LCD will prompt you when the bleach cycle is over and the rinse cycle about to begin.
  • Page 46 GeneChip Fluidics Station 450 User’s Guide ® THE RINSE CYCLE Once the bleach cycle has finished, the second part of the protocol is a rinse step. This step is essential to remove all traces of bleach from the system. Failure to complete this step can result in damaged arrays.
  • Page 47 chapter 3 | Instrument Care and Maintenance Press down on the needle levers to begin the rinse cycle. The fluidics station will empty the lines and rinse the needles. When the rinse is completed after approximately one hour, the fluidics station will bring the temperature back to 25°C and drain the lines with air.
  • Page 48 For systems in routine use, Affymetrix recommends monthly replacement of the tubing. To ensure proper performance, use only tubing available from Affymetrix. This tubing is manufactured to the required specifications to ensure proper fluid delivery and array performance. You can obtain additional tubing by ordering from...
  • Page 49 chapter 3 | Instrument Care and Maintenance Peristaltic Tubing Figure 3.6 Module door open showing peristaltic tubing Open the white clamps to release tubing on both sides. See Figure 3.7. Do not attempt to replace the tubing on a module where the module has been removed from the case of the fluidics station.
  • Page 50 GeneChip Fluidics Station 450 User’s Guide ® White Clamp Figure 3.7 Releasing peristaltic tubing Pull tubing off while gently turning the peristaltic pump head. Discard old tubing. Replace tubing with new peristaltic tubing supplied with the accessory kit as described below: Attach one end of the new tubing to the fitting on the right at the top of the pump enclosure.

  • Page 51: Troubleshooting And Assistance

    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 Affymetrix Technical Support for assistance. TROUBLESHOOTING DECISION TREE The following simple flow charts (Figure 3.8...
  • Page 52 GeneChip Fluidics Station 450 User’s Guide ® Figure 3.8 Troubleshooting decision tree, page 1...
  • Page 53 chapter 3 | Instrument Care and Maintenance Figure 3.9 Troubleshooting decision tree, page 2...
  • Page 54 Clean or Prime script fluidics station. with fresh deionized (DI) water to flush out salt blockage. Call Affymetrix Techni- Missing Fluid Failure of one of the cal Support for service. fluidics sensors. Error Loosen the tubing...
  • Page 55 Common error messages, their meanings, probable causes and solutions Error Message Problem Possible Cause Solution Recovered less Loose tubing attach- Call Affymetrix Techni- sample than ini- ments inside the flu- cal Support for service. tial input during idics station. Recover script.
  • Page 56 Recovery script. • Attempt to rerun script if sample loss can be Invalid tolerated. If problem Command persists, contact Affymetrix for service • If sample loss cannot be tolerated, do not attempt to rerun script. Contact Affymetrix for service Temperature...
  • Page 57 Possible Cause Solution Home script and Valve Motion run desired script again If problem persists, con- Error tact Affymetrix for ser- vice. Home script and Valve Not run desired script again If problem persists, con- Homed tact Affymetrix for ser- vice.
  • Page 58 GeneChip Fluidics Station 450 User’s Guide ® MEANING OF ERROR MESSAGES The following lists some of the common error messages and what they mean (Table 3.4). Table 3.4 Common error messages Error Message Meaning The script contains a command that can not be executed because its command “Invalid Command”...
  • Page 59 chapter 3 | Instrument Care and Maintenance Table 3.4 Common error messages Error Message Meaning “Stage C” “WashA” “Sense/Threshold” “960/890” The Pump command completed its step count before the conductivity sensor determined that the cartridge contained a solution with conductivity below the set threshold value.
  • Page 60 Extra flashing on the Use another cartridge, cartridge. or call Affymetrix Tech- nical Support for service. Salt buildup on the car- tridge needles. Run the Clean script with fresh DI water to flush out salt blockage.

  • Page 61: When To Contact Technical Support

    • if, after service or calibration, the instrument does not perform to the specifications stated in Instrument Specifications on page If the instrument must be returned for repair, call Affymetrix Technical Support. Make sure you have the model and serial number.
  • Page 62 Wycombe Lane, Wooburn Green, High Wycombe HP10 0HH United Kingdom E-mail: supporteurope@affymetrix.com Tel: +44 (0) 1628 552550 Fax: +44 (0) 1628 552585 Affymetrix Japan, K. K. Mita NN Bldg 16 Floor, 4-1-23 Shiba, Minato-ku, Tokyo 108-0014 Japan Tel: (03) 5730-8200...

  • Page 63: Appendix A Customer Module Replacement Procedure

    Appendix Customer Module Replacement Procedure...
  • Page 64 Appendix...

  • Page 65: Introduction

    Introduction This section describes the procedure to replace a Fluidics Station 450 or 250 module in the field. Warning: To ensure user safety, avoid contact with any internal components in the instrument base while removing or installing modules unless specifically indicated by these instructions.
  • Page 66 GeneChip Fluidics Station 450 User’s Guide ® MODULE REMOVAL The procedure below shows you how to remove a module. You can also refer to quick reference card, P/N 08-0099, Fluidics Station 450/250 Module Replacement Procedure Tools Needed: Standard flathead screwdriver When making connections, always turn off power to all devices in the chain.
  • Page 67 appendix A | Customer Module Replacement Procedure Grounding Drain Tube (Waste Conduit) Clear Waste Lines Color-Coded Reagent Lines 1/8 -turn Quck Release Fitting Figure A.1 Components under the fluidics station cover. Note that in some of the newer FS-450 versions, the side buttons may no longer be present and the drip tray and supply lines may be different.
  • Page 68 GeneChip Fluidics Station 450 User’s Guide ® quick-disconnect fittings, and tuck the lines into the space around the eight-way valve. See Figure A.2. Figure A.2 Disconnect the color-coded reagent line tubes Open the software and run the DRAIN_450 script until completion. The DRAIN script pumps the residual liquid in the reagent lines out to waste to reduce the probability that a droplet of buffer will fall from the disconnected ends of the lines onto one of the PC boards.
  • Page 69 appendix A | Customer Module Replacement Procedure is the large chrome-angled tube running along the back). See Figure A.3. Figure A.3 Disconnect the clear, waste line tubes from the waste line. Ensure that no scripts are running on the supporting workstation and no scripts are running on the FS450 for which the module replacement is required.
  • Page 70 GeneChip Fluidics Station 450 User’s Guide ® base of the module, between the vial holder and pump door. See Figure Figure A.5. Take care not to strip the retaining screw. This screw is captive on the module panel; you cannot remove it from the panel. You must gradually pull the module out toward you as you turn the screw otherwise you will strip the screw.
  • Page 71 Grasp the module using both hands as shown and gently pull module out. Place the defective module in the new module shipping packaging for return to Affymetrix. Instructions for returning the module are contained within the package. To ensure safety, avoid contact with any internal components in the...

  • Page 72: New Module Installation

    GeneChip Fluidics Station 450 User’s Guide ® New Module Installation The procedure below shows you how to install a new module. Holding the new module in a secure manner, position the module such that it straddles the exposed rails in the base. See Figure A.6.
  • Page 73 appendix A | Customer Module Replacement Procedure base to avoid pinching. Ensure module tubing is not in a position to be pinched. See Figure A.7. Figure A.7 Ensure that the module tubing will not be pinched by the new module. Reconnect the clear, waste line tubing to the drain tube.
  • Page 74 GeneChip Fluidics Station 450 User’s Guide ® drain tube). See Figure A.9 Figure A.10 for waste line tubing identification and inlet locations. Figure A.8 Reconnect the clear, waste line tubes from the module to the drain tube.
  • Page 75 appendix A | Customer Module Replacement Procedure From Cartridge to C on drain tube From Valve to V on drain tube Figure A.9 The “C,” or cartridge, waste line tubing and the “V,” or valve, waste line tubing...
  • Page 76 GeneChip Fluidics Station 450 User’s Guide ® Figure A.10 The locations of the C inlet and V inlet Align the screw at the bottom of the module into the threaded hole on the base. Using a slotted screwdriver, slowly rescrew the module retaining screw until the module is flush with the other modules.
  • Page 77 Appendix Using More Than One Fluidics Station...
  • Page 78 Appendix...
  • Page 79 Introduction Using one computer workstation, you can connect up to eight fluidics stations together. Follow these steps to connect more than one fluidics station to the computer workstation. When making connections, always turn off power to all devices in the chain.
  • Page 80 GeneChip Fluidics Station 450 User’s Guide ® Table B.1 Guide to setting DIP switches Left Middle Right The FS450 only reads the station address switch when power is first switched on. If the address is changed while the station is already powered on, the new address will not take effect until the station is turned off and then turned back on again.
  • Page 81 Appendix Specifications...
  • Page 82 Appendix...
  • Page 83 appendix C | Specifications Introduction INSTRUMENT SPECIFICATIONS Fluidics Station Dimensions: (height, depth, width) 40.2 x 41.0 x 71.1 cm or 15 13/16 x 16 1/8 x 28 inches Product Weight: Approximately 80 pounds or 36.3 kg Power Input: 100 to 240 V~, 3 A 300 watts or less Main supply voltage fluctuations not to exceed 10% of the nominal supply voltage.
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  • Page 85 Appendix Warranty...
  • Page 86 Appendix...
  • Page 87 D | Warranty Warranty The Affymetrix GeneChip Fluidics Station 450 and 250 are warranted to the ® ® buyer by Affymetrix. Please refer to the Affymetrix Terms and Conditions received with this instrument at time of sale for information on the warranty.
  • Page 88 GeneChip Fluidics Station 450 User’s Guide ® This page left blank.
  • Page 89 Appendix Parameters and Messages...
  • Page 90 Appendix...
  • Page 91 appendix E | Parameters and Messages Introduction This section describes the user alterable parameters and the LCD script messages and their meaning. USER-ALTERABLE PARAMETERS The following list shows the various parameters that you can change in configuring the fluidics station for a 4 wash staining (Table E.1).
  • Page 92 GeneChip Fluidics Station 450 User’s Guide ® The following are parameters for a 2-wash staining (Table E.2). Table E.2 Parameters for a 2-washing staining Parameter Name Description Parameter Values Default VAR: HybTime Hybridization Time (seconds) 86399 1800 VAR: HybTemp Hybridization Temperature (°C) VAR: FlushTemp1 Flush A Temperature (°C) VAR: FlushCycles1...
  • Page 93 appendix E | Parameters and Messages Table E.3 LCD Messages Message Meaning Purging with A Purges chip with ~ 2ml of buffer A at 25°C from bottom to top then to waste. Draining to Vial 1 Recovers stain to Vial #1 for reuse or disposal. Draining to Vial 2 Recovers stain to Vial #2 for reuse or disposal.
  • Page 94 GeneChip Fluidics Station 450 User’s Guide ® Table E.3 LCD Messages Message Meaning LOAD 3 EMPTY VIALS Prompt to load vials. Purging with water Purge with 5ml water to clean line. Washing needle 1 Performing wash needle #1 procedure. Purging with air Purge with air.
  • Page 95 Index...
  • Page 96 Index...
  • Page 97 I n dex Index dimensions 81 installation category 81 address more than one 77 setting 77 operating altitude 81 operating humidity 81 operating temperature 81 pollution degree 81 bubbles power input 81 power requirements 81 priming 20 care weight 81 components fluidics station operation instrument 10...
  • Page 98 GeneChip Fluidics Station 450 User’s Guide ® priming fluidics station 20 probe array handling problems and solutions protocol customizing 32 staining 13 regulatory remove vials setting the address setting up an experiment shutting down specifications starting up support information technical support troubleshooting and assistance warnings...

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