Affymetrix® GeneChip® Fluidics Station 400
Contents
1. WARN Affymetrix Fluidics Station User s Guide 1 Open the drop down door to the module to access the peristaltic pump tubing See Figure 3 2 on page 31 Peristaltic Tubing Figure 3 2 Module open showing peristaltic tubing 2 Open the white clamps to release tubing on both sides See Figure 3 3 on page 32 Do not attempt to replace the tubing on a module where the module has been removed from the case of the fluidics station AFFYMETRIX 31 32 CHAPTER 3 Instrument Care and Maintenance White Clamp Figure 3 3 Releasing peristaltic tubing 3 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 a Attach one end of the new tubing to the fitting on the right at the top of the pump enclosure b Insert the tubing into the clamp under the fitting without stretching the portion of the tubing between the fitting and the clamp There should be a small amount of slack in that portion of the tubing c Work the tubing into the pump head while slowly turning the pump d Insert the free end of the tubing into the other clamp and attach it to the other fitting e Close the drop down module door Order more replacement tubing Affymetrix Fluidics Station User s Guide 33 Troubleshooting and Assistance If problems2. Guide 700103 1 How the Fluidics Station Works For further instructions see Using the Fluidics Station 400 on page 17 Standard Hybridization and Wash Protocol 1 fluidics station protocol Use the Microarray Suite software to define an experiment and start the After preparing the target in the laboratory according to the relevant GeneChip probe array package insert place the labeled target solution into a sample vial Then place the vial into the sample holder on the fluidics station Place the appropriate cartridge into the cartridge holder on the selected module of the fluidics station and close the cartridge holder by pushing the holder into the module until it clicks into place Remove your hand from the exterior of the cartridge holder and engage the cartridge holder by lifting the cartridge lever quickly Avoid performing these two steps in the opposite order as doing so may damage the cartridge needles AFFYMETRIX s 11 12 CHAPTER 1 Introduction The target circulates through the cartridge and hybridizes to the GeneChip probe array The fluidics station will perform the following actions to hybridize the target to the cartridge The fluidics station will m draw target solution from the sample vial into the cartridge and mix it by alternately draining and filling the cartridge at a selected temperature m expel the target solution into the waste or into the sample vial m wash the cartrid
3. THE WRITTEN INSTRUCTIONS PROVIDED THEREWITH THAT BUYER PURCHASES FROM AFX OR ITS AUTHORIZED REPRESENTATIVE THE PURCHASE OF ANY PRODUCT S DOES NOT BY ITSELF CONVEY OR IMPLY THE RIGHT TO USE SUCH PRODUCT S IN COMBINATION WITH ANY OTHER PRODUCT S IN PARTICULAR i NO RIGHT TO MAKE HAVE MADE OR DISTRIBUTE OTHER PROBE ARRAYS IS CONVEYED OR IMPLIED BY THE PROBE ARRAYS ii NO RIGHT TO MAKE HAVE MADE IMPORT DISTRIBUTE OR USE PROBE ARRAYS IS CONVEYED OR IMPLIED BY THE INSTRUMENTS OR SOFTWARE AND iii NO RIGHT TO USE PROBE ARRAYS IN COMBINATION WITH INSTRUMENTS OR SOFTWARE IS CONVEYED UNLESS ALL COMPONENT PARTS HAVE BEEN PURCHASED FROM AFX OR ITS AUTHORIZED REPRESENTATIVE FURTHERMORE PROBE ARRAYS DELIVERED HEREUNDER ARE LICENSED FOR ONE 1 TIME USE ONLY AND MAY NOT BE REUSED THE PRODUCTS DO NOT HAVE FDA APPROVAL NO PATENT LICENSE IS CONVEYED TO BUYER TO USE AND BUYER AGREES NOT TO USE THE PRODUCTS IN ANY SETTING REQUIRING FDA OR SIMILAR REGULATORY APPROVAL OR EXPLOIT THE PRODUCTS IN ANY MANNER NOT EXPRESSLY AUTHORIZED IN WRITING BY AFX IN ADVANCE Patents Products may be covered by U S Patent No 6 114 122 and other U S or foreign patents Copyright 1997 2001 Affymetrix Inc All rights reserved Affymetrix Fluidics Station User s Guide Contents CHAPTER 1 _ Introduction 5 Warnings and Precautions 5 Regulatory 7 Customer Support Information 8 Instrument Components 8 Accessory Kit 10 How the Fluidics Station Wor
4. User s Guide 25 6 Shutting Down Click the Close button to leave the dialog box You should perform the Shutdown procedure at the end of a session Do not keep the fluidics station on if you will not use it again within the next 12 hours The instrument runs the risk of salt buildup 1 2 Replace wash bottles with bottles filled with deionized water From the Protocol drop down list choose Shutdown for all modules and then click the Run button for all modules Follow the instructions that appear in the LCD window As with the prime procedure a 1 5 mL microcentrifuge tube is required for each module After the Shutdown protocol is complete flip the ON OFF switch to the OFF position AFFYMETRIX s 26 CHAPTER 2 Using the Fluidics Station 400 Chapter 3 y Instrument Care and Maintenance 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 This will prevent salt crystals from forming within the fluidics system When not using the instrument leave the sample holder in the raised position with an empty vial in it This will prevent leakage of any fluids from the sample line into the system or onto the tabletop Always use distilled or deionized water
5. appear to pass through the centers of the holes in the 49 50 APPENDIX C washblock and gently tighten the screws Repeat this step until no leaks occur during priming 10 With the three horizontal screws on the top of the bezel and using the 5 32 hex key included in the accessory kit attach the white bezel to the front of the fluidics station 11 Attach the four screws to the bottom of the front bezel of the fluidics station using the same hex key included in the accessory kit 12 Close the top of the fluidics station iu D Fi A A Fag E z he E Specifications 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 Power Input 100 to 240 V 3 A 300 watts or less Main supply voltage fluctuations not to exceed 15 of the nominal supply voltage Temperature Operating 15 to 30 C Storage non operating 10 to 60 C Humidity Operating 10 90 RH non condensing Storage non operating 10 to 95 RH Other Pollution degree 2 Installation category II Electrical Supply The electrical supply shall meet the input specified on the instrument label Voltage fluctuations shall not exceed 15 nominal supply voltage Altitude lt 2000m 53 54 APPENDIX D hil E a Y Ag am a Warranty Warranty The Affymetrix Genech
6. appropriate wash buffer solutions or contact your Affymetrix Technical Support representative 2 Hitis not already open open Fluidics under the Run menu on the computer workstation gt The Fluidics Station dialog box appears If more than one fluidics station is present select the one to be primed in the drop down list 3 In the Fluidics Station dialog box click Protocol then choose Prime for each module under the Protocol drop down list Click the Run button for each module to be primed gt Follow the instructions in the LCD window as the prime progresses You must load a standard 1 5 mL microcentrifuge tube in the sample holder of each module that is to be primed The LCD window on the fluidics station and the Fluidics Station dialog box will indicate the status of the prime and when priming is completed Hybridizing the Target Solution to the Probe Array After you have primed the fluidics station it is ready to hybridize a sample For more specific information on hybridizing the target to the probe array cartridge refer to the appropriate package insert Affymetrix Fluidics Station User s Guide 21 Y Note il If it is not already open click Fluidics under the Run menu on the workstation gt The Fluidics Station dialog box appears If more than one fluidics station is present select the appropriate instrument from the drop down list In the Fluidics Station dialog box select the module that is ready
7. fits inside the sample vial Sample is pulled up and into the system through the sampling tube Cartridge Needles not shown in figure fit inside the septa on the cartridge or the washblock Fluids are circulated through the cartridge via the cartridge needles AFFYMETRIX s 9 10 CHAPTER 1 Introduction 6 LCD Window 5 Cartridge Lever 7 Lid Release Buttons 4 Washblock 8 WashB 9 DI Water Bottle 3 Cartridge Holder 2 Module Door 11 Metal Sampling Tube 1 Sample Holder Figure 1 1 The GeneChip Fluidics Station 400 and components Accessory Kit The GeneChip Fluidics Station 400 also includes an accessory kit Contents of Accessory Kit Component Item Part Number Terminator Plug Assembly 340011 1 Cable Assembly CPU DB9P M F 350001 1 Affymetrix Fluidics Station User s Guide Contents of Accessory Kit Component Item Part Number Power Cord 350014 1 4A Fuse 5 x 20 mm 370013 1 8 5 Silicone Peristaltic Tubing 400110 4 5 32 Handle Ball Tip Hex Driver 400113 1 1 4 Tip Flathead Screwdriver 400115 1 Washblock Assy 400116 2 500 mi Square Media Bottle Fluidics DI 400118 5 Water Buffer 1000 ml Square Media Bottle Fluidics Waste 400119 1 Bottle 9 64 T Handle Hex Driver 400127 1 Pre drilled Bottle Cap 400137 4 Sample Needle 410016 4 GeneChip Fluidics Station 400 User s
8. located on the sides of the fluidics station See Figure 1 1 on page 10 2 Unscrew the two screws on the bottom of the front bezel of the fluidics station using the 5 32 hex key included in the accessory kit 3 Unscrew the three horizontal screws on the top of the bezel inside the instrument using the same hex key included in the accessory kit 4 On all the modules remove all cartridges latch all cartridge holders and place the cartridge levers in the neutral or horizontal position 5 Pull the white bezel off the front of the fluidics station 6 Eject the washblock by pushing the cartridge lever down 7 Using a Phillips head screwdriver unscrew the two screws in the cartridge holder of the washblock that needs replacing 8 Mount the new washblock in the cartridge holder Confirm that the washblock is in the proper orientation i e that the top of the washblock is even with the top of the sensor block and that the dimples on the washblock lock into the front of the cartridge holder Apply a small amount of Loctite 222 ms to the nylon screw threads or the washblock threads Install screws and tighten until the screws bottom out Back off approximately 14 turn 9 Prime the module During priming observe the new washblock for leaks If leaks occur stop the Prime script loosen the four Phillips screws in the corners of the cartridge holder adjust the front part of the cartridge holder until the cartridge needles
9. to prevent contamination of the lines Change buffers with freshly prepared buffer at each system startup The fluidics station should be positioned on a strong level bench away from extremes in temperature and away from moving air Instrument Maintenance To ensure proper functioning of the fluidics station you should perform periodic maintenance Weekly Maintenance 1 To open the top to the fluidics station firmly push the lid release buttons located on the sides of the fluidics station See Figure 1 1 on page 10 Check the overflow tray for liquid If liquid is present absorb it with disposable wipes See Figure 3 1 on page 30 29 30 CHAPTER 3 Instrument Care and Maintenance U J 7 Waste Conduit a Fhe ASS Bee CW 4 Overflow Tray L Figure 3 1 Open chassis of fluidics station 3 Check for salt deposits around tubing and fittings Clean around tubing and fittings with a cotton swab if deposits are present If deposits persist there may be a leak in the tubing or fittings Call Affymetrix Technical Support if you suspect a leak Preventive Maintenance Peristaltic tubing is included in the accessory kit that comes with the fluidics station As needed replace the peristaltic pump tubing as follows IN Wear gloves when changing tubing and do not allow fluid from old tubing to spill onto surfaces
10. Affymetrix GeneChip Fluidics Station 400 User s Guide Version 5 0 For use with Affymetrix Microarray Suite Software For Research Use Only Not for use in diagnostic procedures Affymetrix Confidential 700103 rev 5 AFFYMETRIX Trademarks Affymetrix GeneChip BASTI AM 4 4 ly HuSNP GenFlex Jaguar MicroDB 417 427 418 428 Pin and Ring NetAffx CustomExpress and Flying Objective are trademarks owned or used by Affymetrix Inc Microsoft is a registered trademark of Microsoft Corporation Oracle is a registered trademark of Oracle Corporation GeneArray is a registered trademark of Agilent Corporation Limited License EXCEPT AS EXPRESSLY SET FORTH HEREIN NO RIGHT TO COPY MODIFY DISTRIBUTE MAKE DERIVATIVE WORKS OF PUBLICLY DISPLAY MAKE HAVE MADE OFFER TO SELL SELL USE OR IMPORT PROBE ARRAYS OR ANY OTHER PRODUCT IS CONVEYED OR IMPLIED WITH THE PROBE ARRAYS INSTRUMENTS SOFTWARE REAGENTS OR ANY OTHER ITEMS PROVIDED HEREUNDER EXCEPT FOR CERTAIN ARRAYS AND REAGENTS DESIGNATED AS ANALYTE SPECIFIC REAGENTS SEE APPLICABLE PACKAGE INSERT WHICH ARE LICENSED FOR USE AS ANALYTE SPECIFIC REAGENTS OR RESEARCH USE ALL PRODUCTS INCLUDING THE PROBE ARRAYS INSTRUMENTS SOFTWARE AND REAGENTS DELIVERED HEREUNDER ARE LICENSED TO BUYER FOR RESEARCH USE ONLY THIS LIMITED LICENSE PERMITS ONLY THE USE BY BUYER OF THE PARTICULAR PRODUCT S IN ACCORDANCE WITH
11. a selected temperature m fill the cartridge with wash solution for scanning m clean the metal sampling tube and module tubing for the next cartridge to be processed After staining and washing the Agilent GeneArray scanner scans the cartridge by laser light to obtain fluorescence intensity data For more information on how the scanner works refer to the appropriate scanner manual Kam In addition to the preceding protocols the fluidics station can perform variations of the steps described in both procedures For more information about the protocols that can be performed on the fluidics station please contact your Affymetrix Technical Support representative AFFYMETRIX s 14 CHAPTER 1 Introduction Chapter 2 Using the Fluidics Station 400 This section describes how to use the Affymetrix GeneChip Fluidics Station 400 with sample protocols Starting Up 1 Check to ensure that the fluidics station is connected to the power main through the power cord provided 2 Check to ensure that the fluidics station is connected to the workstation CommLink connections are located on the back of the fluidics station See Figure 2 1 on page 18 3 Flip the ON OFF switch for the fluidics station to the ON position The switch is located on the left side of the fluidics station See Figure 2 1 on page 18 The LCD window should display the following Power On Done NOT PRIMED 25 C 4 Turn on the wor
12. arise with the fluidics station use the following table to locate the description that matches the problem If you cannot find a solution call Affymetrix Technical Support for assistance Problem Cartridge nat filling completely with sample solution or buffer during initial stages of hybridization wash or staining protocol Displayed as Missing Fluid Error Possible Cause Possible holes in the septa of the cartridge Sample or staining solution not in place properly Insufficient volume of sample or staining solution 500 uL Blocked sampling tube or line of the fluidics station Failure of one of the fluidics sensors Pump tubing stretched too tightly around the pump Solution Run Recover script then use another cartridge Run Recover script Make sure sample or stain vial is in the sample holder Run Recover script Add more sample solution to the sample vial Run Recover script Run the Clean or Prime script with fresh deionized DI water to flush out salt blockage Call Affymetrix Technical Support for service Loosen the tubing clamps allow tubing to relax close the clamps Cartridge not filling completely with buffer during wash script Displayed as Missing Fluid Error Buffer bottle empty Deionized water used instead of buffer Module not primed Fill buffer bottles Replace water with buffer and prime instrument lines Prime module Recovered less samp
13. ation wash script Air bubble in wash line See Hybridizing the Target Solution to the Probe Array on page 20 Buffer leaking inside the fluidics station Loose tubing attachments inside the fluidics station Washblock requires replacement Salt buildup in the lines of the fluidics station Call Affymetrix Technical Support for service Refer to Appendix C Replacing the Washblock on page 49 Run the Clean or Prime script with resh DI water to flush out salt blockage Cartridge needles of the fluidics station not engaging with the cartridge Possible defective septa on the cartridge Extra flashing on the cartridge Salt buildup on the cartridge needles Cartridge holder aligned and attached to the fluidics station improperly Cartridge holder not properly engaged to the fluidics station Use another cartridge Use another cartridge or call Affymetrix Technical Support or service Run the Clean script with fresh DI water to flush out salt blockage Clean cartridge needles with a wet cotton swab Call Affymetrix Technical Support for service Place the cartridge into the cartridge holder Push the holder door shut and firmly lift the lever to engage the cartridge needles Affymetrix Fluidics Station User s Guide 35 When to Contact Affymetrix Technical Support Under any of the following conditions unplug the instrument from the power source and contact Affymetrix Techni
14. be carrying an electric charge Affymetrix Fluidics Station User s Guide Caution Notices CAUTION The power supply cord is used as the main disconnect device Ensure that the socket outlet is located and installed near the equipment and is easily accessible ATTENTION gt Lecordon d alimentation est utilis comme interrupteur g n ral La prise de courant doit tre situ e ou install e proximit du mat riel et tre facile d acc s ACHTUNG Zur sicheren Trennung des Ger tes vom Netz ist der Netzstecker zu ziehen Vergewissern Sie sich da die Steckdose leicht zug nglich ist Regulatory This device complies with Part 15 of the FCC rules Operation is subject to the following two conditions 1 This device may not cause harmful interference and 2 this device must accept any interference received including interference that may cause undesirable operation AGS NRTL C Ge 10244 C AFFYMETRIX s 7 8 CHAPTER 1 Introduction Customer Support Information AFFYMETRIX INC 3380 Central Expressway Santa Clara CA 95051 USA Tel 1 888 362 2447 1 888 DNA CHIP Fax 1 408 731 5441 sales affymetrix com support affymetrix com AFFYMETRIX UK Ltd Voyager Mercury Park Wycombe Lane Wooburn Green High Wycombe HP10 OHH United Kingdom Tel 44 0 1628 552550 Fax 44 0 1628 552585 saleseurope affymetrix com supporteurope affymetrix com ww
15. cal Support m when the power cord is damaged or frayed m if any liquid has penetrated the instrument m if after service or calibration the instrument does not perform to the specifications stated in Appendix D If the instrument must be returned for repair call Affymetrix Technical Support AFFYMETRIX INC 3380 Central Expressway Santa Clara CA 95051 USA Tel 1 888 362 2447 1 888 DNA CHIP Fax 1 408 731 5441 sales affymetrix com support affymetrix com AFFYMETRIX UK Ltd Voyager Mercury Park Wycombe Lane Wooburn Green High Wycombe HP10 OHH United Kingdom Tel 44 0 1628 552550 Fax 44 0 1628 552585 saleseurope affymetrix com supporteurope affymetrix com www affymetrix com AFFYMETRIX s 36 CHAPTER 3 Instrument Care and Maintenance a A A A Fag E a he Removing a Module for Servicing Removing a Module for Servicing gt E gt El Affymetrix Technical Support may request that a module be disconnected to be serviced Follow these steps to disconnect a module from the fluidics station 1 Open the top to the fluidics station by firmly pushing the lid release buttons located on the sides of the fluidics station See Figure 1 1 on page 10 Disconnect the three reagent tubing lines from the tubes that connect to the reagent manifold 44 turn quick disconnect fittings leaving them attached to the module Loosely tuck the tubi
16. col before starting it on the fluidics station Protocol changes will not affect runs in progress For more specific instructions refer to the Microarray Suite user s guide or contact your Affymetrix Technical Support representative 1 Select Edit Protocol from the Tools menu on the workstation gt The Edit Protocol dialog box appears 2 Inthe Edit Protocol dialog box under Protocol Name click the arrow to open a list of protocols Click the protocol to be changed gt The Protocol Name text box displays the protocol name The conditions for that protocol are displayed on the right side of the Edit Protocol dialog box 3 Select the item to be changed and enter the new parameters as needed The parameters must be within the ranges shown below Parameter Valid Range Hybridization or Stain Time Seconds 0 to 86 399 Temperature C 15 to 50 Number of Wash Cycles 0 to 99 Mixes per Wash Cycle 1 to 99 Par ai Enter 0 zero for the hybridization time if you desire only a wash Enter O zero for the number of wash cycles for a wash solution that you will not use 4 To return to the default values for the protocol selected click the Defaults button 5 Once you have modified all the protocol conditions click the Save button to save the modified protocol To save the modified protocol under a different name enter the new name in the Protocol Name box before clicking the Save button Affymetrix Fluidics Station
17. for use and choose the experiment name in the drop down Experiment list Check to ensure that the experiment name matches the sample and cartridge to be run In the Protocol drop down list choose the protocol that matches the cartridge type You can also choose a customized hybridization wash or wash protocol here Refer to the Microarray Suite user s guide or to Customizing the Protocol on page 24 If you are running a customized protocol check the parameters of each of the protocols chosen to be sure they are appropriate for your experiment This can be done in the Fluidics Protocol dialog box found by choosing Edit Protocol under the Tools menu Click the Run button to begin hybridization of the sample The protocol will begin The LCD window on the fluidics station and the Fluidics Station dialog box on the workstation will indicate the status of the hybridization as it progresses Follow the instructions on the LCD window or in the Fluidics Station dialog box A selection of the available prompts is given below as examples a If prompted to Remove Vial remove any remaining vial from the sample holder of the fluidics station b If prompted to Load Cartridge open the cartridge holder by pressing down on the cartridge lever to the Eject position Place the appropriate cartridge into the cartridge holder corresponding to the module set up in the experiment Push the cartridge holder back to engage the latch See Fig
18. ge repeatedly with wash solutions at selected temperatures m fill the cartridge with wash solution for scanning m Clean the metal sampling tube and module tubing for the next sample After hybridization the Agilent Gene Array scanner scans the cartridge by laser light to obtain fluorescence intensity data For more information on how the scanner works refer to the appropriate scanner manual Sample Recovery and Staining Protocol 1 Use the Microarray Suite software to define an experiment and start the fluidics station protocol After the hybridization of the sample to the cartridge place the cartridge into the cartridge holder on the selected module of the fluidics station Place an empty sample vial in a sample vial holder The fluidics station transfers the sample to the empty sample vial Remove the sample vial and place a vial containing the stain solution into the sample vial holder The fluidics station will perform the following actions to stain the bound target on the cartridge and prepare it for scanning The fluidics station will m wash the array with wash solution or solutions at selected temperatures m draw staining solution from the vial into the cartridge and mix it by alternately draining and filling the cartridge at a selected temperature m expel the staining solution to the waste line Affymetrix Fluidics Station User s Guide 13 m wash the cartridge with wash solution or solutions at
19. h the three horizontal screws on the top of the bezel using the 5 32 hex key included in the accessory kit Attach the two screws to the bottom of the front bezel of the fluidics station using the hex key included in the accessory kit Connect the two waste tubing lines on the module to the waste conduit Connect the three reagent tubing lines on the module to the reagent manifold following the color code red to red white to white blue to blue Close the top of the fluidics station and restore power Prime the module AFFYMETRIX s 42 APPENDIX A dali B a A A Fag E a he Using More Than One Fluidics Station Using one workstation you can connect up to eight fluidics stations together Follow these steps to connect more than one fluidics station to the workstation CAUTION When making connections always turn off power to all devices in the chain Failure to do so can cause loss of information Setting the Address Setting the address on the fluidics stations will enable the computer to recognize and correctly control each of the fluidics stations Each fluidics station connected to a given workstation must have a unique address You must assign addresses consecutively starting with 1 It is preferable though not necessary to number the fluidics stations in the order in which they are connected Fluidics station Fluidics station Fluidics station Workstation terminator Fig
20. he fluidics station you must first define an experiment For information on defining an experiment refer to the Microarray Suite software user s guide or to the appropriate package insert Defining the Experiment In the Microarray Suite software open the Experiment Info dialog box under the Run menu An Experiment Information dialog box appears 1 In the Experiment Information dialog box fill in the name of the experiment and select cartridge name from the drop down list Do this for each experiment Refer to the Microarray Suite software user s guide or to the appropriate package insert for additional information about the Experiment Information dialog box 2 Save the experiment by clicking the Save button AFFYMETRIX s 20 CHAPTER 2 Using the Fluidics Station 400 3 Close the Experiment Information dialog box Priming the Fluidics Station A prime is necessary to ensure that the wash lines are full of the appropriate buffer and that the fluidics station is ready to process a cartridge You should prime the fluidics station m whenever you first start the fluidics station and whenever you change the wash solutions m before processing a cartridge if you have performed a shutdown on any module and m if the LCD window instructs you to run a prime 1 Check to ensure that all the wash lines are in the appropriate wash bottles Please consult the probe array package insert that came with the cartridge kit for the
21. ip Fluidics Station 400 is 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 57 58 APPENDIX E Affymetrix Fluidics Station 400 User s Guide Index A accessory kit 10 C care 29 components instrument 8 customizing protocol 24 E experiment setting up 19 F fluidics station more than one 45 fluidics stations connecting 46 hybridization standard 11 hybridization and wash protocol 11 hybridizing target solution 20 instrument components 5 maintenance 29 modules 8 P precautions 5 preventive maintenance 30 probe array 18 protocol customizing 24 staining 12 wash 11 R recovery staining 12 regulatory 7 removing module 39 S sample recovery 12 setting up an experiment 19 shutting down 25 staining protocol 12 starting up 17 T target solution hybridizing 20 W warnings and precautions 13 warranty 57 AFFYMETRIX s s 61
22. ks 11 CHAPTER 2 Using the Fluidics Station 400 17 Starting Up 17 Handling the Probe Array Cartridge 18 Setting Up an Experiment 19 Defining the Experiment 19 Priming the Fluidics Station 20 Hybridizing the Target Solution to the Probe Array 20 Customizing the Protocol 24 Shutting Down 25 AFFYMETRIX s il CONTENTS CHAPTER 3 Instrument Care and Maintenance 29 Instrument Care 29 Instrument Maintenance 29 Troubleshooting and Assistance 33 When to Contact Affymetrix Technical Support 35 APPENDIX A_ Removing a Module for Servicing 39 Removing a Module for Servicing 39 Replacing a Module 40 APPENDIX B Using More Than One Fluidics Station 45 Setting the Address 45 Connecting Fluidics Stations Together 46 APPENDIX C Replacing the Washblock 49 Replacing the Washblock 49 APPENDIX D Specifications 53 Instrument Specifications 53 APPENDIX E Warranty 57 Warranty 57 Chapter I E odano This chapter introduces the Affymetrix GeneChip Fluidics Station 400 and its components gives an overview of how the fluidics station works and covers the safe use of the fluidics station Warnings and Precautions m The fluidics station is for research use only It is not for use in diagnostic procedures a All biological specimens and materials with which they come in contact should be handled as if capable of transmitting infection and should be 6 CHAPTER 1 Introduction disposed of
23. kstation The Microarray Suite software should automatically open If it does not open the software program by double clicking its icon 17 18 CHAPTER 2 Using the Fluidics Station 400 Lid Release Butt S utton N CommLink Out Connector to terminator or cable to next fluidics station vo CommLink In Connector N ON OFF Switch Power Cable Figure 2 1 Location of the serial ports and ON OFF switch Handling the Probe Array Cartridge The GeneChip probe array chip comes mounted in a plastic package to form a cartridge See Figure 2 2 on page 19 The probe array chip contains a collection of oligonucleotide probes that have been arrayed on the inner glass surface A chamber in the plastic package directly under the chip acts as a reservoir where hybridization and washing occur Although the inner glass surface is protected any contamination or scratches on the outer surface of the glass can compromise the integrity of the scan Avoid touching the surface of the chip with your fingers Skin oils and other Affymetrix Fluidics Station User s Guide 19 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 Plastic Package Probe Array on Glass Chip Figure 2 2 The GeneChip probe array cartridge Setting Up an Experiment Before running a hybridization on t
24. le than initial input during Recover script Loose tubing attachments inside the fluidics station Call Affymetrix Technical Support for service Fluidics Station X Does Not Respond error message on workstation Power not switched on at the fluidics station Incorrect fluidics station designated for communication Loose cables Turn fluidics station power on then try to connect again Designate correct fluidics station on workstation Firmly connect cables to fluidics station Sensor Timeout error message on workstation No user response to Remove Vial prompt or other prompt Start the selected script again AFFYMETRIX s CHAPTER 3 Instrument Care and Maintenance Problem Error While Draining or Error While Filling error message on workstation Possible Cause Defective septa in cartridge Insufficient sample or stain volume Excessive bubbling in cartridge Buffer conductivity too low Failure of one of the fluid sensors Solution Use a new cartridge Add more sample solution to sample vial Change the buffer reduce detergent Change the buffer increase salt Call Affymetrix Technical Support for service Temperature Timeout error message on workstation Fluidics station not at the designated temperature in time Call Affymetrix Technical Support for service Air bubbles left in cartridge at the end of a hybridiz
25. ng into the top of the module Open the Fluidics Station dialog box on the computer workstation and select the module to be removed Choose Drain for the module to be removed and click the Run button After the Drain is completed turn the power off to the fluidics station and unplug it from the outlet Do not attempt to remove a module without turning off power to the fluidics station Disconnect the two waste tubing lines connected to the waste conduit leaving them attached to the module Loosely tuck the tubing into the top of the module Do not allow liquid from the tubing lines to drip into the main compartment or module 39 40 APPENDIX A Unscrew the two screws on the bottom of the front bezel of the fluidics station by using the 5 32 hex key included in the accessory kit Unscrew the three horizontal screws on the top of the bezel inside the instrument using the 5 32 hex key included in the accessory kit On all modules remove all cartridges latch all cartridge holders and place all cartridge levers in the neutral or horizontal position Pull the white bezel off the front of the fluidics station With the flathead screwdriver included in the accessory kit unscrew the bottom screw of the module to be removed Unscrew the two top screws using the 9 64 hex key included in the accessory kit Pull the module forward to disconnect it from the fluidics station Replace the front bezel and
26. return power to the fluidics station You can continue to use the remaining modules Replacing a Module A To replace a serviced module follow these instructions 1 Turn the power off to the fluidics station and unplug it from the outlet Do not attempt to replace a module without turning off power to the fluidics station Open the top to the fluidics station by firmly pushing the lid release buttons located on the sides of the fluidics station See Figure 1 1 on page 10 Unscrew the four screws on the bottom of the front bezel of the fluidics station using the 5 32 hex key included in the accessory kit Unscrew the three horizontal screws on the top of the bezel inside the instrument using the hex key included in the accessory kit Remove all cartridges latch all cartridge holders and place all cartridge levers in the neutral or horizontal position on all modules Affymetrix Fluidics Station User s Guide 41 10 11 12 13 14 15 Pull the white bezel off the front of the fluidics station Push the serviced module back into its housing in the fluidics station Be sure it connects to the connector in the back Attach the two top screws by using the 9 64 hex key included in the accessory kit With the flathead screwdriver included in the accessory kit attach the bottom screw of the module to the fluidics station Attach the white bezel to the front of the fluidics station wit
27. the cartridge and inspect it again for bubbles If no bubbles are present it is ready to scan Proceed to step 10 If you have made ten attempts to fill the cartridge without bubbles and have been unsuccessful the fluidics station will no longer display EJECT CARTRIDGE after refilling the cartridge Instead it will terminate with the prompt DO CLEAN CYCLE Remove the cartridge and run the Cleanout procedure on the particular module Fill the cartridge manually by inserting a pipette tip or syringe needle through the bottom septum and by using a second pipette tip or syringe needle in the top septum to permit air to escape Refer to Troubleshooting and Assistance on page 33 for possible causes and solutions to bubbles appearing in the cartridge Latch the cartridge holder by pushing up on the lever to engage it You should hear a light click Confirm that you have securely latched the cartridge holder before pushing up the lever Engage the washblock by pushing up on the cartridge lever to the Engage Position The fluidics station will automatically perform a Cleanout procedure The LCD window will indicate the progress of the Cleanout procedure When the Cleanout procedure is complete the LCD window should display the following Remove Vial AFFYMETRIX s 24 CHAPTER 2 Using the Fluidics Station 400 11 Remove the sample vial from the sample holder Customizing the Protocol To be effective you must modify a proto
28. ure 2 3 on page 22 After you hear a light click push firmly up on the cartridge lever which inserts the cartridge needles into the septa AFFYMETRIX s 22 CHAPTER 2 Using the Fluidics Station 400 Y Note Do not push the lever all the way up until the cartridge hold is latched Doing so will bend the cartridge needles c If prompted to Load Vial place the experiment sample vial into the sample holder on the fluidics station As the hybridization progresses check to ensure that the cartridge is filling properly and that bubbles are not forming If it is not filling properly see the note below in this chapter Figure 2 3 Inserting the cartridge into the cartridge holder 6 When the hybridization or washing is complete the LCD window should display the following Eject Cartridge Affymetrix Fluidics Station User s Guide 23 7 Y Note Eject the cartridge by pushing down on the cartridge lever The LCD window should display the following Engage Washblock If bubbles are present in the cartridge return it to the cartridge holder Latch the cartridge holder by gently pushing it inward until you hear a light click Engage the cartridge by pushing up on the cartridge lever to the Engage position The fluidics station will drain the cartridge and then fill it with a fresh volume of the last wash buffer used When it is finished if the LCD window displays EJECT CARTRIDGE again remove
29. ure B 1 Addressing fluidics stations consecutively 1 Use a pen or pencil to set each of the three DIP switches on the back of the fluidics station to the ON or OFF position according to the desired address Push up for ON and down for OFF All three DIP switches need to be set Use the following table as a guide 45 46 APPENDIX B DIP Switch Settings for the Fluidics Station Address Left Middle Right ON ON ON 1 ON ON OFF 2 ON OFF ON 3 ON OFF OFF 4 OFF ON ON 5 OFF ON OFF 6 OFF OFF ON 7 OFF OFF OFF 8 Connecting Fluidics Stations Together Insert the plug end of a nine pin serial cable into the serial board on the workstation Insert the other end of the cable into the CommLink In nine pin connector on the back of the first fluidics station Insert a second nine pin serial cable into the CommLink Out socket nine pin connector on the back of the first fluidics station Insert the other end of the cable into the Comm Link In nine pin connector on the back of the second fluidics station Connect the remaining fluidics stations in a chain following the above pattern Insert a terminator plug into the Comm Link Out socket nine pin connector on the back of the last fluidics station in the chain td C a Ag am Ee the Washblock Replacing the Washblock 1 Open the top to the fluidics station by firmly pushing the lid release buttons
30. w affymetrix com Instrument Components The GeneChip probe array Fluidics Station 400 contains four modules each module can hold one GeneChip probe array cartridge The Microarray Suite software on the workstation which is connected to the instrument can control each of the four modules independently of the others A single workstation can control as many as eight fluidics stations You can use any or all of the modules at the same time You can also choose a different protocol for each module The modules are numbered 1 through 4 near the LCD window The GeneChip Fluidics Station 400 includes the following components See Figure 1 1 on page 10 Affymetrix Fluidics Station User s Guide Sample Holder holds the sample vial Module Door protective cover for the peristaltic pump on the module Cartridge Holder holds the cartridge during hybridization Washblock part of the cartridge holder that completes the fluid path when a cartridge is not in place used for cleaning out or draining the fluidics station Cartridge Lever engages or releases the cartridge holder LCD Window displays messages during processes Lid Release Buttons one on each side Wash Bottles 2 hold wash buffers and tubing that pulls buffer through system DI Water Bottle holds deionized water and tubing that pulls water through system Waste Bottle collects waste from hybridizations and washes Metal Sampling Tube
31. with proper precautions in accordance with federal state and local regulations including adherence to the OSHA Bloodborne Pathogens Standard 29 CFR 1910 1030 for blood derived and other samples governed by this act Never pipette by mouth Avoid specimen contact with skin and mucous membranes Wear gloves when using the fluidics station Exercise standard precautions when obtaining handling and disposing of potentially carcinogenic reagents Do not send your instrument elsewhere for service or attempt to service it yourself To protect your warranty and ensure safe operation the instrument should be serviced only by Affymetrix or its representatives If the instrument is not working correctly please contact your 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 See AN Figure 1 1 on page 10 Under fault conditions the area behind the cartridge holder can have temperatures that rise to 100 C or higher 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 Use OSHA standards for lifting techniques The LCDs in front of the instrument are sensitive to static discharge Avoid touching them with the fingers or any object that may
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