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manual, GeneTitan Instrument User Guide for Expression Array Plates

1. Scan Tray with Holding buffer Figure 4 5 Chapter 4 Wash Scan Workflow 39 NOTE The sandwich of the HT Array Plate and the hybridization tray must remain in the hybridization oven until the Wash B buffer reaches the set point temperature during the initial setup in Step 2C 2 Click Next Figure 3 7 on page 24 displays the System Setup tab and the information in this pane NOTE If there is not enough disk space a message is displayed Delete or move dat files to another location to free up enough disk space for the data that will be generated by eight Array Plates The GeneTitan Single Channel has the following space requirements 96 Array Plate requires 24 GB 24 Array Plate requires 6 GB 16 Array Plate requires 4 GB The GeneTitan MC system has the following space requirements 96 Array Plate requires 100 GB 24 Array Plate requires 18 GB 16 Array Plate requires 8 GB A Plate Information a Barcode Scan or manually enter the Array Plate barcode and click Next The first six characters of the barcode identify the type of plate being loaded the protocol GeneTitan Instrument will use to process the plate and the imaging device parameters required for this type of plate Protocol Name The protocol name is automatically selected Click Next B Refill fluidics bottles with buffer Table 4 1 1 Fill these bottles u Wash A fill with Wash Buffer A keep at 2 L full a
2. IMPORTANT The lamp bulb faces away from the fan and toward the reflecting mirror Chapter A 61 Resetting the Lamp Counter You must alert the software application that you have replaced the lamp so that the hours of the lamp counter are reset to zero 1 On the software application click Tools gt Reset Counter for Life Remaining Figure A 11 This menu option is available only if the system is not processing any plate Figure A 11 Inserting the Lamp EI AGCC GeneTitan Instrument Control Shutdown System Check Available Disk Space Reset Counter for Lamp Life Remaining System Status Scan Status Estimated Completion Time Estimated Time Window to Run Next Hyb VYash Scan HT Array Type Same plate type v System is available now Hybridization Oven Status Fluidics Status Imaging Device Status Estimated Time Remaining Position 1 Barcode Wash B Temperature Pasition 2 Estimated Time Remaining Current Target 39 C 5 e 7 e a 10 11 12 M Oven Temperature Target Log 11 09 40 AM OSVersion Microsoft Windows NT 5 1 2600 Service Pack 3 11 09 40 4M UserName AFFXUser 11 09 40 AM ExecutablePath C Program Files 4ffymetrix Command Console 11 09 40 AM ProductName HTS6CC 11 09 40 AM ProductVersionS6F 3 0 0 1212 11 09 40 4M Last WriteTime S6F 8 29 2009 10 10 38 PM 11 09 40 AM ProductVer
3. Shutting Down You should perform the shutdown protocol at the end of a session Do not keep the GeneTitan Instrument on if you will not use it again within the next 12 hours This will reduce the risk of salt buildup in the instrument The fluidics automatically performs a cleanout protocol IMPORTANT To avoid contamination the DI water should be replaced with fresh DI water before performing a fluidics run 82 GeneTitan Instrument User Guide for Expression Array Plates
4. Barcode 550001 Plate Type 550001 Protocol Name 550001 protoc Location Load consumables on left side i Stain 3 Tray Stain 3 Tray Hyb Tray Workflow Steps Array Plate 7 _ Trash Bin Enter Array PI ate Barcode Iion im o o e e r Will Be Scanned _ Will Not Be Scanned EH Not Available Select arrays to scan Start Processing Status Please select arrays to scan using array selector Press the Next button to advance to the next step Read barcode completed 32 GeneTitan Instrument User Guide for Expression Array Plates 7 Use the default selections or select arrays as described below Each array on the plate is indicated by a single square The color of the square indicates the array s status dark blue Will be scanned white Will not be scanned gray Not available To manually select arrays A Select the Manual Array Selection checkbox B Select the arrays to be scanned You can select arrays by Clicking and dragging through the grid Pressing the Ctrl button down and clicking in different squares NOTE If there is insufficient disk space on the computer s hard drives to store the data from a plate a notice appears 8 Click Next to start the run The Start Processing dialog box opens Figure 3 17 Figure 3 17 Start Processing notice Start Processing P This will start the HybwashScan in the Left Po
5. G Follow the software prompts and load the array plate and trays as directed pressing the Confirmation button after loading each tray or array plate Figure 4 7 Load Scan Tray ES AGCC GeneTitan Instrument Control File Tools Help la Stop Email Help System Status System Setup Setup Option Plate Information System Layout Array Selection Barcode 5500012888 Plate Type 550001 Protocol Name i Location Load consumables on left side Used Hyb Tray Scan Tray Stain 1 Tray Stain 2 Tray Bat Aray Plate Used Hyb Tray Scan Tray Stain 1 Tray Stain 2 Tray Stain 3 Tray Hyb Tay Manual Array Selection 10 11 12 Workflow Steps Trash Bin rl Dkn im BET san B HE FAR Ked Ebe H Will Be Scanned _ Will Not Be Scanned O Not Available Start Processing Status Load the Scan Tray with cover on Left side of Drawer Press the Confirmation button when done Cancel Drawer 2 opened When you load the scan tray the internal bar code reader reads the barcode to see if it is the right kind of tray in the right orientation If the information is correct the application allows you to proceed to the next step If not the application will prompt you to load the correct tray into the instrument Figure 4 8 and Figure 4 9 illustrate the proper way to install the tray You must load the scan tray with the scan
6. KIRI K K KI KIR ee 63 Probl ms and SOIWIONS sss 2 lt s lk ala x lk lan a ak wendy n n jk n ee an k Ga eR lan nan an a 63 Insufficient Disk Space Notice Ak kk kk kk kK kK KK KK KI KK KI KK KK KI KI K KII KI KI KIRI K R KI KK YJ 63 Problems and Solutions kk kk kk kk KK KK KK KK KI KK KK KIRI IK KI KI KI KI KI KI Pewee oes 64 EIPOO IMIGSSA0CS sre 54ers eee Hl a erdmrm na mn ae MH HH 66 Using AGCC E mail Notification with GeneTitan MC Instrument 66 Context Specific Messages kk kk kk kk KK KK eee ee 66 GeneTitan Instrument Recovery Procedure 0000e cece 79 Recovering the Instrument from a Power Interruption 0 KK KK KI K K K K K eee 79 Recovering the Process After a User Power Interruption 79 Procedure for Recovering a Process Ak kk kk kK KK eee 79 Recovering the Process After a Power Failure Ak kk KK K K ee 80 UPS Low Battery Condition nnana aaa kk KK KK KI KK KI KK KI KK KK KI KI KI KIRI KI KIRI KI KI KI KI KI KK KK 80 Resuming the Process from a Workstation or Application Freeze 81 SHUG DOWN EET ER 81 Before Using the GeneTitan Instrument This chapter illustrates the consumables associated with the GeneTitan Instrument and their proper care and handling Topics covered in this chapter include a Equipment Reagents and Consumables Required on page 1 Proper Installation of the GeneTitan
7. Stain 1 Tray Stain 2 Tray Stain 8 3 Tray Hyb Tray Trash Bin p til SS O SE E E Drawer 6 opened Used Hyb Tray Manual Array Selection Zina mio no gt m Will Be Scanned Will Not Be Scanned 10 SENSE E Not Available 44 GeneTitan Instrument User Guide for Expression Array Plates When you load the array plate on the Hyb Tray The internal bar code reader reads the barcode of the array plate and compares it with the barcode and the plate type specified in the Barcode field and Plate Type field on the Setup page If the information is correct the application allows you to proceed to the next step If the instrument is unable to read the barcode it will push the tray out and will prompt you to load the correct plate with the proper orientation into the instrument Figure 4 12 Figure 4 12 Barcode error notice E Verily Drawer 6 Loa EE Waning The system was not able to verify the GeneTitan Consumable Tray using the barcode on the Tray Please venty that the tray on the left side of the drawer is a blue cover and if applicable an array plate in the correct ORIENTATION The right side of the drawer should contain a hyb tray if applicable in the corect ORIENTATION Detals The consumable is ether not the correct consumable not loaded comectly or its barcode is not readable Proceeding with ar incorect or incorrectly loaded consumable can result in a loss
8. The times shown will differ for 3 IVT and WT expression array plates When the system is available 1 Click the System Setup tab 2 Go through the Instrument setup process following the software prompts as described in the section on Loading the Instrument for Hyb Wash Scan Workflow on page 20 E WARNING The bottles are pressurized in normal operation Wait until you see the prompt that the buffer bottles have been depressurized before opening and refilling or emptying the bottles El IMPORTANT When running a series of array plates through the hyb wash scan workflow it is recommended to fill the fluid bottles to the full mark with wash and rinse fluids Wash A fill with Wash Buffer A keep at 2 L full Wash B fill with Wash Buffer B keep at 1 L full a Rinse fill with DI Water keep at 1 L full 3 Perform the loading procedure as described in Loading the Instrument for Hyb Wash Scan Workflow on page 20 Follow the software prompts to make sure that the plates and trays are loaded into the proper side of the drawer Figure 3 22 Ea IMPORTANT When running a series of array plates through the Hyb Wash Scan workflow you must be careful to remove and load the proper array plate and trays and pay careful attention to the software prompts that tell you which side of the open drawer to remove or place a plate or tray In addition you need to follow the restrictions for running plates with different numbers of array
9. or the Affymetrix call center AGCC Log Files The following files apply to the GeneTitan Instruments All the AGCC log files from C Command_Console Logs The different log files include Systemlog XML XML file with system information DEC log Text file with information on the use of the Data Exchange Console DECError log Text file with information on errors created while using DEC AGCC LibFilelmporter log Text file with info on use of the Library File Importer with date and time code Other AGCC Files Your FAS and or FSE may request you to send the following files for troubleshooting 1 Library files PARAMS MASTER WORKFLOW SMD MEDIA located in C Command_Console Library excluding the large analysis library files CDF PSI GRC 2 Provide a list of all sub folders and their contents under the library files folder located in C Command_Console Library Please ensure there are no duplicate library files as these can cause problems 3 AGCC system configuration file located at C Command_Console Configuration Calvin System config Pending job order files located in C Command_Console Jobs 5 Other AGCC related information such as A The number of files under C Command_Console Data including sub directory B If the system is a networked system or a standalone system C Other applications installed on the system such as antivirus application MS Office Internet Explorer versions Chapter A 63 AGCC L
10. 550001 Protocol Name 1 Location Load consumables on left side Workflow Steps Jare vyvasf Empty trash bin Remove consumable trays and plates Load consumable trays and plates Select arrays to scan Start Processing Status Preparing WashB for Wash Scan Filling WashB Heating WashB See Fluidics Status Log for WashB Temperature status Please wait Cancel D Empty trash bin F 1 Open the trash bin and empty If already empty the trash bin remains locked and the Status pane reads Trash bin is empty 2 Press the Confirmation button to continue Remove consumable trays and plates 1 Remove used trays and plates when drawers open If no consumables to remove the Status window reads Drawers are empty 2 Press the Confirmation button to continue Load consumable trays and plates as follows 1 Follow the prompts in the Status window 2 Once loaded examine each cover for droplets of liquid 3 Ifany liquid is present remove the tray clean the cover and top of the tray with Kimwipes and reload the tray Chapter 4 Wash Scan Workflow 41 CAUTION a Orient trays as indicated by the guide inside the drawer Improper orientation may cause the run to fail a Examine each cover for droplets of liquid after loading Liquid on the cover can result in capillary phenomenon As a result the tray may stick to the cover and be lifted out of place inside the instrument
11. Buffer A keep at 2 L full u Wash B fill with Wash Buffer B keep at 1 L full a Rinse fill with DI Water keep at 1 L full 2 Empty the waste bottle 3 Press the Confirmation button on GeneTitan Instrument to continue A fluidics check is run 1 minute NOTE The instrument control software will display a warning if it detects a problem during the fluid dispense operations The filters in the GeneTitan Wash A Wash B and DI Water bottles should be replaced if the software displays such a warning Refer to Replacing the Bottle Filters on page 55 for the message displayed to the user and the procedure for replacing the filters a Table 3 3 shows the minimum volumes of Wash A and B buffer and DI Water that are required for processing one or two plates Table 3 3 The Minimum Volumes of Buffer and Rinse Required to Process on GeneTitan l Minimum Level in Bottle Amount Required for Fluid Type One Array Plate One Array Plate Two Array Plates Rinse 300 mL 450 mL 900 mL Wash A 920 mL 1 040 mL 2 000 mL Wash B 300 mL 450 mL 600 mL C During the initial setup the application prompts you the system is warming the Wash B buffer to the preset temperature Figure 3 8 When the Wash B target temperature is reached the application prompts you to press the Confirmation button 26 GeneTitan Instrument User Guide for Expression Array Plates Figure 3 8 Wash B prep For Wash Scan workflow only Setup Option
12. KK KI KII KII KI KI KIRI KI K K KI K KK 10 E mail and Telephone Notifications from the GeneTitan Instrument 11 Starting the GeneTitan Instrument and AGCC 13 Starting Command Console Launcher and the GeneTitan Instrument Control Software 13 Setup Options for Array Plate Processing 0 0 kk KK KI KIRI KI KI KI K KI K K KI KII KI KI KIRI KI KII KI KI 16 Hyb Wash Scan kk kk kk kk KK KK KK KK KI KK KK KK KK KK KI KK KK KK KI KIR KI KK KI KK KK KK KK K 16 BSN EET 66a toe he E EEE E E ee ees eh daa es 17 Wash SCAN Xa a su ak weed d e he hi di keviya lk dak danl k el d ead di kerta d x r a 17 Scan DEH HH H HH HrHHHHHHHDDmHrDHHHH HE HHHHNEHEHH 17 UlOo a PIES 2 sas sa ak bout cases LE e E ou abo nuns ees eha h lan dirk ee oak os 17 Wash Scan Resume kk kk kk kk kK KK KK KK KK KI KK KK KK KK KK KK KK KI KI KI KIRI KI K K KK KK 17 Hyb Wash Scan Workflow 2 kk kK ee KIRI KK IK KK k 19 Hybridization Buffer Stains and Wash Buffer Volumes Required for the GeneTitan Instrument kk kk kk kk KK KK KI KK KK KI K KI KI KK KI KII KI KI KI KI KIR K K KI KI KK K KK KI KK 19 Loading the Instrument for Hyb Wash Scan Workflow kK KK KRI KIRI KII eee 20 Loading Plates and Trays into the GeneTitan Instrument KK IIIIII KIIV 24 Running Multiple Workflows at the Same Time for Expression Arrays 34 Running the Hyb Wash Scan Workflow on a Series of Array
13. Plate Information Barcode Plate Type 550001 Protocol Name Location Load consumables on left side Workflow Steps Enter Array Plate Barcode Refill tles v iffer epare VWashB for Wash Scan Empty trash bin Remove consumable trays and plates Load consumable trays and plates Select arrays to scan Start Processing L Status Preparing WashB for Wvash Scan Please wait Filling vashB Heating WashB see Fluidics Status Log for WvashB Temperature status Cancel Empty trash bin 1 Open the trash bin and empty If already empty the trash bin remains locked and the Status pane reads Trash bin is empty 2 Press the Confirmation button to continue Remove consumable trays and plates 1 Remove used trays and plates when drawers open If no consumables to remove the Status window reads Drawers are empty 2 Press the Confirmation button to continue Load consumable trays and plates as follows 1 Follow the prompts in the Status window 2 Once loaded examine each cover for droplets of liquid 3 If any liquid is present remove the tray clean the cover and top of the tray with Kimwipes and reload the tray CAUTION Orient trays as indicated by the guide inside the drawer Improper orientation may cause the run to fail a Examine each cover for droplets of liquid after loading Liquid on the cover can result in capillary phenomenon As a result the tr
14. Scan workflow Only certain types of workflows can be run at the same time and delays may be necessary before starting the second workflow These restrictions exist because an array plate should be scanned immediately after the wash and stain processing is finished and GeneTitan scans one array plate at a time If you want to run a series of Expression array plates through the Hyb Wash Scan workflow you will need to wait for up to five hours after you start the first workflow before loading the second array plate hyb tray and consumables to allow the first array plate to finish being scanned When running a series of Expression array plates there are restrictions on the sorts of arrays you can run through in a series because of Differences between the workflow for 3 IVT and WT Expression arrays The number of arrays on a plate There are limitations on your ability to mix array plates with different numbers of arrays due to timing differences in the scan and other issues GeneTitan can process array plates with 16 24 or 96 arrays on a plate The delay time varies depending upon the number of arrays on the first array plate Approximately five hours if the first array is a 96 array plate Approximately two and a half hours if the first array is a 16 or 24 array plate The Workflow pane of the System Status screen Figure 5 8 displays the time you need to wait before beginning a second workflow The instrument will sho
15. The proper installation of the GeneTitan tray consumables the image shows the Stain Tray and the Stain Tray cover as an example Barcode faces in and back fs 2 aah RSE FOR RESEARCH ns FOR RESEARCH ASE Notch faces out and left Affymetrix For Research Use Only faces out Chapter 1 Before Using the GeneTitan Instrument 5 Proper Tray Alignment and Loading Proper alignment and loading of plates covers and trays is critical when using the GeneTitan Instrument Each plate cover and tray has one notched corner The notched corner of plates trays covers and bases must be in vertical alignment with each other and placed in position Al per the Tray Alignment guide inside each GeneTitan Instrument drawer Figure 1 3 and Figure 1 4 on page 7 K IMPORTANT When running a multi plate workflow you must pay careful attention to the software prompts that tell you which side of the drawer to place or remove a plate tray El TIP Mark the notched corner of each plate cover and tray with permanent marker to help ensure proper alignment and loading onto the GeneTitan Instrument Clear Tray Shipping Cover To be Discarded Array Plate ee 7 b ay Piste i Protective base Array Plate Array Plate with protective packaging Array Plate with shipping cover removed i IMPORTANT The clear tray shipping cover must be discarded prior to loading the array plate Th
16. Tray 4 Shipping Cover To be Discarded Array Plate Protective base Array Plate Array Plate with shipping cover removed Array Plate with protective packaging 22 GeneTitan Instrument User Guide for Expression Array Plates o Hybridization Tray for the Hyb ready cocktail Figure 3 2 o SAPE 1 Stain tray with cover Figure 3 3 o AB Stain tray with cover Figure 3 4 Chapter 3 Hyb Wash Scan Workflow 23 o SAPE 2 Stain tray with cover Figure 3 5 ee a a n N NER RETE OE Kard ke J UD RR DD RD rig U r e 3 0 gt CanNn iray Wi li UMS gt cdil Udy COVEI WA A Nn pes fb ey J ENI kewn oa RE ERE a tNOUT tne black OFOLECLIVE The software will direct you to load each plate or tray opening the drawer and displaying the proper side for the tray or plate En IMPORTANT When running a series of array plates through the Hyb Wash Scan workflow you must pay careful attention to the software prompts that tell you which side of the open drawer to remove or place a plate or tray If you load the array plate and trays for a second Hyb Wash Scan while the first workflow is still proceeding you must be careful to remove and load the proper array plate and trays See Running the Hyb Wash Scan Workflow on a Series of Array Plates on page 35 for more information 24 GeneTitan Instrument User Guide for Expression Array Plates Loading Plates and T
17. Wash B fill with Wash Buffer B keep at 1 L full a Rinse fill with DI Water keep at I L full 2 Empty the waste bottle 3 Press the Confirmation button on GeneTitan Instrument to continue A fluidics check is run 1 minute a Table 4 1 shows the minimum volumes of Wash A and B buffer and DI Water that are required for processing one or two plates Table 4 1 The Minimum Volumes of Buffer and Rinse Required to Process on GeneTitan l Minimum Level in Bottle Amount Required for Fluid Type One Array Plate One Array Plate Two Array Plates Rinse 300 mL 450 mL 900 mL Wash A 920 mL 1 040 mL 2 000 mL Wash B 300 mL 450 mL 600 mL C During the initial setup the application prompts you the system is warming the Wash B buffer to the preset temperature Figure 4 6 When the Wash B target temperature is reached the application prompts you to press the Confirmation button 40 GeneTitan Instrument User Guide for Expression Array Plates NOTE The instrument control software will display a warning if it detects a problem during the fluid dispense operations The filters in the GeneTitan Wash A Wash B and DI Water bottles should be replaced if the software displays such a warning Refer to Replacing the Bottle Filters on page 55 for the message displayed to the user and the procedure for replacing the filters Figure 4 6 Wash B prep For Wash Scan workflow only Setup Option Plate Information Plate Type
18. before loading the scan tray with the scan tray cover The Black Scan tray cover in the package is used to protect the scan tray glass from damage The black scan tray is distinct trom the Blue Array Plate Cover and must not be used with the Array Plate Remove and discard the protective base rom the scan tray before loading The GeneTitan Scan tray must be loaded with the scan tray cover into the GeneTitan instrument a Do not load the scan tray with the protective base Chapter 1 Before Using the GeneTitan Instrument 3 Table 1 1 GeneTitan Instrument consumables Continued Item Part Number Labware Image Information GeneTitanStain 501025 Trays The GeneTitan stain trays are packaged in ziplock bags to keep them free of dust The GeneTitan stain trays are barcoded and tray have separator walls that are flush with the frame of the stain tray as shown by the yellow line GeneTitan Scan 202757 and Stain Tray cover The GeneTitan scan and stain tray covers are provided to prevent any evaporation of the stains in stain trays and the array holding buffer in the scan tray u All stain and scan trays must be placed in the GeneTitan instrument with the GeneTitan stain tray cover u All tray covers must be de ionized to remove static electricity prior to placing the cover on the tray See the section Anti Static Procedure for GeneTitan Instrument Trays and Covers on page 9 for the anti static procedure GeneTit
19. have not selected any array to scan Please select arrays to scan No arrays selected for scan When running a Hyb Wash Scan Wash Scan Wash Scan Resume or Scan at least 1 array must be selected for scan If no arrays are selected when the user selects Next the following message is displayed The user can continue the array selection process after selecting OK Table A 4 GeneTitan Instrument Error Messages Continued Chapter A 77 Message Meaning Do vou want to load another plate in the Left Position Please press the Yes button to confirm Cancel setup another tur re vou sure All open drawers will be closed Reagent loading workflow prompts Loading another plate for a workflow Some products including Axiom have a reagent load step which occurs at the end of the hyb reagent trays are not loaded when the HTA plate is loaded into the system After loading all reagent trays the user will be asked if they want to load another plate to start hyb before the fluidic process starts up for a plate which is about to come out of the hyb oven If the user intends to process 2 plates per day for a workflow sustained through the week then the response must be Yes The Left or Right refers to the drawer 2 location which will be allocated to the scan tray and hyb output sample tray If two plates are already in the oven then the side will be the same as the side of the plat
20. in Figure 3 4 4 Aliquot 105 uL of the Stain 2 into the GeneTitan Stain Tray identified with the label GeneTitan Stain Tray P N 501025 on the tray 5 Use the stain tray cover provided with the GeneTitan Consumable Upgrade kit to cover the Stain 2 tray as shown in Figure 3 4 6 Aliquot 105 uL of the Stain 3 into the GeneTitan Stain Tray identified with the label GeneTitan Stain Tray P N 501025 on the tray 7 Use the stain tray cover provided with the GeneTitan Consumable Upgrade kit to cover the Stain 3 tray as shown in Figure 3 5 8 Aliquot 150 uL per well of the Array Holding Buffer into the GeneTitan Scan Tray identified with the label HT Scan Tray P N 501006 on the tray En IMPORTANT You must fill all 96 wells with the Array Holding Buffer whether you use 16 24 or 96 well format HT array plates 9 Use the scan tray cover provided with the GeneTitan Consumable Upgrade kit to cover the scan tray as shown in Figure 3 6 Chapter 3 Hyb Wash Scan Workflow 21 This process will require the following GeneTitan consumables o Array plate with cover tray Figure 3 1 The HT Array Plate shipping package includes the following The clear Stain Tray shipping cover for the array plate must be discarded after removing the array plate from the pouch The Array Plate must be protected at all times from damage or exposure to dust The Array Plate must be in the Blue Array Plate Cover at all times Clear
21. mode operation Table A 4 GeneTitan Instrument Error Messages Continued Chapter A 69 Message Meaning There are plate s in the oven that can be recovered after drawer 1T output positions are cleared Do vou want to open drawer 1 to remove those plates now This will allow plate s in the oven to be recovered Plate detected in oven during system startup If the system has a plate on drawer 1 during this recovery the user will be prompted to remove the plate before the recovery can proceed The following message is displayed If no is selected the plate will not be removed from the oven If Yes is selected the drawer will open for plate removal before proceeding to unload the plate from the oven Remove platels from drawer 1 If Yes is selected then drawer will be opened and the following message will be displayed Remove all plates from drawer 1 and select OK to resume recovery of the plate in the oven to drawer 1 Once the plate is on drawer 1 use the normal Unload operation to unload the plate Plate present in Scanner but not removed because Aight side of drawer 2 is not empty Please remove plate on right side of drawer 2 Drawer 2 will open for plate removal Please remove plate on right side of drawer 2 Press the OF button when done Scanner drawer needs to be cleared at startup If a plate is detected in the scanner at startup the system will move the plates from the scanner to
22. of consumables boss of samples and may require a field Samt engineer lo serinca ihe instrument Refer to the System Setup Tab or the User Guide provided with the Assay or AGCO for instructions on proper consumable placement Fress the flashing blue confirmation button or Press OF GeneTitan wil verify the baraode and orientation Press Skip GeneTitan will NOT verity the barcode and orientation 4 Click OK to retry and check the loading of the array plate or Click Skip if the instrument has problems reading the barcode and after verifying that the trays have been placed in the proper orientation After the trays and plates have been loaded the application prompts you to select the array s to be scanned Figure 4 13 The application makes the default selection based on the barcode of the array plate You can select the specific array to scan by overwriting the default selection The default selection is all the pegs and they are selected by pressing the lt NEXT gt button Chapter 4 Wash Scan Workflow 45 Figure 4 13 Selecting array s ES AGCC GeneTitan Instrument Control File Tools Help lal Stop Email Help ji System Status System Setup Setup Option Plate Information Barcode 550 IOTZKKKEKKKKERKER System Layout Array Selection Used Hub Tray Scan Tray Plate Type 550001 Protocol Name 550001 protocol Stain 1 Tray Stain 2 Tray Location Load consu
23. on the Biomek FX Target Prep System Instrument the robot will aliquot the hyb cocktail stains and array holding into the appropriate GeneTitan consumables Refer to the appropriate user guide for the target preparation for additional information The static electricity from stain trays must be dissipated before the consumables are placed on the Biomek FX TPE system The stain tray covers and scan tray cover must be processed as described in this user guide to remove Static electricity NOTE The hyb cocktail must be aliquoted into the GeneTitan Hyb Tray as described in the user guide for the appropriate expression assay Refer to the specific user guide for that assay for further information 1 Place all the stain trays and scan and stain tray covers required to process a run on a table top Use the anti static gun and follow the de static procedure described in Anti Static Procedure for GeneTitan Instrument Trays and Covers on page 9 El IMPORTANT When aliquoting the reagents be careful to prevent bubbles from forming If bubbles should form remove them using a pipette tip IMPORTANT You must dissipate the static electricity from every cover before placing on top of the stain trays 2 Aliquot 105 uL of the Stain 1 into the GeneTitan Stain Tray identified with the label GeneTitan Stain Tray P N 501025 on the tray 3 Use the stain tray cover provided with the GeneTitan Consumable Upgrade kit to cover the Stain 1 tray as shown
24. out via e mail configured through the AGCC e mail configuration editor Since the user is not likely present this is the best way to alert the user to a problem in a timely manner It is strongly urged that users keep at least one on call e mail contact in the AGCC e mail configuration editor to respond to an event requiring user intervention E mail contact can include a cell phone to receive the e mail as a text message e g 4151234567 att mms txt Context Specific Messages Context specific error messages exist in the software that will be tailored to an error condition occurring in specific process steps It is not possible to list all possible combinations of events here In certain cases the error message will be shown to alert the user but the process may attempt to continue without waiting for acknowledgement This is done to try to ensure that a condition occurring on one plate will not affect processing for other plates If the error requires a specific user response processing for all plates may suspend at the next logical pause point for each plate being processed Table A 4 GeneTitan Instrument Error Messages Chapter A 67 Application launch 93 2009 11 42 15 AM Message Meaning Help About Machine ame 3300 G T J6YFER 1 OSY ersion Microsoft Windows NT 5 1 2600 Service Pack 3 User ame AFFRUser Product ame HT SECC Product ersiory 3 001212 Bar de cay reli aps HRe ic ree space ra alate i
25. plate failure An error similar to the message below will be reported This message is an indication a previous drain was incomplete or that a sensor is malfunctioning or out of adjustment The problem is usually intermittent and the plate currently running may complete without additional problems Do not start any additional plates on the system until the problem has been addressed Solution o Allow the current plate to finish processing if no other system is available oO Contact Affymetrix Field Service to have the sensor adjusted or replaced o Do not start any new plates until the problem is resolved Warming Scanner already launched Click OF to relaunch Recommended Click Cancel to skip relaunch For debugger use only Imaging system scanner error messages Scanner re launch option The production release code should never provide the option seen below which allows the user to skip re launching the application during application launch This is available only in development If seen outside development contact Affymetrix field service to verify proper installation of the current production released AGCC software which includes GeneTitan Table A 4 GeneTitan Instrument Error Messages Continued Chapter A 73 Message Meaning Error Scanner pp launch timeout Scanner is disabled Please exit program and resolve the Scanner problem IF you choose to continue with Scanner disabled thie Wi
26. process provides guidance on how to use the anti static gun on the stain and scan tray covers only See Figure 1 9 EE WARNING The deionization steps 4 and 5 will damage the HT arrays on the plate Before using the anti static gun ensure that the HT array plates remain in their protective pouch and placed away from the deionization area You must place the scan tray and hybridization tray away from the area where you are performing deionization Treat the plate or lid as if it were divided into 6 sections and deionize as follows Place a Kimwipe on the benchtop Place the stain tray on a table top Use the anti static gun to aim at the center of each of the six sections on cover or tray and pull the trigger Ensure that a stream of ionized particles settles on all wells of the stain tray or cover to dissipate the static electricity Squeeze and release the trigger slowly 3 times over each section Squeeze for approximately two seconds and release for approximately two seconds 4 Place the stain tray cover with the flat surface facing upward on the Kimwipe Aim the anti static gun P N 74 0014 approximately one half inch away from the flat surface and pull the trigger As you pull the trigger move the gun across the cover so that the stream of 1onized particles settles on all areas of the cover and dissipates the static electricity Squeeze and release the trigger slowly 3 times over each section Squeeze for approximately two seconds and rele
27. scanner application is killed and re launched If it still fails then the use has an opportunity to be informed and correct the problem and then press Retry If the problem cannot be corrected the scanner is placed offline Any plate currently in the scanner will stay in the scanner until GeneTitan can be re launched to again Any plates moving through the system will automatically be aborted after fluidic processing completes they will not attempt to move into the scanner Error Cannot relaunch Scannerdpp Plate detected in scanner handoff 55000112345678901 2345 Please resolve the problem before retry Plate detected in scanner handoff If GeneTitan cannot clear a plate detected in the scanner handoff the scanner application cannot be started Solution o Re launch GeneTitan o If the problem persists contact Affymetrix Field Service Are you sure Processing plates Aborting a run confirmation When the user selects a plate to abort from the STOP button the following confirmation is presented The system is running on battery Plate processing is not supported Running on battery unable to start process When the GeneTitan system detects that it is running on battery this indicates that the facility power is currently down If the user attempts to start a run the following message will appear Solution o Verify the UPS has not been accidentally unplugged from the facility power o Wait for t
28. side of the open drawer to remove or place the plate GeneTitan Instrument Care and Troubleshooting GeneTitan Instrument Care This chapter provides instructions on caring for and maintaining the instrument and on troubleshooting if problems arise 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 a Always use deionized water to prevent contamination of the lines Change buffers with freshly prepared buffer at each system startup The GeneTitan Instrument should be positioned on a sturdy level bench away from extremes in temperature and away from moving air En IMPORTANT Before performing maintenance turn off power to the instrument to avoid injury in case of an electrical malfunction Cleaning and Maintenance Monthly The GeneTitan family of instruments require little in the way of customer maintenance The instruments must be kept clean and free of dust Dust buildup can degrade performance Wipe the exterior surfaces clean using a mild dish detergent solution in water Do not use ammonia based cleaners or organic solvents such as alcohol or acetone to clean the system because they may damage the exterior surfaces The following tasks should be performed regularly to ensure the Imaging Device remains in working order Wipe down the outer surface of the Imaging Device with a dry cloth Every Six Months R
29. tab Figure 2 4 Figure 2 4 Setup options for processing array plates FE 4GCC GeneTitan Instrument Control File Tools Help Stop Email Help System Status System Setup H jb ash S can Plate Information Barcode IE Wash Scan Resume Scan Plate Type oO Unload Plates Protocol Name 2 Click the Setup Option drop down list box to view options a Hyb Wash Scan u Hyb Wash Wash Scan a Wash Scan Resume Scan Unload Plates Hyb Wash Scan This setup option enables you to hybridize wash stain and scan an array plate on the GeneTitan Instrument Li IMPORTANT When running a multi plate workflow you must pay careful attention to the software prompts that tell you which side of the drawer to place or remove a plate tray a Hyb the array plate is moved to the hybridization oven inside the instrument Each sample in the Hyb Tray is hybridized to an array on the Array Plate Wash samples on arrays are washed and stained Scan The array plate is moved to the imaging device in the GeneTitan Instrument and each array is scanned Please go to Chapter 3 Hyb Wash Scan Workflow on page 19 for instructions on the Hyb Wash Scan Workflow for expression array plates Chapter 2 Starting the GeneTitan Instrument and AGCC 17 Hyb Wash If this setup option is selected array plate processing will stop after the array has gone through fluidics processing Use this option if an array plate cannot b
30. the prompts shown below appear then a i r AE by scanning the barcode or library file for the product is either not installed or i missing some components Solution S50001 protocol does not exist o Use the Library file installer available via the Barcode or Protocol file selection may be incorrect Affymetrix Launcher to load the library files required for the product you are running o Re launch GeneTitan after installing the library files Media file C Command_ConsolesLibran550032 med does not exist Barcode may be incorrect Please resolve the problem before pressing Retry Press Cancel to exit Setup Error GetMediaFilePath failed MediaFilePath Media File for barcode 5S50032test Axes does not exist Possible causes Incorrect barcode Incorrect library installation Incorrect Command Console installation Please resolve the problem and retry setup again Array file arayFileName does not exist Barcode may be incorrect Please resolve the problem before pressing Retry Press Cancel to exit Setup Please select Setup Option Table A 4 GeneTitan Instrument Error Messages Continued Chapter A 75 Message Meaning Unable to verify trav type using the tray barcode Verify orientation and that the tray type loaded is a scan tray Press Ok or the flashing blue Confirmation button when ready Barcode read failure for scan stain or hyb tray During the reagent load steps plate set
31. the run is restarted or resumed It only makes sense to select YES if you will restart the run immediately either in either Wash Scan or Wash Scan Resume mode operation If a Hyb Wash Scan is started as the next operation any saved reagent in the Wash A or Wash B reservoir will be disposed of since HWS starts a new run The Lamp Life Remaining is less than 60 hours Lamp Life Remaining is 59 kours Using the lamp beyond the recommended tre period result in poor quality data Please exit the program and replace the lamp n IF you have replaced the lamp please reset the counter For lamp life remaining Press OK to reset the counter for lamp ite remaining Press Cancel to ship reset Lamp life remaining less than 60 hours This message will be displayed when the lamp life is expiring Click OK if you changed the lamp prior to starting GeneTitan This will reset the lamp life counter Click cancel if you have not replaced the lamp 70 GeneTitan Instrument User Guide for Expression Array Plates Table A 4 GeneTitan Instrument Error Messages Continued Message Meaning Error processing 5500321212121212 while trying to process fluidic macro Fillw ashB Event detected at 9 6 2009 4 55 45 PM 4 possible leak has been detected and valve power is disabled through a hardware interlock Software control of the valve system has been disabled Corect the problem before continuing Select Ret to continue proce
32. till processing is complete or abort processing before shutting down the system Running shutdown The shutdown menu available from the tools menu drop down explains the special steps it will take before closing the application Shutdown while processes running If the user attempts to shut down GeneTitan when processes are running the user is prevented from exiting Before attempting to exit the running processes should be aborted using the STOP button HTS6CE is closing because 4 5Abnormal application exit If the application exits unexpectedly but ina controlled manner the reason for the exit will be included in the message below Typically this message will be oriented to a software developer and not be GeneTitan application specific If this happens get a screen capture of the message box and note the circumstances leading up to the event Report the failure to Affymetrix field service Note reason will appear in the message box Solution o Reboot the computer o Launch GeneTitan o Perform appropriate resume and recovery operations as required oHyb can be completed off line or by restarting GeneTitan and choosing to leave the plate in the oven oFluidic process can be resume using Wash Scan Resume mode operation Table A 4 GeneTitan Instrument Error Messages Continued Chapter A 71 Message Meaning Motion movement error Movement that cannot be completed is reported as an error Man
33. tray cover as shown You must load the scan tray into the instrument with the Affymetrix For Research Use Only label facing out towards you and the notch on the left front side The tray barcodes should be in the back facing away from you and into the instrument 42 GeneTitan Instrument User Guide for Expression Array Plates Figure 4 8 Loading the scan tray and cover The correct orientation in the loading of the scan tray into Drawer 2 the notch faces out and to the left You must remove the black base Scan Tray with cover loaded in drawer 2 Do NOT load the protective black base packaged with the Scan Tray Figure 4 9 Loading the scan tray into Drawer 2 Chapter 4 Wash Scan Workflow 43 Figure 4 10 Confirm tray type FE Waming The system was not able to verify the GeneTitan Consumable Tray using the barcode on the Tray Please verify that the tray in the drawer is a SCAN tray and that it has the correct ORIENTATION The scan tray should have a cover or array plate as applicable in the correct orientation Details The consumable is either not the correct consumable not loaded correctly or its barcode is not readable Proceeding with an incorrect or incorrectly loaded consumable can result in a loss of consumables loss of samples and may require a field service engineer to service the instrument Refer to the System Setup Tab or the User Guide provided with t
34. BI gray To manually select arrays Will not be scanned Not available A Select the Manual Array Selection checkbox B Select the arrays to be scanned You can select arrays by Clicking and dragging through the grid a Pressing the Ctrl button down and clicking in different squares C Click Next NOTE If there is insufficient memory on the computer s hard drives to store the data from a plate a notice appears 5 Click the Next button to start the run The Start Processing dialog box opens Figure 5 7 Chapter 5 Scan Workflow 51 Figure 5 7 Start Processing notice Start Processing Please press the CK button to confirm i Cancel Wi This will start the WashScan in the Left Position 6 Click OK to begin the Scan workflow The instrument performs the workflow steps for Scan and can be tracked in the Status window Running Multiple Workflows at the Same Time for Expression Arrays When processing expression arrays the GeneTitan Instrument can run two different workflows at the same time This enables you To load a series of array plates with hyb trays and consumables for the Hyb Wash Scan workflow to process arrays more quickly Ba IMPORTANT You cannot load Genotyping and Expression array plates at the same time To run an array plate that was processed using a different system through the scan workflow while another array plate is going through earlier stages of the Hyb Wash
35. It is critical that the Hyb Tray and the Stain Trays be labeled on the front edge of the tray only The front edge of the tray is the short side with the lettering A1 through H1 Do NOT mark these trays on any other side as this can interfere with sensors inside the of GeneTitan Instrument and result in experiment failure To ensure proper placement of lids onto stain trays and trays onto the GeneTitan Instrument you can also mark the notched corner of the trays and lids Figure 1 6 Marking GeneTitan Hyb Trays and Stain Trays Do NOT write or make notes along the long side of tray Use front of tray to Notch should kele write or make notes face the front Do not write w aa or label trays ST Na CU n Use area in front along the long side of tray to write or make notes Notch should face the front Chapter 1 Before Using the GeneTitan Instrument 9 Anti Static Procedure for GeneTitan Instrument Trays and Covers Use the following technique to destatic GeneTitan Instrument Stain Tray trays and lids n IMPORTANT Except for the HT array tray and the hybridization tray you must deionize all GeneTitan stain trays stain tray covers and scan tray covers using an anti static gun You must do this before you fill the trays with reagents and before you place the covers on the trays Deionization removes the static electricity The presence of static electricity on the underside of the cover can cause the grip
36. KG Affymetrix User Manual GeneTitan Instrument User Guide for Expression Array Plates P N 702933 Rev 1 For research use only Not for use in diagnostic procedures Trademarks Affymetrix Axiom Command Console DMET GeneAtlas GeneChip GeneChip compatible GeneTitan Genotyping Console NetAffx and Powered by Affymetrix are trademarks or registered trademarks of Affymetrix Inc All other trademarks are the property of their respective owners Limited License Subject to the Affymetrix terms and conditions that govern your use of Affymetrix products Affymetrix grants you a non exclusive non transferable non sublicensable license to use this 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 In particular no right or license is conveyed or implied to use this Affymetrix product in combination with a product not provided licensed or specifically recommended by Affymetrix for such use Patents Arrays Products may be covered by one or more of the following patents U S Patent Nos 5 445 934 5 744 305 6 399 365 6 733 977 and other U S or foreign patents Products are manufactured and sol
37. Plates 35 Wash Scan Workflow kk kk kk kk kk kk KK KK KI KK kK kk kk kk kk kk kk ka 37 Loading Instrument for Wash Scan Workflow kk kK KK KK ee rene 37 Scan Worktiows acca wuca kk ca ada ak anal ad kd SEE woe a dr dnd d t ar di ewes di 47 Loading Instrument for Imaging Workflow Aa kk kK KK KK KK eee 47 Running Multiple Workflows at the Same Time for Expression Arrays Bl Running the Scan Workflow with Other Workflows kK cece eee oy GeneTitan Instrument User Guide for Expression Array Plates Appendix A Appendix B GeneTitan Instrument Care and Troubleshooting 53 GeneTitan Instrument Care A kk kk kk kK KK KK K KI KK KII KI KI K KI KI KI KI KI KI KI KI KI KI KI KI K K KII KI KK K D3 Cleaning and Maintenance kk kk kk KK KK KK KI KK KI KK KI K KI KI K KI KI KI KI KI KI KI KI KIR KI KI KK KK 53 al N EEEE E EET E E E E E 53 Every SIX MORT S ocd aw oo a k da a al ene ene ewe gow be ob eed dk ron d dew dO eh ee os 53 Servicing the Outer Enclosure Fan Filters AA KV KK KIRI KK ee 53 Replacing the Bottle Filters kk kk kk kK KK eee DD Replacing the Xenon Lamp in the GeneTitan MC Instrument 57 TROUDICSMOOUING se sieaa e sedaane 2a ann ak hnek a d EDR di n dis s a n al d ln d rana AE c h sk R GG d Hb dli d dli dk J 62 oe FREE SEE E E EET EEE E EE ene ere 62 AGCC Log Files for GeneTitan MC Systems kk KK KK KIRI K
38. Plates Starting the GeneTitan Instrument and AGCC This chapter provides instruction for starting the GeneTitan Instrument and Affymetrix GeneChip Command Console Software AGCC An overview of the expression array plate processing options is presented Starting Command Console Launcher and the GeneTitan Instrument Control Software Use the Affymetrix GeneChip Command Console AGCC software Launcher to access the AGCC GeneTitan Instrument Control IC software Starting the Command Console Launcher The Command Console Launcher Figure 2 1 provides a convenient way to open the AGCC software applications 1 Click the Microsoft Windows Start button Ht start and select Programs Affymetrix gt Command Console Affymetrix Launcher or double click the Launcher shortcut on the desktop The Command Console Launcher opens Figure 2 1 Figure 2 1 Command Console Launcher window the GeneTitan Family of instruments Command Console LJ A AGCC Viewer GeneTitan GeneTitan Instrument Control Instrument Control EE LEL Analysis Applications Command Console components for performing Array Processing Workflow 3 E Ren Affymetrix Analysis Applications for analyzing cell intensity data Tools Data Exchange Console Eita Fil init Affymetrix Tools for migrating data A and installing necessary support files a Reconnector GeneTitan Library File Installer A Email Configuratio
39. TA CON MOCNE naw ev Have you teplaced the fers Select YES to continue processing using mew filters NO to continue processing without changing fiters thes waning may appear each time GeneTilan ic launched No BE Filter Change R equire d BUFFERA_TO_WASHA 3 17 2010 3 50 53 AM Wang The ferm the Genelitan reagent buffer bottles and or DI water bottle should be replaced before processing any more atay plates You need 3 hber GeneTiten instrument Possible iter foe BUFFERA TO WASHA Recent fd dala shows a trend of increanng fil imes Median value for time remaining before bmeout i eB a Mosi recent average fill lima remaining is 6 166 rec Amay plates processed wih duty liers in reagent buffer or rinse bottle may exhibit quality issues The bottles are depressunzed and hikers can be c FiA Do not change fiters while Bene Talan is process Pleste contact your local Alfymetix representative or FSE to obtain information on procuring new fiters Have you replaced the fikers Select YES to conhnwe processing using mew NO to continue ya RE rewino iis his warin na appek each tiya Girat kan ir arched TT The message boxes displayed in Figure A 2 will provide information on fluid dispense errors that were detected by the instrument for any of the bottles or when the instrument detects an increase in the amount of time that is required to perform the fill operations NOTE The reagent bottles are depressurize
40. Tray Consumables on page 4 Proper Tray Alignment and Loading on page 5 Correct Placement of Stain Trays and Covers on page 7 Labeling GeneTitan Reagent Trays on page 8 Anti Static Procedure for GeneTitan Instrument Trays and Covers on page 9 a E mail and Telephone Notifications from the GeneTitan Instrument on page 11 Equipment Reagents and Consumables Required Consumables for the GeneTitan Family of Instruments All consumables for the GeneTitan Family of Instruments are provided by Affymetrix The following table provides guidance on the consumables that are shipped with the Array Plate B IMPORTANT All covers must have barcodes Discard any cover without a barcode Table 1 1 GeneTitan Instrument consumables Item HT Array Plate Package Part Number Labware Image Information All array plates have The HT Array Plate shipping package the PN 202091 etched n includes the following on the on the plastic a The function of the clear plastic cover for the Array Plate is to protect the Array Plate during transport You may discard this after removing the Array Plate The Array Plate must be protected at all times from damage or exposure to dust The Array Plate must be in the Blue Array Plate Protective Base at all times The Blue Array Plate Protective Base in the package must be used to protect the Array Plate from damage Gear Tray an i Shipping Cover To be Distarded 2 GeneTit
41. an Instrument User Guide for Expression Array Plates Table 1 1 GeneTitan Instrument consumables Continued Item protective base Scan Tray with cover Part Number HT Scan Tray Packaging Black Scan Tray PN 202096 Scan Tray 501006 Cover 202757 Labware Image Information Harcodaed Sean bay Cover PM 202757 GeneTaan Scan Tray Ph S000 ior PN SCBA Notched comer of bay end cover line up NOTE The Scan Tray cover should have a barcode on the plastic If the tray cover you received does not have a barcode or does not match the scan tray cover shown in this picture please contact your Field Application Specialist The HT Scan Tray shipping package includes the following a The HT Scan tray includes a Scan Tray cover The tray cover should be used to cover the scan tray before placing the tray in the GeneTitan MC Instrument The Tray cover should be deionized before use See the section Anti Static Procedure for GenetTitan Instrument Trays and Covers on page 9 for the anti static procedure The Scan tray must be protected at all times from damage or exposure to dust The Scan Tray must be in the Black Plate Cover at all times The Black Scan tray cover in the package is used to protect the scan tray glass from damage The black scan tray is distinct trom the Blue Array Plate Protective Base and must not be used with the Array Plate Remove the protective base trom the scan tray
42. anStain Tray 501025 Tray cover Cover 202757 The GenetTitan stain trays must be placed in the GeneTitan instrument with the GeneTitan stain tray cover It is important to remove the static electricity on the cover and the stain tray prior to loading the tray into the GeneTitan instrument See the section Anti Static Procedure for GeneTitan Instrument Trays and Covers on page 9 for the anti static procedure GeneTitan Hyb 500867 Tray The GeneTitan hybridization trays are packaged in white pouches with the label HT Hybridization Tray After aliquoting the hyb cocktail into the hybridization tray the tray should be loaded into the GeneTitan instrument with the barcode facing away from the operator i e Barcode should be on the back side 4 GeneTitan Instrument User Guide for Expression Array Plates Proper Installation of the GeneTitan Tray Consumables It is very important that you install the GeneTitan tray consumables in the proper orientation The barcode faces into the instrument IMPORTANT You must rotate and install the trays so that the barcode faces into the instrument See Figure 1 1 on page 4 for additional details Notch This faces out and left FRONT OF INSTRUMENT FACING YOU Barcode This faces BACK TO THE REAR of the instrument Turn the tray and cover combo so that the barcode faces BACK AND INTO the instrument and the notch faces OUT AND TO THE LEFT Figure 1 1
43. appropriate recovery procedure based on the condition of the process when the event occurred Recovering the Instrument from a Power Interruption Recovering the Process After a User Power Interruption If you cycle the power of the instrument the GeneTitan Instrument can recover itself from its last position whenever you restore the power to the instrument and only when you initiate another run This means that the GeneTitan Instrument will automatically home all stages in the instrument without any hardware crashes or damage regardless of the positions of the stages at the time of the power interruption If the power interruption occurs while the plate gripper is handling the array plate the instrument can home all of its stages without any damage to the array plate Procedure for Recovering a Process 1 Resume power 2 Initiate another run For this procedure see the Affymetrix GeneChip Command Console User s Guide P N 702569 The plate confirmation button light Figure B 1 will flash blue while the system homes Confirmation Button to open close drawers 3 The flashing plate confirmation button light will stop If required the AGCC application will prompt you to remove the plates Follow the unload plate procedure in the AGCC application 80 GeneTitan Instrument User Guide for Expression Array Plates Recovering the Process After a Power Failure The intent of this recovery procedure is to recover the ar
44. ase for approximately two seconds Place the treated cover or tray on the Kimwipe and lift it up Do one of the following a If the Kimwipe does not adhere to the plastic proceed with the step a If the Kimwipe adheres to the plastic then perform steps 3 and 4 again If it continues to adhere to the plastic then the gun 1s not working and you should replace it Chapter 1 Before Using the GeneTitan Instrument 11 Figure 1 9 Removing the static charge from Stain Trays and lids Treat the inside surface of Stain Trays right and cover left IMPORTANT Remove static gun cover before use If a Kimwipe sticks to treated surface treat again following this procedure If the Kimwipe still adheres replace the antistatic gun E mail and Telephone Notifications from the GeneTitan Instrument We strongly recommend that you configure the Affymetrix GeneChip Command Console AGCC software to send you GeneTitan Instrument notifications It is critical that you know when the instrument requires your attention either for sample handling or troubleshooting Rapid notification can lessen the risk of sample loss Notifications can be sent to e mail addresses and telephones Refer to the AGCC user manual for instructions The types of notifications available will let you know when a process Starts Completes a Aborts Encounters an error 12 GeneTitan Instrument User Guide for Expression Array
45. ay may stick to the cover and be lifted out of place inside the instrument Follow the software prompts and load the array plate and trays as directed pressing the Confirmation button after loading each tray or array plate Chapter 3 Hyb Wash Scan Workflow 27 BE AGCC GeneTitan Instrument Control Workflow Steps Select arrays to scan Start Processing Plate tray position indicators 28 GeneTitan Instrument User Guide for Expression Array Plates Figure 3 10 Scan tray loaded in drawer 2 Scan Tray with cover loaded in drawer 2 Do NOT load the protective black base packaged with the Scan Tray When you load the scan tray the internal bar code reader reads the barcode to see if it is the right kind of tray in the right orientation If the information is correct the application allows you to proceed to the next step Ifthe instrument is unable to read the barcode it will push the tray out and will prompt you to load the correct plate with the proper orientation into the instrument Figure 3 15 Figure 3 11 Confirm tray type Verily Scan Tray Load Waming The system was not able to verify the GeneTitan Consumable Tray using the barcode on the Tray Please verify that the tray in the drawer is a SCAN tray and that it has the correct ORIENTATION The scan tray should have a cover or array plate as applicable in the correct orientation Details The
46. barcode and the plate type specified in the Barcode field and Plate Type field on the Setup page If the information is correct the application allows you to proceed to the next step If not the application will prompt you to load the correct plate into the instrument Figure 5 5 Figure 5 5 Barcode error notice FE verify Drawer 2 Left Side Array Plate Lond Waming The system was not able to verify the array plate barcode Please venty that the tray on the left side of the drawer is a SCAN tray with an ARRAY PLATE in the correct ORIENTATION Details The consumable is either not the correct consumable not loaded corectly or its barcode is not readable Proceeding with an incorrect or incorrectly loaded consumable can result in a loss of consumables loss of samples and may require a field service engineer to service the instrument Refer to the System Setup Tab or the User Guide provided with the Assay or AGCC for instructions on proper consumable placement Press the flashing blue confirmation button or Press OF Gene Titan wil venty the barcode and orientation Press Skip Gene Titan wall NOT venfy the barcode and onentation The barcode entered at registration will be used se 3 Click OK to retry and check the loading of the array plate or Click Skip if the instrument has problems reading the barcode and after verifying that the trays have been placed in the proper orientation The applicati
47. cation and then restart it If the same error occurs shut down both the application and the computer and then restart If it still occurs shut down the entire unit and then restart Insufficient Disk Space Notice If there is not enough memory on the computer s drives to save the data from an array plate a notice appears when You first initialize the software and instrument You select arrays for imaging Figure A 14 Insufficient Disk Space Notice Insufficient Disk Space Error Barcode DrivelD SpaceRegob Freespaceob Plate State Scannerstate SoU032123456 7890125456 C 12 311 Hyb Waiting DrivelD FreeSpaceob FreespaceRemainingSB Status 299 Insufficient disk space Please free up sufficient disk space before scanning starts You can check for sufficient disk space with the the menu command under Tocls Check vailable Disk Space Failure to do so will result in lost of data If you see this notice you will need to free up sufficient disk space before imaging starts 64 GeneTitan Instrument User Guide for Expression Array Plates Problems and Solutions The following tables list possible problems and their solution that you might encounter in the use of the GeneTitan Instrument Table A 1 lists common power problems and possible solutions Table A 1 Common Power Problems and Possible Solutions Problem Probable Cause Possible Solutions The instrument cannot be powered up or do
48. consumable is either not the correct consumable not loaded correctly or its barcode is not readable Proceeding with an incorrect or incorrectly loaded consumable can result in a loss of consumables loss of samples and may require a field service engineer to service the instrument Refer to the System Setup Tab or the User Guide provided with the Assay or AGCC for instructions on proper consumable placement Fress the flashing blue confirmation button or Press OK Gene Titan will verity the barcode and orientation Press Skip Gene Ttan will NOT verty the barcode and orientation Chapter 3 Hyb Wash Scan Workflow 29 4 Click OK or press the Confirmation button to continue or click Skip to continue without confirming the barcode read operation Click Skip if the instrument has problems reading the barcode and after verifying that the trays have been placed in the proper orientation and are in the correct drawer location NOTE This message can be triggered when using consumable trays or tray covers that do not have barcodes or if the barcodes are un readable The message can also appear if the barcode reader inside the instrument is in operational or out of alignment Please call your local Field Application Specialist if the Confirm tray type message is repeatedly displayed The software prompts you to load the stain trays After the trays have been loaded the software prompts you to load the Array Plate and Hybrid
49. correct orientation select No The system will continue processing using the bar code you typed or scanned with the external bar code reader o If you are unsure that you loaded the correct plate in the correct orientation select Yes to retry loading the plate If No is selected the selected the user is given the following message to acknowledge that the barcode being used was provided by the user not verified by the internal bar code reader Setup will continue when the user selects OK Cannot proceed because Different bar code Part number from Barcode read by instrument is different from one registered If the GeneTitan system successfully reads a bar code Part number from Barcode read by intrument 550001 Part number from Barcode registration 500002 and it does not match the bar code entered by the user the system will force you to reload the plate The Please redo setup and register with the correct barcode following message is displayed Barcode for this plate is already used by the plate in the system Duplicate bar code i Please setup again with the correct barcode If the barcode being set up matches any actively running plate in the system the user must re enter a barcode that is not already in use The following message is displayed Cannot find the protocol file for the entered barcode Missing library and or protocol files Please make sure the protocol files are properly installed and or If any of
50. d a half hours if the first array is a 16 or 24 array plate Chapter 3 Hyb Wash Scan Workflow 35 When running a series of expression array plates there are restrictions on the sorts of arrays you can run through in a series because of a Differences between the workflow for 3 IVT and WT expression array plates The number of arrays on a plate There are limitations on your ability to mix array plates with different numbers of arrays due to timing differences in the scan and other issues GeneTitan can process array plates with 16 24 or 96 arrays on a plate The Workflow pane of the System Status screen Figure 3 20 displays the time you need to wait before beginning a second workflow The instrument will show prompts on plate load time based on the plate you run first Figure 3 20 Workflow pane Work Flow Barcode Plate Type Location Hyb Status Fluidics Status Scan Status Estimated Completion Time 50001403749512100841 550001 Left Position Running Waiting Waiting 9 9 2008 11 17 47 AM Estimated Time Window to Run Next Hyb Wash Scan HT Array Type Same plate type v 9 9 2008 12 28 06 PM 9 9 2008 11 12 48 AM NOTE The times shown will differ for 3 IVT and WT expression array plates If you are performing the Hyb and Wash processes on array plates in a different system you can load a second array plate for the scan workflow shortly after you begin a hyb wash scan workflow The Scan workflow opti
51. d under license from OGT under 5 700 637 and 6 054 270 Scanner Products may be covered by one or more of the following patents U S Patent Nos 6 141 096 6 262 838 6 294 327 6 403 320 6 407 858 6 597 000 7 406 391 and other U S or foreign patents Software Products may be covered by one or more of the following patents Products may be protected by one or more of the following patents U S Patent Nos 6 090 555 6 611 767 6 687 692 6 829 376 7 130 458 7 451 047 and other U S or foreign patents Copyright 2010 Affymetrix Inc All rights reserved Contents Chapter 1 Chapter 2 Chapter 3 Chapter 4 Chapter 5 Before Using the GeneTitan Instrument 2 000 eee eee 1 Equipment Reagents and Consumables Required 0 0 kk KK KK KI KI KI KI KII KI KI eee 1 Proper Installation of the GeneTitan Tray Consumables A KK R eee 4 Proper Tray Alignment and Loading kk kk kk kK KK KK KI KI KI KI KI KI K KI K K KI KI KI KI K K KI KI KI KI K K KK 5 Correct Placement of Stain Trays and Covers kk kk kK KK eee 7 Labeling GeneTitan Reagent Trays 0 kk kk kK KK KK KK KK KI KK KI KI KI KI KI KI KII KI K K KI K K KI KII KK 8 Anti Static Procedure for GeneTitan Instrument Trays and Covers 9 Testing the Anti Static GUN 21 kk kK KK KK KI KK KK KI KI KI K KI KI KI KIRI KI KI KII KI KI KI KI KI KI KI KI KI KI k 10 Deionization Procedure AA kk kk kk kk KK KK KK KK KK KI KK KI KI
52. d when this warning message is displayed It is safe to change the filters in all three fluidic bottles when this message is displayed After changing the filters in all three bottles using the procedure described below please press the Yes button to continue If you choose to ignore the error message press the No button This warning message will be displayed each time AGCC instrument control software is launched You may also experience data quality issues if particulate matter cannot be trapped by the filters if they are clogged We recommend that your site keep three spare filters in the event they need to be replaced The procedure for replacing the filters is simple 56 GeneTitan Instrument User Guide for Expression Array Plates Part details Affymetrix P N 01 0671 Figure A 3 Replacing the Filter Filter Holder Removing and inspecting the Filter 1 Loosen and remove the cap on the bottle 2 Carefully remove the filter from the end of the filter body Use a firm stick to remove the filter from the end of the filter holder 3 Visually inspect the filter If one of the filters appears to have a concentration of dirt or contaminate in it discard it and obtain a new one Replacing the Filter 1 Insert the filter into the end of the filter body 2 Replace the cap onto the bottle and tighten it 3 Repeat for each bottle IMPORTANT Replace one filter at a time to ensure the correct connection of the b
53. drawer 2 If the required position on drawer 2 is not available then the user will be prompted to clear drawer 2 with the following messages WashB is curently filled with BUFFERB_TO_WASHB Wash temperature set point is 39C WashB current temperature is 27 70 Was a plate process interrupted or aborted that you intend to resume using this current fill The setpoint will be reset when vou resume the run and will be based on the fluidic protocol selected Selecting NO will dran the current fill IF you do not intend to resume an interrupted run immediately select NO IF you select YES the system will maintain the temperature at this setting until the fluidic protocol resets the it Resume option for filled Wash A or Wash B detected at startup In a case where the system may have been interrupted abruptly there may be Wash B or Wash A filled already when the system starts up The Wash B may already be at the process temperature and draining would cause a process delay As an aid to resuming the operation as fast as possible the user is provided the option to retain the current fills when the system starts up If you do not intend to resume the run immediately select No so the indicated reservoir will be drained If restarting the run be sure there is sufficient reagent in each bottle since this draining operation means the reagent will need to refill for the current operation This message and option to drain will be presented again when
54. e UPS battery dropping below 50 is detected then the instrument moves the array plate to the scan tray b IMPORTANT The system does not have any resume capability from this condition Chapter B 81 If the plate was in a final wash A it is then possible for you to resume the run using the scan mode only You will need to use your Judgement on this as to whether it is worth continuing the run The 50 charge required on the battery is a configured setting and may change to a higher or lower setting in the future You might just refer to that level as the minimum allowed UPS battery charge which just happens to be 50 in this release Resuming the Process from a Workstation or Application Freeze If the workstation has locked up you must reboot the workstation If the application has crashed you must relaunch the AGCC application Neither of these actions will cause the instrument to home all the stages These stages shall remain in the same positions as before the reboot or the relaunch Follow these procedures 1 Ifthe scanner freezes during the scanning of an array plate reboot the Affymetrix GeneChip Command Control AGCC application After the application has opened you may initiate a scan of the unscanned wells 2 Ifthe scanner freezes when the scanner is scanning an array plate while the GeneTitan Instrument is processing another plate A If the other plate is in a fluidic process 1 Wait until the GeneTitan Instru
55. e array plate must be loaded with the blue protective base 6 GeneTitan Instrument User Guide for Expression Array Plates Figure 1 3 Proper alignment and loading of plates covers and trays in the GeneTitan Instrument See rt ES Tj 277 S gt i Xw gt Notched corner of Array Plate aligned with notched corner of blue base Tip Mark the notched corner of each plate cover and tray with permanent marker to help ensure proper alignment and loading Plates and trays must be seated in this groove The notched corner of all plates bases and covers and must be seated in this corner of the drawer per the Tray Alignment guide Chapter 1 Before Using the GeneTitan Instrument 7 Figure 1 4 Array Plate with protective blue base and the Hyb Tray aligned and properly loaded into drawer 6 Array Plate with protective blue base Hyb Tray En SEAT Ty AN Fare ME ve Frost JEG DAN a F xue FOR RESEARCH USE ONLY KR IMPORTANT Always place the flat side of the cover against the Stain Tray Figure 1 5 Placement of covers on trays Correct placement of cover on Stain Tray Incorrect placement of cover on Stain Tray 8 GeneTitan Instrument User Guide for Expression Array Plates When preparing the reagent trays to be loaded onto the GeneTitan Instrument it is convenient to mark the front of each tray in a way that identifies its contents En IMPORTANT
56. e lamp power switch is in the ON position 4 The scanner is not busy Failure to replace the lamp will cause poor quality data Failure to turn on the lamp will cause Scanner error Ves Mo 62 GeneTitan Instrument User Guide for Expression Array Plates 3 Click Yes if you want to reset the counter The software will display a message that confirms that the software has reset the counter Figure A 13 Figure A 13 The counter is reset Lamp Life Management x Lamp life remaining has been reset to 500 hours Troubleshooting Log Files This section provides instructions on how to identify and solve simple problems with the GeneTitan MC Instrument If a problem or error occurs that is not listed in this chapter contact a Affymetrix technical support for assistance For software errors that do not involve hardware crashes the most common solution is to shut down the application and then restart it If the same error occurs shut down both the application and the computer and then restart If it still occurs shut down the GeneTitan MC Instrument and then restart The log files are produced by different AGCC 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 These files may be requested by your field application specialist FAS field service engineer FSE
57. e scanned on the same GeneTitan Instrument as the one used for hybridization and fluidics processing If the array plate cannot be scanned immediately after the Hyb Wash process is complete 1 Wrap the array plate in the scan tray with black protective base in aluminum foil to protect from light No lid is required Do not invert the plate stack If inverted the Hold Buffer will spill out of the tray 2 Store at 4C 3 Scan the array plate within 3 days or less When ready to scan the array plate 1 Keeping the plate protected from light bring the plate to room temperature for 20 min 2 Remove the aluminum foil and load onto the GeneTitan Instrument Please go to Chapter 3 Hyb Wash Scan Workflow on page 19 for instructions on the Hyb Wash Workflow for expression array plates Wash Scan Use this option if You wish to bypass the Hybridization step and perform only the Wash Stain and Scan steps In this mode of operation you can process one array plate at a time Please go to Chapter 4 Wash Scan Workflow on page 37 for instructions on the Wash Scan Workflow Scan Use this option To rescan an entire array plate or specific arrays on a plate that failed to scan for reasons such as bubbles or gridding failure a If you have hybridized and performed the fluidics processes off the GeneTitan Instrument In this mode of operation you can process one array plate at a time Please go to Chapter 5 Scan Workflow on
58. e that is ending hyb now In other situations the side may change to whichever side is available based on plates running in the system at the time While setting up the run for the new plate if the user selects Cancel in the setup tab the following message is displayed Cancel setup another run refers to the new plate being set up not the original plate that is still waiting to come out of hyb when the process is resumed This will resume the Hyb VWfash Scan in the Left Position Please press the OF button to confirm No do not load another plate If No is selected then the message shown below is displayed to confirm the original plate coming out of hyb will continue processing Note this may be left or right side position Selecting cancel at this prompt will abort the plate from the hyb oven and bring it out to drawer 1 for unloading This will resume the Hyb Mfash Scan in the Left Position and This will start another plate with Hyb Wash Scan mn mode in the Aight Position Please press the OF button to confirm Cancel resume setup Are you sure All open drawers will be closed Yes load another plate If Yes is selected the user will be prompted to load the new plate and sample on drawer 6 Then the message shown below is displayed to confirm the original plate coming out of hyb will continue processing along with the new plate that was just loaded into the system If the user selects Canc
59. el the following confirmation message is displayed Please remove any Trays loaded for Setup Another Aun Make sure on Left Drawer there is a Blue Tray bottom WITHOUT cover or ArayPlate on top Press OK when done Canceling setup leaving the blue tray Canceling during setup while other plates are still running will prompt the user to remove their sample tray and HTA plate It is essential that the user leave a blue cover in place on the left side of drawer 6 This will be used by other plates waiting to be processed in the system AGCCEmailConfigurationE ditor already running AGCC interface E mail configuration editor already running If this message is displayed locate the currently running configuration editor on the Windows task bar Only one instance of the application can be run at a time Error Cannot find 4AGCCEmailConfigurationE ditor exe Cannot find e mail application If this message is displayed the AGCC installation may be corrupt AGCC Command Console should be re installed Error Command Console not installed properly Failed at GetLibraryPaths Please exit Application and resolve problem before relaunching this Application Command Console not installed properly If this message is displayed the AGCC installation may be corrupt AGCC Command Console should be re installed 78 GeneTitan Instrument User Guide for Expression Array Plates Table A 4 GeneTitan Instrument Error Me
60. eplace the cooling fan air filters at the rear of the instrument Replace the Micropore filters in the Wash A Wash B and Rinse bottles If you run 4 8 plates week then the micro pore filters need to be replaced more frequently Servicing the Outer Enclosure Fan Filters Cleaning Schedule The GeneTitan fan filter cartridge Figure A 1 should be cleaned at least every 90 days of service Note that in some service locations the presence of excessive dust or particulate matter may necessitate cleaning the cartridge more often than 90 days A plugged filter cartridge can cause excessive temperatures within the machine that can cause unwanted evaporation on test media Part details Affymetrix P N 01 0669 Number of parts per assembly 3 54 GeneTitan Instrument User Guide for Expression Array Plates Cleaning Procedure 1 Slide the filter cartridge from the fan filter cartridge at the rear of the GeneTitan Instrument 2 Submerse in clean DI water Rinse and agitate gently to dislodge material 3 Remove from water and dry with clean compressed air or towels 4 When the filter cartridge is completely dry to the touch re install the cartridge Chapter A 55 Replacing the Bottle Filters The bottles used in GeneTitan Instrument contain a filter to remove particulates that may exist in the buffers and DI water The filters in the GeneTitan fluidics bottles Wash A Wash B and DI Water need to be replaced when the f
61. error messages will normally present after this general error message They are for field service reference if the solution listed below is unable to resolve the startup issue Likely cause USB disconnected no power or a safety mechanism front panel door switch open or trash bin missing Solution o Make sure all USB connections are made between the scanner fluidic system computer and UPS power backup o Remove any external USB memory drives that are not normally connected to the system o Reboot the computer o Log into the AffxUser account n If the trash bin has been removed from the system replace it into its normal location o If a drawer is visibly open before GeneTitan starts up hold the switch on the left side of the drawer down while starting GeneTitan Error initializing amp Y on node 25 System Auntime InteropSenvices COMException 080004005 The referenced object has not been initialized at CMLCOMLIib AmpObjClass Relrit at 0 FanelAttyk otor niti Error on axis Y Error initializing amp lt on node 26 System Auntime InteropSenvices COMException 080004005 The referenced object has not been initialized at CMLCOMLib AmpObjClass A elniti at 0 Panel Atuk otor niti Error on axis Z Error initializing amp Gripper on node 27 System Auntime nternpSenvices COMException Ox80004005 The referenced object has not been initialized at CMLCOMLib AmpObyjClass Relrit at 0 Panel AttyMotor Ir
62. es not start up properly Cause 1 Power has been disconnected Check the connections to facility power and UPS power Confirm that they are secure Shut down and restart the application Shut down and restart the computer u Shut down and restart the Imaging Device by unplugging and reconnecting the power cord on the back of the unit Do not use the power switch located on the front of the Imaging Device Shut down and restart the Fluidics by unplugging and reconnecting the power cord on the back of the unit Cause 2 USB cables are unplugged or plugged into wrong USB port or USB memory stick placed on system by user Exit the application Properly eject any user inserted memory stick that may have been inserted into the computer s USB ports Confirm that the USB connections to the labeled USB ports for the Imaging Device Fluidics and UPS are correct USB connections should be to the correct labeled USB port the ports cannot be moved Verify drive G is connected and the directory G tasks appears in windows explorer Verify drive F is connected and the directory F HT96 Fluidic Tasks appears in Windows explorer Verify the Windows Control panel gt Device manager gt Ports lists COM3 COM4 and COM5 where COM4 and COM5 are listed as a Prolific USB to Serial Comm Port If all three ports do not show up recheck USB connections Close and re open device manager to refresh the IO list when
63. etract Hybln 10 59 11 AM Gripper Close 10 59 17 AM Verify plates are securely clamped550001 1 x8888K8KKKRKKEE 10 59 17 AM 10 59 17 4M Press flashing Confirmation button 11 00 03 4M Retract Drawer6R 11 00 03 4M Gripper Close 11 00 08 4M 11 00 08 4M Press OK or flashing Confirmation button 11 00 44 AM StartStep 11 00 44 AM Waiting for Hyb to reach target 48C 11 00 44 AM Oven target 48 Current temp 30 11 00 59 AM Oven target 48 Current temp 30 11 01 14 4M Oven target 48 Current temp 30 1 GMM oO NEN EO ji35 E Will Be Scar ned O Will Not Be Scanned c Now Scanning E Scan Completed x Scan Failed Arrays Total Will Be Scanned Scanned 11 01 29 4M Oven target 48 Current temp 30 3 ee Fluidics Status Scanner Status System Ready At the start of hybridization after the array plate has been loaded on the hybridization tray the drawer opens and the software prompts you to check the positioning of the array plate on the tray Figure 3 19 34 GeneTitan Instrument User Guide for Expression Array Plates Figure 3 19 Verify Clamping notice and location of clamping points on the array plate and hyb tray Verify Clamping Verify plate clamping is secure Press Ok or the blue Confirmation button when ready Cancel Clamping points on Array Plate and Hyb Tray lt ____ Array plate Hyb Tray C
64. fer A or Buffer B Missing reagent bottle Or cap not secure a or low facility pressure or reagent bottle empty a or clogged filter Verify that all bottle caps are installed on the correct bottle and that they are snug Check facility CDA pressure is up and running Verify that the reagent bottle is not empty Replace the filter if all other options do not resolve the issue Select Retry to continue processing or Cancel to abort the run 66 GeneTitan Instrument User Guide for Expression Array Plates Error Messages Table A 4 lists various error messages Messages may occur as a result of normal operation of the GeneTitan system and are also used to report error conditions to the user This document outlines the most common message boxes the user may encounter normal operation as well as potential errors Practical recovery methods are detailed were recovery is possible by the user Using AGCC E mail Notification with GeneTitan MC Instrument Mail notification Once you configure the e mail with contact and notification information the software sends the e mail notification concurrently as the software displays the dialog box Message boxes that occur when the user is already present generally are not sent out through AGCC e ma il since the user is already present to be notified by a dialog box prompt Messages that occur as a result of an error while processing on GeneTitan are usually sent
65. files Copied 19 9 27 11 AM AuditLogDir set to C Command_ConsoleLogs S6F 9 27 11 AM LogFileDir set to CACommand ConsoleYLogsY96F 39 27 11 AM Timer started with Interval 1000 msec 9 27 77 AM Homing HTS6F and Scanner 9 27 23 AM Set HybO ven temperature to 30 9 27 23 AM Set WashB temperature to 25 C 9 28 12 AM Homing HTS6F completed 9 28 12 AM Initializing Scanner 9 28 12 4M Status Scanner drawer not extended or no plate present 9 28 12 AM Scannen Option is on 9 29 27 AM Scanner homing completed 9 29 27 AM Checking and removing plate from scanner 9 29 53 AM Status Mo Plate in Scanner System ready for running 3 29 56 AM System Ready 9 29 56 AM System Ready The software interface has the following components Figure 2 2 a Menu bar Provides access to IC functions Tool bar Provides quick access to frequently used functions System Status tab Use to track the progress of array plates through the workflow System Setup tab Use to set up the GeneTitan Instrument for different workflows Status bar and Progress bar Displays information about the status of the GeneTitan Instrument and the workflow in progress 16 GeneTitan Instrument User Guide for Expression Array Plates Setup Options for Array Plate Processing The processes setup options available for processing array plates are shown in Figure 2 4 A brief description of each option is given below 1 In AGCC select the System Setup
66. he Assay or AGCC for instructions on proper consumable placement Press the flashing blue confirmation button or Press OK GeneTitan will verify the barcode and orientation Press Skip GeneTitan will NOT verify the barcode and orientation 3 Click OK or press the Confirmation button to continue or press the Skip button if the instrument has problems reading the barcode and after you have verified that the trays are placed in the proper orientation The software prompts you to load the stain trays After the trays have been loaded the software prompts you to load the Array Plate on the Hyb Tray and the Array Plate cover Figure 4 11 Figure 4 11 Load Array Plate on Hyb Tray with cover HE AGCC GeneTitan Instrument Control 3 Stop TE Help System Status System Setup Setup Option B issc l System Layout Array Selection Plate Information Used Hyb Tray Barcode li mm Plate Type 550001 Protocol Name Localion Load consumables on left side Workflow Steps Enter Array Plate Barc ode consumable trays and plates Load consumable trays and plates Select arrays to scan Start Processing Status Load the Blue Cover on Left side of Drawer Load the Array Plate Hyb Tray combo on Right side of Drawer Press the Confirmation button when done Cancel Scan Tray Stain 1 Tray Stain 2 Tray Stain 3 Tray Array Plate Scan Tray
67. he power out condition to end When the UPS is once again online the run can be started Please register aray plate by scanning the barcode or Type in the barcode Plate registration missing bar code When starting a new process setup the barcode must be entered If the user fails to enter the barcode either by using the hand held bar code reader or typing it in the user will be prompted to register the plate with the following message 74 GeneTitan Instrument User Guide for Expression Array Plates Table A 4 GeneTitan Instrument Error Messages Continued Message Meaning Instrument cannot read barcode HTA plate barcode read error Do you want to Retry Unreadable bar code Yes Reload ArapPlate Tray combo with corect onentation and retry reading barcode After the HTA plate has been loaded into the system No Use barcode in textbox scanned with external barcode reader or entered manually the Fluidic system tries to read the plate bar code using its internal bar code reader This is to verify that the correct plate was loaded and that the plate was loaded in the correct orientation If the bar code read by the system does not exactly match the bar code entered by the user the following message is displayed It is also displayed if the bar code is unreadable by the system Warming Barcode in testbos used 550001123456 79901 2345 Solution o If you are certain that correct plate was loaded in the
68. ilters are clogged The software displays warning message boxes for the filter in each reagent bottle when it detects a problem or shows a trend of increased fill times during fluid fill operations If an error is detected as described above then a message box titled Filter Change Required is displayed along with the information on the specific dispense operation You should change all three filters when a warning is displayed for any one of the three filters Figure A 2 EI Filter Change Required BUFFERA TO WASHA 3 9 2010 5 21 00 FM wana g e DA RE e ee ee ia ili ou need ers Problem dispense for BUFFERA_TO_ WASHA is Ested below 17270200 4 29 16 PM dispense time remaming before timeout was too short 1 75 sec 1 27 2010 4 41 45 PM dispense time remaining before timeout was too short 1 407 sec This warming will have been replaced c 5 acceptable depentes have been ded The last 0 sisperise erties lor BUFERA TO WASHA Were a a ae 1 22 2010 4 23 16 PM dipenta lime temaning 1275 sec 1227 2010 4 41 45 PM dispense time remaning 12 407 sec 1272010 4 26 28 Pid dapenre lime remaning 12616 lee el 1 27 2011 0 4 23 15 PM depense lime remaning 1 Vereen 4 41 45 PM dispense time remam ng 1 Fl Anay plates processed with dety lilters im re JE ehe tt Met uta The bottles ae depressunmed and fiers can changed now Do not change filters while GeneTiian ie processing PIATE CINA sour seal AERAN CAMAATA cr FSE tn ODAN FAN
69. irm j Cancel 7 Click OK to begin the Wash Scan workflow The instrument performs the workflow steps for the Wash Stain workflow and can be tracked in the Status window Scan Workflow Loading Instrument for Imaging Workflow The Scan Workflow allows you to scan the array plate on the GeneTitan Instrument Imaging Device This mode allows you to bypass the hybridization and wash stain step of the process workflow You can scan only one array plate at a time You must load the array plate and scan tray as shown in Figure 5 1 Figure 5 2 and Figure 5 4 You must load the array plate and scan tray into the instrument with the Affymetrix For Research Use Only label facing the out towards you and the notch on the left front side The tray barcodes should be in the back facing away from you and into the instrument To load the Array Plate and Scan Tray 1 Select Scan for the Setup Option The application opens the Input Output drawer 2 and prompts you to load the array plate scan tray combo on the drawer 48 GeneTitan Instrument User Guide for Expression Array Plates Figure 5 3 Load Array Plate Scan Tray prompt FE AGCC GeneTitan Instrument Control Wet Ae CIN RG File Tools Help Stop Email Help System Status System Setup Setup Option Scan TE System Layout Array Selection Erme Fer B Manual Array Selection Plate Information f Used Hyb Tray Sca
70. it Error on axis Gripper Error initializing amp Unclamp on mode 21 System Auntime Intenopservices COMException 20004008 at CMLCOMLib AmpObjClass Reinet at OP anelAtfyMotor nit Error om axis Timeout waiting on SDO Unclamp Stage initialization error messages All or some of these messages may appear after the error initializing hardware message box They can usually be cleared following the instructions above If not cleared using the steps outlined above then these messages may be used by service personnel to diagnose a specific subsystem malfunction The amplifier motor encountering the error may be any one of the fluidic system motion components X Y Z Unclamp station Wash B lid or Gripper 68 GeneTitan Instrument User Guide for Expression Array Plates Table A 4 GeneTitan Instrument Error Messages Continued Message Meaning Digital I0 failure event occurred at 9 2 2009 12 10 29 PM Error on BeckhoflO tomodule tnitializel for node 3 GeneTitan must be restarted after exiting by using Windows Task Manager All motors and DIO taken offline Syetem Auntime nteropsenvices COMException Ux80004005 Timeout at CMLCOMLib I0 0 bjiClass O06 _Initialze canOpenOUb canUpenUby Intl nodelD at 10 Panel BeckhofflO Module rit Digital lO Initialization error messages This message may appear after the error initializing hardware message box It can usually be cleared following
71. ization Tray Figure 3 12 The proper installation of the GeneTitan tray consumables the image shows the Stain Tray and the Stain Tray cover as an example nA Con Barcode faces in and back hi I B j HE CC Adi Vibe trig FOR RESEARCH AN RM USE ONLY 5 r m ee FOR RESEARCH SUSE ONLY Notch faces out and left Affymetrix For Research Use Only faces out 30 GeneTitan Instrument User Guide for Expression Array Plates Figure 3 13 Loading the Array Plate and Hyb Tray Stop Email System Status C Gene Titan Instrument Control eza PEN So Help System Setup Setup Option Plate Information Barcode Plate Type Protocol Name Location Workflow Steps Load consumables on left side System Layout Array Selection Used Hyb Tray B sed H yb Tray Scan Tray _ Sean Tray Stain 1 Tray Stain 1 Tray Stain 2 Tray FEED See tents Hyb Tray Manual Array Selection 101 11 12 ji Trash Bin bottles with buffer bin consumable trays and plates x Om m o m o J gt Load consumable trays and plates Select arrays to scan Start Processing Not Available Kl Will Be Scanned Will Not Be Scanned Status Load the Array Plate Tray on Left side of Drawer Load the Hyb Tray without cover on Right
72. l After changing the lamp it is necessary to reset the lamp life clock manually EE WARNING You must turn off the lamp using the power switch in the rear of the unit and remove the power cord Allow the lamp to cool before attempting to replace the lamp Removing the Xenon Lamp 1 Unscrew the four retaining bolts They should be finger tight Figure A 7 Figure A 7 Unscrewing the Bolts Unscrew these four bolts WARNING HIGH VOLTAGE DISCONNECT POWER BEFORE REMOVING LAMP ACCESS PANEL i autltna Risi af VA le Ahk 2 Place each hand on each side of the blue plastic flange and lift out the lamp in a vertical motion Figure A 8 You must use both hands to remove the lamp successfully Apply equal pressure on each side of the lamp and gently lift Chapter A 59 Figure A 8 Lifting out the lamp Replacing the Lamp CAUTION Ensure that you install the lamp in the correct orientation 1 Hold the lamp by the blue plastic flanges Ensure that the lamp bulb faces inward toward the reflecting mirror Figure A 9 and vertically insert the lamp Figure A 10 2 Replace the warning cover and hand tighten the bolts Figure A 7 60 GeneTitan Instrument User Guide for Expression Array Plates Figure A 9 The Reflecting mirror Reflecting Mirror ER Them ETT SEDA RAY E sven sm oarn a a asa a en Figure A 10 Inserting the Lamp
73. l ate rf ae ean Yahi SS00S40S1 226020510909 Ci La L96 OR ak bs all Drivel Free5pereGE i lae 179 3 FreeSpaceRemaining sB Status reespace SE FreeSpace thy Aherat t ara ao 240 Disk Ste required for one peg Joo lao Disk Space Check Connection error Error initializing hardware No can bus found or an error initializing an amp was encountered Check USB connections Make sure drive F has become visible before attempting to restart the application The application must be exited and restarted when the problem is fixed Possible cause A fluidic system drawer door is open or not completely closed and the switch on the left side of the drawer is not closed If this is the case make sure the drawer is moved into the system and close the drawer completely If the system state is such that the gripper is actively holding the door open you will not be able to push the drawer in In this case you will need to hold the switch closed while the application starts up to allow the homing procedure to complete If the problem cannot be resolved as outlined above contact Affymetrix Field Support Error initializing hardware Symptom The system gives a warning that there was an error initializing the hardware when the GeneTitan application starts up The following message will appear note formatting of this message produces a message box larger than the screen and will be corrected in a future release Other more specific
74. ll allow You to remove plates in the system But processing involving scanning will be aborted in the scan step Scanner launch timeout If the following message is received hyb and fluidic operations will be enabled but plates will stop processing without going into the scanner Solutions o Exit GeneTitan o Verify all cable connections including USB and fire wire between the scanner and the computer It is critical that the USB cable is inserted into the proper labeled location on the computer o Unplug the scanner wait 10 seconds and plug the scanner back in o Reboot the computer o Wait for the USB drive in the scanner to become visible G drive If the G drive does not become visible in Explorer contact Affymetrix Field Service to correct the configuration problem o Restart GeneTitan Scanner error detected scanner relaunched but failed You have the following options 1 Retry resolve the problem and press the Retry button IF retry is successful there ig no interruption to the workflow 2 Cancel Abort the current plate and put the scanner offline b Processing of plates already loaded in the system will continue But plates that require scanning will be aborted at the scanning step You have to wait til the gripper is available to remove the plate 15 43 40 4218750 a You have to wait til the gripper it available to remove the current plate Scanner re launch failure If ascanner failure is detected the
75. m persists contact Affymetrix Field Service 0000 An Unexpected plate it detected on Left side of drawer Please remove the plate Error during plate unloading Unexpected plate detected The user placed a plate on the drawer or failed to remove the plate during an unload step Solution remove the requested plate and select OK fou removed the plate on Left side of drawer Please put the plate back Unexpected plate or tray removal The user removed a plate or tray required by some other plate process during an unload step The wrong plate was probably removed left vs right side Solution Return the plate or tray that was accidentally removed to its proper location and orientation If the tray had a cover when it was removed it should continue have a cover If the system had already removed the cover return the tray to the system without a cover Note this may be left or right side An eror occured during plate loading Setup has to be aborted Error during plate loading An error caused by improper loading of plates or a motion system error may cause the plate loading process to exit setup and display the following error message Solution o Perform a new setup being careful to load the proper plates and in the correct orientation o If restarting setup does not clear the problem re launch the GeneTitan application Contact Affymetrix field service if the problem persists even after re launch You
76. mables on left side Workflow Steps Stain 3 Tray Array Plate Used Hub Tray Scan Tray Stain 1 Tray Stain 2 Tray Stain 3 Tray Hyb Tray Trash Bin Manual Array Selection 101 11 12 B E D E F G H TE Will Be Scanned C Will Not Be Scanned Status Please select arrays to scan using array selector Press the Next button to advance to the next step Cancel Read barcode completed EH Not Available 5 Use the default selections or select arrays as described below Each array on the plate is indicated by a single square The color of the square indicates the array s status dark blue Will be scanned _ white i eray To manually select arrays Will not be scanned Not available A Select the Manual Array Selection checkbox B Select the arrays to be scanned You can select arrays by Clicking and dragging through the grid Pressing the Ctrl button down and clicking in different squares NOTE If there is insufficient memory on the computer s hard drives to store the data from a plate a notice appears 6 Click Next to start the run The Start Processing dialog box opens Figure 4 14 46 GeneTitan Instrument User Guide for Expression Array Plates Figure 4 14 Start Processing notice Start Processing This will start the WashScan in the Left Position Please press the OK button to conf
77. ment completes the wash and stain protocol on the other plate and ready to scan 2 Reboot the GeneTitan AGCC application 3 Unload plates 4 Reload and scan both plates following the scan mode procedure B If the other plate is undergoing hybridization 1 Reboot and relaunch the AGCC application to force the instrument to unload the plate from the oven and to transfer it to Drawer 1 2 Unload the hybridizing plate and finish hybridization offline 3 Unload and reload the plate that was in the scanner and scan the remaining wells IMPORTANT Relaunching AGCC will cause the scanner plate to eject back onto the drawer location from which it originated 3 Ifthe workstation or application freezes while the GeneTitan Instrument is processing an array plate in the wash and stain procedure reboot the workstation and relaunch the AGCC application 4 Ifthe workstation or application freezes while one or two array plates are hybridizing in the oven the power to the controller will continue to maintain the oven temperature Reboot the workstation or AGCC application The software will offer the option of leaving the plates in the oven or removing them for offline hybridization If you elect to leave the plate in the oven you will need to remove the plates at a later time by again relaunching the AGCC application or by removing the plates manually through the front of the system You can then resume the plate processing using wash scan mode
78. n Editor q 2a Data Uploader Resources Ae Affymetrig com Web resources to learn more about the Command Console software and other AM Support at Affyrnetris corn Affymetrix p roducts A N eb lin 14 GeneTitan Instrument User Guide for Expression Array Plates The launcher enables you to start AGCC software components and tools including a AGCC Instrument Control Software for the GeneTitan family of instruments AGCC GeneTitan Control For more information on AGCC Controls please refer to the Affymetrix GeneChip Command Console User Manual P N 702569 Starting the AGCC GeneTitan Instrument Control software The AGCC GeneTitan Instrument Control software is used to control the GeneTitan Instruments 1 Click the AGCC GeneTitan Instrument Control icon in the Affymetrix Launcher or Click the Microsoft Windows Start button l Start and select Programs Affymetrix gt Command Console AGCC GeneTitan Control The AGCC GeneTitan Instrument Control window opens Figure 2 2 Figure 2 2 AGCC GeneTitan Control software System Status Tab Menu Bar Tool Bar System Setup System Status tabs Status Bar a AGCC GeneTitan Instrument Control Ol x Fie Tools Help Stop Email Help Hyb Status Scan Status Estimated Completion Time Location Fluidics Status Barcode Plate Type System is available no
79. n Tray Scan Tray 10 1112 Stain 1 Tray Stain 1 Trap Stain 2 Tray Stain 2 Tray Barcode Plate Type 550001 Protocol Name 550001 protocol L jj Stain 3 Tray Stain 3 Tray Workflow Steps _ Array Plate Hyb Tray H rash Bin Location Load consumables on left side Enter Array Plate Barcode in Tx Om m fo m mo gt onsumable trays and plates oad consumable trays and plates Select arrays to scan J mij izi Ez imaj laj Eza izi in i i aiei ea ee Will Be Scanned Will Not Be Scanned Not Available Start Processing mi a Is E j E war bewar Me e ezo Ti r r N Status Load the Array Plate Scan Tray combo on Left side of Drawer Press the Confirmation button when done Plate tray position ind icators Cancel Drawer 2 opened 2 Load the array plate scan tray combo into the indicated side of the drawer Figure 5 4 and press the Confirmation button En IMPORTANT When running a series of array plates through the Scan workflow you must be careful to remove and load the proper array plate and pay careful attention to the software prompts that tell you which side of the open drawer to remove or place the plate Figure 5 4 Loading Array plate on scan tray in drawer 2 Chapter 5 Scan Workflow 49 The internal bar code reader reads the barcode of the array plate then compares it with the
80. new connections are made DO NOT reassign port addresses using device manager Contact Affymetrix field service if connections are verified but the ports do not appear as indicated Re launch the user application Chapter A 65 Table A 2 shows possible problems dealing with the array plates This includes what to do if a power failure or user initiated power shutdown leaves array plates in the instrument or if you have left a plate in the hybridization oven during the GeneTitan AGCC application startup Table A 2 Recovering Plates From The Instrument Problem Probable Cause Solution Array plates are trapped in the instrument Power loss or abnormal application exit for any reason leaves plates in the system 1 2 Exit and restart the GeneTitan AGCC application Wait for flashing blue light on the confirmation button to stop and homing to complete Respond to dialog box prompts and or questions about plate disposition that may occur before during or after the stage homing sequence At the end of the startup homing routine the instrument will return all plates to the front of the system unless the you select to leave a plate in the oven When homing is complete run Unload Plates from the setup tab to remove plates from the system Plates are left in the hybridization oven during the GeneTitan AGCC application startup If a plate is in the oven the user is offered the option to remove the
81. ns ranging from user induced to sensor malfunction or facility supply line problems Depending on the type of error and where in the process the error occurred the system may not stop processing until the error is corrected Some errors are simply reported in a message box but the process continues In such cases the purpose of the message box is to inform the user of an abnormal event The event should be investigated after the plates running on the system are finished running 6 1Bottle pressure too low Symptom Message box similar to that shown here is displayed If you choose to Cancel the fluidic process being performed will stop but you may still need to abort the overall plate process using the STOP button or Cancel button during a plate setup operation Solution o Verify facility line pressure into the system is ON o Verify all bottle caps are secure and that no bottle cap is crimping a supply line o Do not refill bottles or empty waste except when prompted to by the GeneTitan application Plate SystemT ask Time 9 2 2009 2 15 21 PM Unable to achieve vacuum vac start 1415 50 28512500 end 14 16 20 4375000 Check CDA house pressure and bottle caps are firmly attached Vacuum failure Symptom Message box similar to that shown here is displayed If you choose to Abort the fluidic process being performed will stop but you may still need to abort the overall plate process using the STOP button or Cancel button du
82. og Files for GeneTitan MC Systems Log files for the GeneTitan MC Instrument control processes are placed in subdirectories of the Command Console Logs folder Affymetrix may need the following files for troubleshooting GeneTitan MC Fluidics 1 C Command_Console Logs 96F A subdirectories named by date e g Log7 29 2009 1 Collect all dated directories and contents since the GeneTitan application was started not just the date of the event some logging goes into files from the date the application started so this can be critical for us 2 Absolutely required are all the log directories from the date the run was started to the date of the event 2 C Command_Console Logs 96F FluidicErrorLog all files in this directory GeneTitan MC Imaging Device 1 C Affymetrix GeneChipHTScanControlIMC Log collect all dated directories and contents since the GeneTitan application was started 2 C Affymetrix GeneChipHTScanControlIMC RunLog collect all dated directories and contents since the GeneTitan application was started Problems and Solutions This section provides instructions on how to identify and solve problems with the unit If problems arise with the instruments use the following tables to locate the description that matches the problem If you cannot find a solution call Affymetrix technical support for assistance For software errors that do not involve hardware crashes the most common solution is to shut down the appli
83. on prompts you to select the array s to be scanned Figure 5 6 The application makes the default selection based on the barcode of the array plate You can select the specific array to scan by overwriting the default selection 50 GeneTitan Instrument User Guide for Expression Array Plates Figure 5 6 Selecting array s HE AGCC GeneTitan Instrument Control File Tools Help lal Stop Email Help System Status System Setup FEER Setup Option Plate Information Barcode 550 Plate Type 550001 Protocol Name Location Load consumables on left side Used Hyb Tray Scan Tray Stain 1 Tray Stain 2 Tray Stain H 3 Tray Array Plate Stain 3 Tray Hyb Tray Manual Array Selection System Layout Array Selection Used Hyb Tray _ Scan Trap Stain 1 Tray Stain 2 Tray 10 11 12 Trash Bin swith buffer crim fm O co yr and plates s E Will Be Scanned _ Will Not Be Scanned O Not Available Select arrays to scan Start Processing Status Please select arrays to scan using array selector Press the Next button to advance to the next step Read barcode completed 4 Use the default selections or select arrays as described below Each array on the plate is indicated by a single square The color of the square indicates the array s status dark blue Will be scanned T white
84. on will not be available when there is not enough time to finish the scan workflow before the first array plate finished the wash and stain process Running the Hyb Wash Scan Workflow on a Series of Array Plates The GeneTitan Instrument allows you to load a second array plate hybridization plate and other consumables into the trays before the first array plate has finished going through the workflow Since the array plate should be scanned immediately after the wash and scan processing is finished you need to wait before loading the second array plate to give the system time to scan the first plate The delay time varies depending upon the number of arrays on the first array plate Approximately five hours if the first array is a 96 array plate a Approximately two and a half hours if the first array is a 16 or 24 array plate The time you need to wait is displayed in the Workflow pane Figure 3 21 of the Status tab NOTE GeneTitan can process array plates with 16 24 or 96 arrays on a plate Figure 3 21 Workflow pane Work Flow Barcode Plate Type Location Hyb Status Fluidics Status Scan Status Estimated Completion Time 550001 4037495121008417 550001 Left Position Running Waiting Waiting 9 9 2008 11 17 47 AM Estimated Time Window to Run Next Hyb VYash Scan HT Array Type Same plate type 97972008 12 28 06 PM 3 3 2008 11 12 48 AM 36 GeneTitan Instrument User Guide for Expression Array Plates NOTE
85. onfirm that the array plate is properly clamped and click OK The drawer closes and hybridization proceeds Running Multiple Workflows at the Same Time for Expression Arrays When processing expression arrays the GeneTitan Instrument can run two different workflows at the same time This enables you To load a series of array plates with hyb trays and consumables for the Hyb Wash Scan workflow to process more arrays EE IMPORTANT You cannot load Genotyping and Expression array plates at the same time To run an array plate that was processed using a different system through the scan workflow while another array plate is going through earlier stages of the Hyb Wash Scan workflow Only certain types of workflows can be run at the same time and delays may be necessary before starting the second workflow These restrictions exist because an array plate should be scanned immediately after the wash and stain processing is finished and GeneTitan scans one array plate at a time If you want to run a series of expression array plates through the Hyb Wash Scan workflow you will need to wait for up to five hours after you start the first workflow before loading the second array plate hyb tray and consumables to allow the first array plate to finish being scanned The delay time varies depending upon the number of arrays on the first array plate Approximately five hours if the first array plate is a 96 array plate Approximately two an
86. ot the correct consumable not loaded correctly or its barcode is not readable Proceeding with an incorrect or incorrectly loaded consumable can result in a loss of consumables loss of samples and may require a field service engineer to service the instrument Refer to the System Setup Tab or the User Guide provided with the Assay or AGCC for instructions on proper consumable placement Press the flashing blue confirmation button or Press OK GeneTitan will verify the barcode and orientation Press Skip GeneTitan will NOT verify the barcode and orientation The barcode entered at registration will be used Skip 6 Click OK to retry and check the loading of the array plate or click Skip to continue without confirming the barcode read operation After the trays and plates have been loaded the application prompts you to select the array s to be scanned Figure 3 16 The application makes the default selection based on the barcode of the array plate You can select the specific array to scan by overwriting the default selection Figure 3 16 Selecting array s FE AGCC GeneTitan Instrument Control Fie Tools Help a Stop Email Help System Status System Setup Setup Option i Hyb Wash Sca System Layout Array Selection Manual Array Selection Plate Information Used Hyb Tray Used Hyb Tray 550001 AEEA NI Scan Tray Scan Tray ig Stain 1 Tray Stain 1 Tray Stain 2 Tray Stain 2 Tray
87. page 47 for instructions on the Imaging Workflow Unload Plates Use this option to unload plates and trays from the instrument when Array plate processing is complete a Array plate processing has been aborted Wash Scan Resume The intent of the recovery procedure is to save the array plate array plate process and the instrument when a power interruption power blackout or emergency shutdown or the user cycle the power of the instrument occurs or if the workstation and application unexpectedly freezes during the operation Please go to Appendix B GeneTitan Instrument Recovery Procedure on page 79 for further instructions 18 GeneTitan Instrument User Guide for Expression Array Plates Hyb Wash Scan Workflow Hybridization Buffer Stains and Wash Buffer Volumes Required for the GeneTitan Instrument This section describes the reagent consumption per process on the GeneTitan Instrument for processing HT array plates when running the manual assay Table 3 1 The Minimum Volumes of Buffer and Rinse Required to Process on GeneTitan l Minimum Level in Bottle Amount Required for Fluid Type One Array Plate One Array Plate Two Array Plates Rinse 300 mL 450 mL 900 mL Wash A 920 mL 1 040 mL 2 000 mL Wash B 300 mL 450 mL 600 mL Table 3 2 Volumes Required to Process HT Array Plates per Run Number of Plates that can be Processed using the GeneTitan Hybridization Wa
88. per to lift the tray along with the tray cover and can result in an aborted run See Figure 1 7 Figure 1 8 and Figure 1 9 Deionize the inner surface of each tray and lid The surface of the tray with the wells that will hold reagents The surface of the lid that will cover the reagents CAUTION Do not deionize the scan tray or hybridization tray Figure 1 7 Scan Tray with Cover Deionize only the cover Figure 1 8 Stain Tray with Cover Deionize the cover and the tray Notched corner should face the front 10 GeneTitan Instrument User Guide for Expression Array Plates Testing the Anti Static Gun Verify that the anti static gun PN 74 0014 Figure 1 9 is in working condition You can use the protective cap on the gun to determine if the anti static gun is releasing ions The procedure is as follows Keep the cap on the gun and press the trigger and release it Observe the discharge through the viewing slot on the cap of the anti static gun There is a visible light observed in the viewing window on the cap when charged ions are discharged If you cannot see the light the gun may be un usable and you should replace it Each anti static gun is capable of 50 000 trigger operations which is sufficient for approximately 200 250 runs on the GeneTitan instrument FE IMPORTANT Make sure you remove the cap from the gun when you deionize a tray or cover Deionization Procedure The following
89. plate or leave it in the oven during application startup In response to this prompt the user may choose to leave plate s in the oven during the program startup homing routine allowing hyb to complete in the oven The plate hyb time is no longer controlled by the software Wait until the hybridization procedure has completed then re start the application This time select the option to remove the plate from the oven when the GeneTitan AGCC application prompts as part of the homing startup routine You may restart the GeneTitan AGCC application at any time to remove the plate and move the hybridization to an offline oven to complete the hybridization process You may later resume the process by starting the plate in wash scan mode normal operation for offline hyb mode processing Table A 3 shows possible problems dealing with the buffer and DI water bottles Table A 3 Problems Related to Wash and Rinse Bottles Problem Probable Cause Solution GeneTitan AGCC application reports that bottle pressure is too low during a run or at startup Missing reagent bottle or bottle cap not secure 1 Verify that all bottle caps are installed on the correct bottle and that they are snug Check that the facility CDA pressure is up and running Select Retry to continue processing or Cancel to abort the run GeneTitan AGCC application reports that the Prime has failed for Rinse Buf
90. ray plate from the instrument which experiences a process interruption in the event of a facility power failure during operation If required the AGCC application will prompt you to following certain procedures Saving the Process You can resume the process at certain process steps The integrated UPS allows you to perform an appropriate recovery procedure to recover the array plate at the following process steps At the Hybridization step The instrument removes the array plate from the oven and places it on Drawer 1 Plates remain in the drawers available for the user to initiate an unload process from the setup tab a At the Wash Stain step The instrument unloads the array plate to its scan tray Plates remain in the drawers available for the user to initiate an unload process from the setup tab a At the Scan step The instrument aborts the scan The scanner unloads the array plate and transfers the array plate into the GeneTitan Instrument where they remain in the drawers available for the user to initiate an unload process from the setup tab Ifthe GeneTitan Instrument was processing two array plates during a power failure the instrument performs the combination of all three procedures above to recover all the array plates from the instrument IMPORTANT If you cannot restore power to the GeneTitan Instrument a trained service technician must manually recover the array plate This recovery procedure may require the disassembl
91. rays into the GeneTitan Instrument To load the plates and trays 1 Select the System Setup tab Figure 3 7 Figure 3 7 System setup tab and the information displayed in this pane File Tools Help System Setup tab Stop Email Help System Status System Setup Setup Option The various options you can choose for processing array plates gt setup Opin Hy Wash Scan Plate Informati Barcode The array plate barcode Can be ee ead ua Protocol Name The protocol that GeneTitan Instrument will run The list of protocols displayed is based on the 550032 protocel first 6 digits of the array plate barcode Only the protocols iteadieonsumabiccen ler cide that are valid for the type of array plate loaded are displayed If there are multiple protocols for an array plate select the appropriate protocol from the drop POEET TEE nEn ter Aray Plate Barcode down list box Workflow Steps This field gt Refil glass bottles with buffer displays an overview of the user Empty trash bin ACTIONS required to process an Remove consumable trays and plates array plate based on the setup Load consumable trays and plates select arrays to scan option se ected start Processing Status Status This field displays the actions that must be performed to prepare or unload the GeneTitan Instrument for the setup option that has been selected After each action you are instructed to click the Next button or to press
92. ring a plate setup operation Solution o Verify facility line pressure into the system is ON o Verify all bottle caps are secure and that no bottle cap is crimping a supply line o Do not refill bottles or empty waste except when prompted to by the GeneTitan application 72 GeneTitan Instrument User Guide for Expression Array Plates Table A 4 GeneTitan Instrument Error Messages Continued Message Meaning TIMEOUT ms 22000 waiting for sensor ON S5Washd_BFOOvertlow Continuing due to time critical nature of the process Fill cannot be guaranteed FilllntiSensorstate Failure on valve group BUFFERA_TO_WASHA Plate SS 00 Satie Time 97272009 2 22 15 PM Fluidic process FillWfash Possible causes for dispense failure include Bottle empty or fluid level too low Replenish bottle Bottle cap not secure Check all bottle caps are secure Clogged filter Replace filter Continuing due to time critical nature of the process Fill cannot be guaranteed Undertill was likely Timeout waiting for fill During processing in the fluidic system the process does not stop if a timeout occurs while trying to fill a wash reservoir In this case the timeout means the sensor that should have detected reagent flowing in the overflow drain did not turn on and stay on long enough The error will be reported similar to the message below The message s typically come in two separate boxes Solution o Ensure there is
93. s as described in the note below Wash Scan Workflow Loading Instrument for Wash Scan Workflow The Wash Scan Workflow allows you to bypass the hybridization step and begin processing the array plate from the Wash Stain and Scan steps without any user intervention In this mode of operation you can process one array plate at a time 1 Select Wash Scan during the initial setup Other options available are described under Setup Options for Array Plate Processing on page 16 This process will require the following GeneTitan consumables a Array plate on Hyb Tray Figure 4 1 Front of plate and tray with For Research Use Only notices and notch us n j I C u 1r l 14 nananet TT mm i Li azas HF Eza ku ig HI lll l _ Jl n aen fit aa Hu Gene 1 1 ET i FEED Plane SSO TUN 1134355314114112 PF dik l i a a amp Notched Corners The Array Plate and Hyb Tray combo should be loaded into the instrument with the For Research Use Only label facing the user and the notch in the left front side as shown on the right Figure 4 1 The HT Array Plate barcode should be on the back side facing away from the user a SAPE 1 Stain tray with cover Figure 4 2 38 GeneTitan Instrument User Guide for Expression Array Plates a AB Stain tray with cover Figure 4 3 SAPE 2 Stain tray with cover Figure 4 4
94. s execution The message will display the plate number if known and current oven settings A target place location is shown where the plate will be moved to when the user selects NO to the prompt Do you want to leave the plate in the oven If there are 2 plates in the oven the process described here will be performed for each plate Solution 1 select Yes o Select Yes if you are not ready to deal with the circumstances that caused the malfunction or if you have no offline oven to complete the hyb The oven is the safest place to leave a plate while waiting to move on to fluidic processing n If the oven output is enabled the set point will be used to bring the oven back into range o Note that if the oven itself did not lose power it will normally retain all settings and temperature control would have been maintained even while the computer lost power from rebooting o If the oven lost power then when power is restored the oven will automatically start to restore the settings displayed by this message even if the GeneTitan application is not launched o When the problem that caused the interruption is resolved restart GeneTitan and this time select No Solution 2 select No o Select No to remove the plate from the oven after the full hyb time is completed or for removal to an offline oven o Make sure the plate is finishing hybing for the full hyb time before continuing the process using Wash Scan
95. sh and Stain Kit for 3 IVT Arrays Amount i Aliquot into Columns P N 901530 Required for One Reagent Array Plate 16 Format 24 Format 96 Format 16 Format 24 Format 96 Format Hybridization Target 90 uL well 5 amp 7 5 7 amp 9 All N A N A N A Wash A 920 mL 1 1 1 Wash B 300 mL 1 1 1 Stain 1 and 3 105 uL well 5 amp 7 5 7 amp 9 All 6 4 1 Stain 2 105 uL well 5 amp 7 5 7 amp 9 All 6 4 1 Array Holding Buffer 150 pL well All All All 6 4 1 Please use GeneTitan Wash Buffers A and B Module PN 901583 for ordering Wash A and B buffers for additional plates NOTE The GeneTitan instrument requires a minimum of 450 mL of Wash B fluid in the Wash B reservoir prior to starting the process For additional plate runs you will need to purchase additional Wash A and Wash B IMPORTANT The instrument must have a minimum of 450 mL of Wash B in the Wash B reservoir of the instrument for each HT array plate prior to starting Hyb Wash Stain and Scan process The waste bottle should be empty 20 GeneTitan Instrument User Guide for Expression Array Plates Loading the Instrument for Hyb Wash Scan Workflow This workflow runs the array plate through all steps In the Hyb Wash Scan workflow for expression arrays the array plate hyb tray scan tray and reagent trays are loaded at the same time To run this workflow you need to a Select Hyb Wash Scan during the initial setup s NOTE If the target preparation is completed
96. side of Drawer Press the Confirmation button when done Plate tray position indicators Cancel Drawer 6 opened 5 Load the Array Plate and Hyb Tray and press the Confirmation button Figure 3 14 illustrates the proper way to install the trays Figure 3 14 Array Plate with protective blue base and the Hyb Tray aligned and properly loaded into drawer 6 Array Plate with protective blue base Hyb Tray AFFYMETRIX FOR RESEARCH ae USE ONLY When you load the Array Plate the internal bar code reader reads the barcode of the array plate then compares it with the barcode and the plate type specified in the Barcode field and Plate Type field on the Setup page Chapter 3 Hyb Wash Scan Workflow 31 If the information is correct the application allows you to proceed to the next step If the instrument is unable to read the barcode it will push the tray out and will prompt you to load the correct plate with the proper orientation into the instrument Figure 3 15 Figure 3 15 Barcode error notice Fe erify Drawer 6 Array Plate Load i ID xl Warning The system was not able to verify the array plate barcode Please verify that the tray on the left side of the drawer is a blue cover and if applicable an array plate in the correct ORIENTATION The right side of the drawer should contain a hyb tray if applicable in the correct ORIENTATION Details The consumable is either n
97. sion96S canner 3 0 0 1212 11 03 40 AM LastWriteTime 96S canner 8 29 2009 10 16 10 PM 11 09 41 AM MED amp 96S files Copied 45 n Will Be Soanned _ Will Not Be Scanned 11 09 41 AM AuditLogDir set to C Command_Console Logs 96F _ Now scanning E Scan Completed DE scan Faited 11 03 41 4M LogFileDir set to Command ConsoleYLogsy96F 11 09 41 AM Timer started with Interval 1000 msec Arrays Total Will Be Scanned Scanned 11 03 41 4M Homing HTS6F and Scanner 11 09 41 AM Set HybOven temperature to 48 11 09 41 AM Set WashB temperature to 39 11 10 13 AM Homing HTS6F completed 11 10 13 AM Initializing Scanner 11 10 13 AM Status Scanner drawer not extended or no plate present 11 10 13 AM ScannerOn Option is on 11 11 13 4M Scanner homing completed 11 11 13 AM Checking and removing plate from scanner 11 11 42 4M Status No Plate in Scanner System ready for running 11 11 45 AM System Ready 11 11 45 AM System Ready 11 11 45 AM Lamp Life Remaining is 143 hours Fluidics Status Scanner Status System Ready 2 The software will display a message that allows you to change your mind Figure A 12 Are you Sure Lamp Life Management xj Reset Counter For Lamp Life Remaining re vou sure Please make sure 1 You had replaced the lamp before resetting the counter For lamp life remaining 2 The lamp is plugged into an active socket and 3 Th
98. sition Please press the CK button to confirm i Cancel 9 Click OK to begin the Hyb Wash Scan workflow The instrument begins processing the array plate and the Status tab appears Figure 3 18 Chapter 3 Hyb Wash Scan Workflow 33 System Status System Setup Wark Flow Barcode Plate Type Location Hyb Status Fluidics Status Scan Status Estimated Completion Time sili beccecsccecesces 550001 Left Position Running Waiting Waiting 6 19 2009 12 38 03 PM Estimated Time Window to Run Next Hyb Wash Scan HT Array Type Same plate type 6 19 2009 12 35 29 PM Hybridization Oven Status Fluidics Status Imaging Device Status Barcode 550001 1 888888KKKKKKEEK Barcode Barcode Position 1 r z P E Estimated Time Remaining 00 04 15 Beste Estimated Time Remaining Estimated Time Remaining Barcode Position 2 Wash B Temperature Plate Status Log Estimated Time Remaining Current 27 9C Target 25 G Oven Temperature Target 48 G Step Task Time Status Log 10 58 29 AM Step STAINSAPE2 10 58 29 AM Step 8 WASHA 2 10 58 30 4M Move HTA onto hyb tray 10 58 30 AM Pick 5500011 xxxxxxxxexxxxee from Htaln 10 58 30 4M Gripper Open 10 58 34 4M Gripper Close 10 58 35 AM Retract Htaln 10 59 07 4M Gripper Open 10 59 08 AM Retract Hybln 10 59 11 AM HTA and sample plate combined 550001 1 xxxxxxxxexxexKx 10 59 11 AM R
99. ssages Continued Message Meaning To avoid potential damage to system If the drawer is extended Please remove any tray on the drawer Press OK button when done Unsupported configurations The messages below should not be encountered in the field If they are there is a configuration problem with the system If any of the following messages appear do not attempt to use your system Contact Affymetrix field support Unload Tray from Scanner Cause This message is encountered if the fluidic system is not properly configured in the system or if the scanner does not have a GeneTitan system attached Solution Remove any plates from the scanner arm before selecting OK If this is field installed contact Affymetrix field service to correct the configuration before continuing to use the system Warming This i for debug use only You should not use this version for real plates For debug use only If this message is displayed the AGCC installation is not a production released software AGCC Command Console should be re installed GeneTitan Instrument Recovery Procedure The intent of the recovery procedure is to save the array plate array plate process and the instrument when a power interruption power blackout or emergency shutdown or the user cycle the power of the instrument occurs or if the workstation and application unexpectedly freezes during the operation The instrument software performs the
100. ssing after the problem is resolved or Cancel to abort the process Sensor 9 located on the bottomleft side of the system has either detected a leak is unpowered of requires adjustment Leak Detected Leak checks are performed at application startup and any time a fluidic process priming filling draining etc is performed The leak detection is a hard wired sensor which will shut off fluid flow without software control Leaks are normally confined to the drip pan located inside the system Causes oO System malfunction o User killing the application using task manager during a fill operation resulting in application exit without stopping flow Solution Contact Affymetrix field support The system cannot be used for any fluidic processing until this is resolved You are about to close the Application Press OK button to close Application Press Cancel button to cancel closing Normal exit If the user attempts to exit GeneTitan when no processes are running the normal application exit message will be displayed Cannot close Application The System ts busy Please wait lil processing is complete or abort processing before closing Application Exit while processes running If the user attempts to exit GeneTitan when processes are running the user is prevented from exiting Before attempting to exit the running processes should be aborted using the STOP button Cannot shut down system The System is busy i i Please wait
101. sufficient reagent loaded when the run is started o Verify facility line pressure into the system is ON o Verify all bottle caps are secure and that no bottle cap is crimping a supply line o Do not refill bottles or empty waste except when prompted to by the GeneTitan application oO Contact Affymetrix Field Service to have the sensor adjusted or replaced if the problem persists even after correcting for the usual causes outlined above Plate 5S50032 plate e od Time 9 4 2009 4 54 53 PM RINSE TO WASHA sensor SSWash4_BFDOverflow time remaining i abnormally short Maximum time remaining limit for fil is 17 seconds Recorded time remaining iz 19 796seconds Fill may not have occured or a previous drain may not have completely drained Contact Affymetris field support to determine if service may be required Possible causes Bottle cap removed while previous drain was in progress Sensor may need adjustment Sensor SOW ash4_BFOOverflowy Process is continuing with this event noted Abnormally fast fill During processing in the fluidic system the process does not stop if an abnormally fast fill occurs while filling a wash reservoir Abnormally fast means the sensor detected the reservoir as being full in an impossibly short period of time starting from when the reagent flow to the reservoir was initiated When this happens the result is that the reservoir is under filled and that particular process step is a likely cause of
102. ted 9 29 27 AM Checking and removing plate from scanner 9 23 53 4M Status No Plate in Scanner System ready for running 9 29 56 AM System Ready 9 29 56 AM System Ready B E D E F G H Ei Will Be Scanned Will Not Be Scanned EF Now Scanning E Scan Completed K Scan Failed Arrays Total Will Be Scanned Scanned p Fluidics Status Scanner Status System Ready a Progress Bar The software proceeds through the initialization process and starts the GeneTitan instrument You can track the initialization process in the Hybridization Status pane Figure 2 3 when the initialization is completed System Ready is displayed in the log and you can display the System Setup tab Chapter 2 Starting the GeneTitan Instrument and AGCC 15 Figure 2 3 Hyb Oven log with System Ready notice Hybridization Oven Status Tl l Position 1 Em EEE fe ooo Position 2 Emm T EEE 9 27 10 AM OSV ersion Microsoft Windows NT 5 1 2600 Service Pack 3 9 27 70 AM User ame AFF User 9 27 70 AM ExecutablePath C Program Files 4ffymetne Command ConsoleYHT 9 27 70 AM Product ame HTS6CC 9 27 70 AM Product ersionS6F 3 0 0 141 9 27 10 4M Last riteT ime SEF 6 23 2009 4 31 34 AM 9 27 10 AM Product Version96S canner 3 0 0 1741 9 27 10 AM LastriteTime 96S canner 6 23 2009 4 37 00 Al 9 27 11 AM MED amp 965
103. ted the system will continue processing without re verifying the barcode This will allow processing to continue in the case where the barcode is unreadable or not present Be sure to verify plate orientation before pressing Ok Verify plate clamping is secure Press Ok or the blue Confirmation button when ready Verify Clamping After clamping the HTA plate to the sample HYB tray for Hyb Wash Scan mode operation the drawer is moved out for inspection to verify the clamping is secure When the drawer is closed again the bar code of the hyb tray is verified again see section 8 6 Barcode read failure for scan stain or hyb tray to verify the user has not replaced the tray in the wrong orientation 76 GeneTitan Instrument User Guide for Expression Array Plates Table A 4 GeneTitan Instrument Error Messages Continued Message Meaning Warming Failed to set WashB target temperature or process aborted by user IF you did not abort the process please resolve problem and retry Setup failure or abort during WASHB preheat Failure or user abort during a setup preheating operation will result in the following message to inform the user Solution If the user did not abort the preheating step then reset the system o Exit the GeneTitan application o Disconnect power from the fluidic system for 10 seconds Reconnect power and wait 30 seconds Reboot the computer Launch GeneTitan Continue processing If the proble
104. the blinking blue Confirmation button located on the GeneTitan Cancel Next Please select the protocol Press the Next button to advance to the next step 2 Select Setup Option Hyb Wash Scan Other options available are described under Setup Options for Array Plate Processing on page 16 3 Click Next Figure 3 7 System Setup tab and the information displayed in this pane Chapter 3 Hyb Wash Scan Workflow 25 NOTE If there is not enough disk space a message is displayed Delete or move dat files to another location to free up enough disk space for the data that will be generated by eight Array Plates The GeneTitan Single Channel has the following space requirements 96 Array Plate requires 24 GB 24 Array Plate requires 6 GB 16 Array Plate requires 4 GB The GeneTitan MC system has the following space requirements 96 Array Plate requires 100 GB 24 Array Plate requires 18 GB 16 Array Plate requires 8 GB A Plate Information Barcode Scan or manually enter the Array Plate barcode and click Next The first six characters of the barcode identify the type of plate being loaded the protocol GeneTitan Instrument will use to process the plate and the imaging device parameters required for this type of plate Protocol Name The protocol name is automatically selected Click Next B Refill fluidics bottles with buffer Table 3 3 1 Fill these bottles u Wash A fill with Wash
105. the instructions above If not cleared using the steps outlined above then this message may be used by service personnel to diagnose a specific subsystem malfunction If this message appears by itself without any of the other stage initialization errors being displayed then there may be a problem with the digital IO Temperature controller failed to initialize on COM pork COMS Temperature Controller failed to Initialize This message may appear after the error initializing hardware message box It can usually be cleared following the instructions above If this message appears by itself without any of the other stage initialization errors being displayed then there may be a problem with the temperature controller com port If this is the case contact Affymetrix field support Oven location 1 has a park UnidentifiedPlate Current oven temperature is 34 20 Set point iz 38C Heater output enabled is True The target recovery position for the plate is on drawer 1 at position HybOL_HtaHyb DOWN left side You may choose to leave the plate in the oven or move it to the recovery location Do vou want to leave the plate in the oven Plate detected in oven during system startup Symptom The system gives a warning that there was an error initializing the hardware when a plate is detected in the oven at startup This may occur if the user used task manager to kill the GeneTitan application or the computer lost power during proces
106. try to save the lamp life by turning OFF the switch on the lamp After the normal life expectancy of the lamp has expired the software application will alert you to the requirement to replace the lamp This procedure is simple but you must follow good health and safety precautions Affymetrix Part Number 01 0740 lt a NOTE The power switch on the shutter box should be ON at all times The OPEN CLOSE switch on the shutter box should be at AUTO position at all times Lamp Life Imaging Device Status Notices The Imaging Status pane displays lamp life and Imaging Device status notices for the GeneTitan MC In normal operation the pane displays the hours of life left in the lamp Figure A 4 Lamp Life above tolerance Imaging Device Status Barcode Estimated Time Remaining Lamp Life Remaining 166 hours It displays a red or yellow notice when the lamp life is getting short Figure A 5 Lamp Life above tolerance Imaging Device Status Barcode Estimated Time Remaining Lamp Life Remaining It also displays a red notice when the Imaging Device is offline Figure A 6 Imaging Device Offline Imaging Device Status Barcode Estimated Time Remaining 58 GeneTitan Instrument User Guide for Expression Array Plates NOTE The 300 Watt Xenon lamp in the GeneTitan MC instrument is warranted for 500 hours To replace the lamp refer to the instructions in the GeneTitan instrument manua
107. uffer supply tube to its respective bottle The color of the buffer supply tubing matches the bottle color code Chapter A 57 Replacing the Xenon Lamp in the GeneTitan MC Instrument This section applies to your site only if you have the GeneTitan Multi Channel MC instrument The GeneTitan MC uses a xenon arc lamp system that is warranted for 500 hours to provide illumination for imaging the array at two wavelengths The xenon lamp has a limited lifetime and needs to be replaced at regular intervals The GeneTitan Instrument Control software provides a timer that indicates the remaining useful life of the bulb and notifies you when it requires replacement It is important to adhere to the warnings specified in the GeneTitan MC User Guide Refer to the GeneTitan MC Instrument User Guide P N 08 0308 or Appendix F GeneTitan amp MC Instrument Care for details on replacing the lamp Refer to the GeneTitan MC Instrument User Guide P N 08 0308 for the Lambda LS and Smart controller system The Lamp and the controller should NEVER be switched ON or OFF manually The GeneTitan MC instrument control software manages the lamp activity and will switch the lamp ON and OFF as required It takes 10 minutes to warm up the lamp In idle mode the lamp will remain ON for 2 hours before it is automatically switched OFF and if there are no more plates being transferred from the fluidics to the imaging station This is by design and intended behavior Please do not
108. up each reagent tray has a bar code which is read by the system to verify the correct tray type is loaded and that it has been loaded in the correct orientation The bar code does not verify tray content It is up to the user to ensure the correct reagent is loaded into the tray at each step The verification is repeated every time the drawer is closed whether it is a load or an unload operation Normally the bar code is read and no message is displayed to the user If the bar code is unreadable or not present the drawer opens and the user is prompted to verify the tray type and orientation No matter what process is being run the drawer close procedure expects the following trays o Drawer 2 scan trays only o Drawer 3 4 and 5 stain trays only may contain stain fixing ligation or other reagents o Drawer 6 blue cover on left side and hyb tray if any plate is present on right side The drawer close verification does NOT check the HTA plate bar code That check is done at a higher level in the GeneTitan application software The drawer close verification is not context sensitive It doesn t know what should be loaded on a specific drawer left or right It does know that if any tray is present it should be the correct type Verify Scan Tray Load for drawer 2 Cause Scan tray bar code not detected Solution o Be sure to verify plate type is a scan tray o Verify correct orientation before pressing Ok When Ok is selected the system
109. w Hybridization Oven Status Fluidics Status Imaging Device Status Barcode Barcode Barcode Position 1 A E Estimated Time Remaining BESES ell Estimated Time Remaining Estimated Time Remaining Lamp Life Remaining Barcode Pasition 2 er B Temperature Plate Status Er Estimated Time Remaining Current Target 25 E rr Oven Temperature Current Protocol Log Target 30 C Step Task Log 9 27 10 AM OSVersion Microsoft Windows NT 5 1 2600 Service Pack 3 9 27 10 4M UserName AFFXUser 9 27 10 AM ExecutablePath C Program Files Affymetrix Command Console HT 9 27 10 AM ProductName HTS6CC 9 27 10 AM ProductVersionS6F 3 0 0 141 9 27 10 AM LastwriteTime 96F 6 23 2009 4 31 34 4M 9 27 10 AM ProductVersion96S canner 3 0 0 141 9 27 10 AM LastWriteTime 96S canner 6 23 2009 4 37 00 AM 9 27 11 AM MED amp 965 files Copied 19 9 27 11 AM AuditLogDir set to C Command_Console Logs S6F 9 27 11 AM LogFileDir set to C Command_Console Logs 96F 9 27 11 AM Timer started with Interval 1000 msec 9 27 11 AM Homing HTS6F and Scanner 9 27 23 AM Set HybOven temperature to 30 C 9 27 23 AM Set WashB temperature to 25 9 28 12 AM Homing HTS6F completed 9 28 12 AM Initializing Scanner 9 28 12 AM Status Scanner drawer not extended or no plate present 9 28 12 AM ScannerOn Option is on 9 23 27 AM Scanner homing comple
110. w prompts on plate load time based on the plate you run first Figure 5 8 Workflow pane Work Flow Barcode Plate Type Location Hyb Status Fluidics Status Scan Status Estimated Completion Time Creare wis 550001 Left Position Running Waiting Waiting 9 9 2008 11 17 47 AM Estimated Time Window to Run Next Hyb Wash Scan HT Array Type Same plate type v 9 9 2008 12 28 06 PM 9 9 2008 11 12 48 AM 52 GeneTitan Instrument User Guide for Expression Array Plates NOTE The times shown will differ for 3 IVT and WT Expression arrays If you are performing the Hyb and Wash processes on array plates in a different system you can load a second array plate for the scan workflow shortly after you begin a hyb wash scan workflow The Scan workflow option will not be available when there is not enough time to finish the scan workflow before the first array plate finished the wash and stain process Running the Scan Workflow with Other Workflows You can load an array plate and scan tray for the scan workflow while another array plate is being run through the Hyb Wash Scan workflow After starting the first workflow you will need to wait a few minutes before loading the array plate and scan tray for the second workflow En IMPORTANT When running the Scan workflow while another workflow is running you must be careful to remove and load the proper array plate and pay careful attention to the software prompts that tell you which
111. will continue processing without re verifying the barcode This will allow processing to continue in the case where the barcode is unreadable or not present Be sure to verify plate orientation before pressing Ok Unable to verity t Yerity onentation and that the tray type d s a Stain tray Referto the System Setup tal tem Layout for tray content Press Ok or the flashing blue Confirmation button when ready Verify Stain Tray Load for drawer 3 4 or 5 Cause Stain tray bar code not detected Solution o Be sure to verify plate type is a stain tray o Verify correct orientation before pressing Ok When Ok is selected the system will continue processing without re verifying the barcode This will allow processing to continue in the case where the barcode is unreadable or not present Be sure to verify plate orientation before pressing Ok Unable to verity orientation and tray type using the tray barcode Verify left side is a blue cover and HTA if required Verify right side is a hyb tray lf required lf You are performing an unload step remove the plate Press Ok or the flashing blue Confirmation button when ready Verify drawer 6 load Cause Hyb tray bar code not detected or a wrong tray placed where the blue cover should reside on the left side Solution o Be sure to verify plate type is a hyb tray on the right is required for the current process r Verify correct orientation before pressing Ok When Ok is selec
112. y of the instrument such as the front or side panel to gain access to the instrument Resuming the Process If you were able to recover the array plate at the hybridization or scan process steps the software will allow you to continue to process the array plate using the modes of operation specified in the section Processing an Array Plate in the Affymetrix GeneTitan Instrument User Guide P N 08 0296 En IMPORTANT If you recovered the array plate at the Wash Stain process steps you cannot resume the Wash Stain process at the step where the power failure occurred UPS Low Battery Condition During a run if the UPS internal battery falls below 50 charge any running processes are automatically aborted and the instrument moves the plates to the front of the system to wait for you to come and deal with the situation unload the plates and continue elsewhere If an array plate hyb tray combo is in the hybridization oven the instrument moves it to the output location in drawer 1 position left or right You will normally remove the plate to an offline hybridization oven and after hybridization return the plate to the instrument and resume the run on the instrument using the wash scan mode of operation on the GeneTitan system If the array plate is not attached to the hybridization tray the plate is in a wash stain process and the instrument has removed the scan tray and stain tray If you initiate an abort or if a power outage with th
113. y things can cause a motion error and may be resolved to continue the run Possible causes and solutions are listed below Cause Drawer opened by user and safety switch stops motion Solution Close the fluidic system front panel drawer and select retry o Cause Trash bin is not positioned properly r Solution Verify the trash bin is seated and select retry o Cause Wrong tray type or wrong orientation r Solution Select Cancel and or use the STOP button to abort the plate and restart the run o Cause System malfunction due to improper plate placement or gripper mishandling r Solution In some circumstances GeneTitan will continue to process by trying to automatically re home the motion system Follow on screen prompts which may lead you to unload plates as part of the recovery process If the machine cannot clear the error automatically exit and re launch GeneTitan If the homing operation done at system startup does not clear the error contact Affymetrix Field Service Error processing SystemTask while trying to process fluidic macro WratlntlPressunzationComplete Event detected at 9 2 2009 2 14 42 PM Bottle pressure too low or intermittent Check that all bottles are securely connected Corect the problem before continuing Select Retry to continue processing after the problem l resolved or Cancel to abort the process Fluidic system error messages Fluidic system error messages may occur for many reaso

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