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HybStation User Manual

1. GENOMIC O GeneTAC HybStation z SOLUTIONS The ON OFF Switch Section 3 1 Initiating the HybStation The Main HybStation Screen GENOMIC ybridisation Station SOLUTIONS Version 3 61 Maintenance Initiating the GeneTAC HybStation To initiate the GeneTAC HybStation first ensure that there is no disc in the disc drive then place the ON OFF switch into the ON position This switch is located at the back of the instrument The system will then start and the main control screen will open O GeneTAC HybStation Section 3 1 Initiating the HybStation Version 4 0 Issued February 2003 Je GENOMIC SOLUTIONS oa le GENOMIC ae SOLUTIONS Select The Dre To Losd Fram 21 GENOMIC SOLUTIONS ka Section 3 2 Running a Protocol Running a Protocol Starting a Run To run a protocol proceed as follows 1 At the Main control screen select Start a run The Select The Drive to Load From screen will then appear prompting for the location of the protocol to be defined Select the location of the protocol Floppy Disk or Internal Storage The Choose a Protocol to Load screen will then open listing all available protocols Select the protocol to be run A marker will appear next to the protocol selected Select Load The Select Slides for the Run screen will then open At this screen select the slides for use during the protocol The selected slides will then become h
2. 11 Press OK A screen appears prompting for the number of times this wash is to cycle 14 Select the step priority The preferred selection is Must not be GENOMIC interrupted The priorities that can be set are as follows Q Normal The program may interrupt the wash cycle on one module to start and perform wash steps on other modules moving back and forth between modules Normal can be used for a single protocol run but if used for a multi protocol run the wash timing may be affected Q Must not be interrupted critical The program goes through the complete wash step on one module before proceeding to the next one This is the preferred choice as it guarantees that all wash steps are performed for the exact length of time specified in the 12 Press the number of wash cycles protocol bis ee ui OF ar 10 To change your entry Q Urgent The program runs an urgent step as soon as possible and plese Vict ana ANEA TNEI MINER does not interrupt the step once it has started A step with Urgent 13 Press OK The Select the Step Priority screen appears scheduling interrupts any other steps that might currently be running but cannot be interrupted itself When this has been set the Protocol Definition screen will appears with the new wash step displayed OoGeneTAC HybStation Version 4 0 Issued February 2003 Adding a Probe Labeled Sample Step This step is used to specify where in the protocol and at what
3. To set the date and time 1 On the Maintenance screen select Set Date amp Time The Date and Time screen opens Press the left and right arrows to edit the year month day hours or minutes when the selection is in the currently editing field Press the up and down arrows until the correct numbers appear near the top of the screen To accept the new settings and return to the Maintenance screen press OK To return to the Maintenance screen without accepting the new settings press Cancel OoGeneTAC HybStation Version 4 0 Issued February 2003 Section 4 9 Setting the Date and Time Section 5 Using the PC Methods Editor Software GENOMIC O GeneTAC HybStation EE SOLUTIONS _____ GENOMIC SOLUTIONS Short File Name y The Tool Bar oe El El New Open Save Print Bee Add Insert Delete Step Step Step ee is Lead from PL1 ES Network lead from PL2 to other HybStations View of HybStation Rear Panel The PC Methods Editor Main Window Section 5 1 Introduction Step Properties Network Status Introduction to the PC Methods Editor Software The PC Methods Editor software runs on a PC and can be networked to the HybStation Using the software protocols can be created edited and printed To connect the HybStation to a PC a communications lead Part No H2001016 is used between port PL1 on the HybStation and the PC as shown above To n
4. Removal of the Array Slides To remove the Array Slides from the assembly first remove the Slide Cover The Array Slide Base can then be positioned onto the Extraction Tool The pins protruding from this tool will release the Array Slides and Slide Pads when the base is pushed down onto it Remove the Array Slide Base from the Extraction Tool when the Array Slides and Slide Pads have been removed Note It must be noted that when removing the Array Slide Cover the Array Slides may stick to the Array Slide Seals This will depend upon the type of protocol being used and is quite normal The slides can carefully be removed from the seals without any damage occurring Section 2 2 2 Using the 21mm Slide Assembly Section 2 3 Using Reagents Using Reagents The GeneTAC HybStation has positions for five reagent or reservoir bottles and two waste bottles Note Before starting any hybridization protocol it is important to empty the waste bottles and dispose of the contents properly Genomic Solutions Reagents Genomic Solutions offers hybridization and wash buffer solutions for the GeneTAC HybStation The GeneTAC Hybridization Kit for 12 to 15 hybridizations includes 2 tubes of 2X HybBuffer Hybridization Solution 1ml each 1 bottle GeneTAC Medium Stringency Wash Buffer 500ml 1 bottle GeneTAC High Stringency Wash Buffer 500ml 1 bottle GeneTAC PostWash Buffer 500ml 1 package of neoprene O rings 2 labeled sample p
5. OrGeneTAC HybStation Section 4 4 Testing the Heating Element Version 4 0 Issued February 2003 of a Module EN SOLUTIONS Section 4 5 Cleaning the Valves and Lines Cleaning the Valves and Lines A machine cleaning cycle should be performed on modules that were used 3 To start the cleaning cycle press Start A message appears after each run The water in this cycle removes solutions to prevent prompting preparation of the HybStation by precipitation in the valves and lines The cleaning program allows the selection of slide positions for cleaning Q Placing tubes 1 through 5 into a single container of ultrapure water Q Fitting slides at all positions selected for cleaning To clean the valves and lines 1 On the Maintenance screen press Machine Cleaning Cycle The Slide Positions screen will then open 4 Press Continue The cleaning cycle will then start 2 To select specific slides press the slides on the screen To select Note To mainiain a clear fluidic system it is good to do a Machine all slides press Select All Clean cycle using warm water at approx 85 C every month Changing the Network Address If multiple HybStations are being run in a network each instrument must have a unique network address The Network Address screen is used to change the network address of the GeneTAC HybStation To change the network address 1 On the Maintenance screen press Network Address The Ne
6. for the desired temperature To change the entry press Clear and enter a different number Press OK A screen appears prompting for the length of time the temperature is to be maintained Je GENOMIC i SOLUTIONS DRE oo mame 0 11 Enter the desired length of time in minutes and or seconds Note To select minutes press Minutes then press the desired number s small marker will appear next to the Minutes button to indicate it is selected Similarly to select seconds press Seconds then press the desired number s To change an entry press Clear and enter a different number 12 Press OK A screen appears prompting for the number of times that the wash is to cycle OoGeneTAC HybStation Version 4 0 Issued February 2003 13 14 15 16 GENOMIC SOLUTIONS Select the desired number of cycles The maximum number of cycles is 10 To change the entry press Clear and enter a different number Press OK The Wash Definition screen appears with the wash step displayed Continue adding wash steps as desired up to 10 steps by repeating the previous procedures When all steps have been added to the multiple wash press Finish The Protocol Definition screen appears listing the Multiple Wash as one step Section 3 12 4 Adding Protocol Steps The Multiple Wash Step Adding a Drain Step The drain step is used to select a specified length of time for which each slide is drained Note
7. left over buffer by switching on the two purge valves the waste valve for waste bottle one and the air intake valve The air intake and the waste valves are left open to allow the proper flow across the slides When the HybStation is within 0 25 C of the target temperature the Probe screen appears showing the appropriate slide positions The order in which labeled sample is added to modules is not necessarily sequential It is dependent upon the order in which the modules reach the required temperature It is important to be aware of which modules are ready to accept labeled sample When Probe is pressed below the first slide position a check mark appears next to the probe button to show it is selected and the inlet valve for the slide is opened Labeled sample is then added through the port by means of a standard 200 pipette with disposal tips yellow When this has been done insert the labeled sample plug and press Finished next to the Probe button The inlet valve for the slide is then closed This process is then repeated for the second slide position and others As prompted add the labeled sample to each slide in turn by module When labeled sample had been added to all slides Finished is pressed at the bottom of the screen to move on to the next protocol step ObGeneTAC HybStation Section 3 11 The Protocol Steps Version 4 0 Issued February 2003 Section 3 11 The Protocol Steps The Temperature Step with Agita
8. 5 5 Editing a Protocol GENOMIC 2 SOLUTIONS Section 5 6 Inserting Steps I nto a Protocol Inserting Steps into a Protocol When a step is inserted into a protocol it will be positioned before a selected step in the protocol To insert a step into a protocol 1 Open a protocol The Main window will then appear showing the steps for the protocol In the step list click the step before the location of the new step Do one of the following e From the Edit menu choose Insert Step e On the toolbar click the Insert Step button The New Method Step dialog box will then open Chaces hs Hope of aden pou raand La akt 4 From the Steps drop down list select the step to be inserted All available steps will be shown in the list Cases fee tune of isp puai ka AGE Sa Gide Tangs spiss bikes Click OK Repeat Steps 2 through 5 to insert additional steps into the protocol Save the changes to the protocol e To save the changes using the same protocol name choose Save from the File menu e To save the changes using a different protocol name choose Save As from the File menu Note Always use a file name with 8 characters or less or make the first 8 characters recognizable Deleting Steps from a Protocol To delete a step from a protocol 1 Open the protocol 5 Click Yes 2 The Main window will then appear showing the steps of the 6 Save the protocol changes protoral e To save the c
9. A drain step is only used for the removal of prehybridization solution To add a drain step 1 Onthe Steps screen press Drain The Define Drain Time screen appears gt GENOMIC SOLUTIONS ina Th Inte F 2 Enter the amount of time that the system is to drain in minutes and or seconds The maximum time is 20 minutes Section 3 12 5 Adding Protocol Steps The Drain Step Note To select minutes press Minutes then press the desired number s A small marker will appear next to the Minutes button to indicate it is selected Similarly to select seconds press Seconds then press the desired number s To change an entry press Clear and enter a different number Press OK Adding a Loop A loop is a series of steps that are defined and saved to use in a protocol where a number of steps is repeated several times Rather than adding all these steps repeatedly they can be saved as a loop that forms part of the final protocol To create a loop 1 On the Steps screen press Start Loop The Keypad screen appears prompting for a name to be entered for the loop 2 GENOMIC gt SOL UT IONS BOE 2 Enter a name of up to eight alphanumeric characters using the alphanumeric buttons Note To delete a character press Bkspc To cancel the operation and return to the Protocol screen press Cancel To accept the entry and continue press OK The Protocol Definition screen will then appear showing a new ste
10. damage occurring to the Array Slides To move the slides into position place the insertion tool into position as shown then slide the tool towards the top of the assembly This will move the Slide Pad and allow the springs to push the slides into the top left hand datum corner When the slides are in position check that Gap between This gap they are properly seated against the datum bottom of Slide and must be bottom of Slide Pad closed corner and that the springs are properly positioned flush with the base and against the edges of the slides Push the Insertion Tool towards the top of the assembly allowing the springs to position the slides at the datum corner CbGeneTAC HybStation Section 2 2 2 Using the 21mm Slide Assembly Version 4 0 Issued February 2003 GENOMIC Z SOLUTIONS or g 7 Place a metal shim onto the top of the assembly as shown 9 After finally checking that the Array Slides are correctly positioned place the Array Slide Cover onto the assembly with the O Ring seals at the top The assembly is now ready for use 8 Prepare the Array Slide Cover for use To do this ensure that four red colored connecting O Rings are correctly positioned into the recesses at the end of the cover and insert two black Array Slide Seals into the rectangular recesses in the cover O Rings Array Slide Seals OoGeneTAC HybStation Version 4 0 Issued February 2003
11. over each slide in turn for the specified time The maximum flow time allowed is 1 minute For each wash the valve for the input solution and the selected waste bottle are open for all of the slides In addition the particular slide s inlet and outlet valves are open for the length of time that is specified Then the countdown for the hold time specified is started All of the wash valves are closed at this stage The priority selected determines how the system continues The priorities are Q Normal The program may interrupt the wash cycle on one module to start and perform wash steps on other modules moving back and forth between modules Q Must not be interrupted Critical The program goes through the complete wash step on one module before proceeding to the next one Q Urgent This step is similar to the Normal priority in that the program interrupts the wash step on one module to perform wash steps on other modules However when Urgent priority is selected the program next starts the wash steps for the module with this priority assigned The Probe Step This step defines where in a protocol the labeled target is to be inserted into each slide of one several or all selected modules The temperature at which the labeled sample is to be inserted can also be set This temperature can be between 0 and 99 When the modules have reached the specified labeled sample temperature the manifolds are purged of their contents that is
12. press Finish Checking a Module Temperature Module temperatures can be checked using the Module Status screen The screen lists the current temperatures of the six modules To view current module temperatures On the Maintenance screen press Module Status The Module Status screen opens To return to the Maintenance screen press Close O GeneTAC HybStation Section 4 2 Checking a Module Temperature Version 4 0 Issued February 2003 Section 4 3 Testing the System Valves Testing the System Valves A number of valves are incorporated into the HybStation systems Each slide has three dedicated valves Q Inlet Valve Q Agitation Valve Q Outlet Valve Additionally there are bottle and air inlet valves waste valves vent and transfer valves and valves for the manifolds called primary and secondary primers The Valve Screen is used to manually open and close valves and run liquid through them To test selected valves 1 Place tubes 1 through 5 into a single container of ultrapure water 2 On the Maintenance screen press Valve The first Valve Screen appears GENOMIC SOLUTIONS ottle 1 Input Input Input Input 3 Select the valve s to be tested Note It must be ensured that an input valve is not selected for an empty or non existent bottle reservoir A check mark appears next to each selected valve 4 Observe the flow of the liquid To select valves for individual s
13. to be used Q Waste bottle to be used Q Specific wash time and temperature Q Specific hold time at that temperature a Number of times the wash will be performed Unlike the single wash step the manifolds are not emptied when the first wash is finished before the new buffer flows into them This results in some mixing of fluids No choice of scheduling is available with this step The Drain Step This option is used to select the amount of time to vent and drain the slides The slides are drained one at a time by having their inlet and outlet valves opened When the air inlet valve is opened it allows airflow over each slide to the waste bottle Start Loop This option is used to create and name a loop A loop comprises a series of steps that are defined and run a specified number of times Using loops relieves the creation of a long protocol as it is only necessary to list repetitious steps only once Once a loop is named it can be added to a protocol in the same way as other steps The Start Loop command sets a flag in the protocol list that indicates the beginning of the loop End Loop This option is used to end a loop and specify the number of times to run the loop When End Loop is pressed having added the desired number of steps you are prompted to enter the name for the loop You must enter the same name you specified when you started the loop The following procedures define how to implement each of the prot
14. For AS Ladki PEI ILL 3 Press the number of the reservoir bottle to be used 1 5 The number appears in the box above the available choices To change the entry press a different number The system overrides the current entry with the new one OoGeneTAC HybStation Version 4 0 Issued February 2003 Section 3 12 4 Adding Protocol Steps The Multiple Wash Step 4 Press OK The Waste Bottle screen appears prompting for selection of a waste bottle for this cycle gt GENOMIC SOLUTIONS OC 5 Press the number of the waste bottle to be used 1 or 2 The number appears in the box above the available choices To change the entry press a different number The system overrides the current entry with the new one 6 Press OK A screen appears prompting for definition of the flow time for the wash Le GENOMIC SOLUTIONS 10 Section 3 12 4 Adding Protocol Steps The Multiple Wash Step Enter the length of time the fluid should flow in minutes and or seconds Note To select minutes press Minutes then press the desired number s A small marker will appear next to the Minutes button to indicate it is selected Similarly to select seconds press Seconds then press the desired number s To change an entry press Clear and enter a different number Press OK A screen appears prompting for a temperature step at which the wash is to cycle ce GENOMIC SOLUTIONS Press the number s
15. GENOMIC SOLUTIONS ter The Time For This 5 Enter the desired amount of time in hours minutes and or seconds 6 Press OK Adding a Multiple Wash Step A multiple wash step is similar to a single wash step but can contain up to 10 washes within the one step Only one definition of a multiple wash can be made for a protocol If a multiple wash is defined and this option is selected again a message appears asking if the multiple wash is to be re defined or if the current multiple wash is acceptable If it is selected to re define the multiple wash either add steps can be added to your multiple wash or steps can be deleted from it A multiple wash consists of multiple steps which are defined on multiple screens To continue from one screen to the next press the OK button at the bottom of a screen If this button is pressed before making a required entry a warning message appears prompting an entry before continuing To add a multiple wash 1 On the Steps screen press Multiple Wash The Multiple Wash Definition screen then appears Py GENOMIC I tiple wasi Note To return to the Multiple Wash Definition screen from any of the following screens without adding a wash step Cancel can be pressed To return to the Protocol Definition screen without adding a multiple wash step press Finish 2 Press Add The Reservoir screen appears prompting you to select a reservoir bottle GENOMIC SOLUTIONS The Reservoir
16. The environment must be dust and vibration free and be controlled to achieve Always keep the work area dry Always work with dry hands and ensure that the work area is kept dry during use e Temperature between 5 C and 40 C Q Maintain proper clearance on underside and sides of the e Maximum relative humidity of 80 for temperatures up to 31 C decreasing linearly to 50 relative humidity at 40 C e Pollution degree 2 environment in accordance with IEC 664 instrument for proper air conduction Power Connection The equipment is supplied with a separate main power lead having an integral ground earth wire The main power lead must firstly be inserted into the power socket at the side of the workstation as shown above The main outlet plug is then inserted into a properly grounded power supply socket If any doubt exists about the power supply socket intended for use a qualified electrician must be contacted for advice It must be noted that the workstation is equipped with a universal power supply However the controlling PC is not equipped with a universal power supply so the PC voltage is factory set prior to dispatch from Genomic Solutions The PC supply voltage setting must therefore not be adjusted except by Genomic Solutions personnel Warning Failure to provide a properly grounded power socket for the equipment could lead to an electrical shock hazard It is also important to ensure that main supply voltage fluctuat
17. acrylic manifold A vacuum source moves fluids through the system to the waste bottles Temperature control and fluidics can be varied on the HybStation to control hybridization of microarrays Temperature control has a range between 1 and 99 C 0 5 C with temperature ramping of 1 C per second By separating the slide from the slide cover with a shim of a specific thickness it is possible to maintain a consistent hybridization volume over time regardless of the changing properties of the O ring System Flowpath The flow path of the acrylic manifolds valves and tubing lines is shown on the page above On the diagram the reagent lines are numbered 1 2 3 4 and 5 The four lines at the back of the manifold are 6 which is open to air 7 for waste bottle 1 8 for waste bottle 2 and 9 which is a vent line open to air There are three valves for each slide Q Inlet valve Q Agitation valve located between the inlet valve and the slide chamber Q Outlet valve OoGeneTAC HybStation Version 4 0 Issued February 2003 Section 2 1 Introduction to the HybStation Section 2 2 Using Slides 21 3mm 0 0 Datum Corner 21 0mm 3 8mm A 1 9mm gt 0 0 Datum Corner N Frosted Area Face Down array element side up 68mm max E amp CO Hybridization Area Frosted Area Face Down array element side up The 21mm Slide Assembly The 18mm Slide Assembly Introduction to Using Sl
18. ails are not repeated again in this section When in use the complete slide assembly is located onto the yellow colored heat exchanger thermal pads positioned on the HybStation heat exchangers It must be noted that these Thermal Pads should always be left in position on the heat exchangers and must not be removed To use the 21mm assembly proceed as follows Heat Exchanger Thermal Pads Section 2 2 2 Using the 21mm Slide Assembly Note When setting up and using the 21mm slide assembly always ensure that the U shaped slot is located at the top of the Array Slide Base U shaped slot at the top Array Slide Base To use the assembly proceed as follows 1 Place two Slide Pads into the recesses of the Slide Base 2 With the slide pads correctly positioned place the insertion tool into the recesses on the left hand side of one of the slide When positioning the pads care must be taken to ensure that they are pads pushed towards the top left hand corner of the recesses and that the springs are properly positioned flush with the base These pads will later be used to compress the springs to allow insertion of the Array Slides This tool will then be used to push the slide pads towards the bottom right hand corner of the base against the action of the springs Position the Slide Pads adjacent to the top left hand corner ObGeneTAC HybStation Section 2 2 2 Using the 21mm Slide Assembly Version 4 0 Issue
19. and at what temperature Q Temperature Enter the temperature at which the GeneTAC HybStation will cycle a Multiple wash Select a solution to flow through the slide chambers for up to 10 wash steps Q Drain Specify the length of time for which you want air to be drawn through the slide to remove a solution Q Start loop Create a series of steps to be repeated multiple times Q End loop Complete the series of steps Any number of steps can be added to a protocol When a step has been added the Protocol Definition screen appears listing the new step The protocol steps are described in detail on the following pages ObGeneTAC HybStation Section 3 11 The Protocol Steps Version 4 0 Issued February 2003 Section 3 11 The Protocol Steps The Single Wash Step This step is used to specify flow and hold times and temperatures for a wash step The reservoir and the waste bottle to be used are also selected together with a definition of the number of times cycles the wash step is to be performed First the modules selected for a run go to the temperature specified in the wash step Once all modules arrive at the proper temperature the manifolds are primed with the wash solution The wash bottle valve and the waste valve are open at this time For twelve slides the two transfer valves one for each manifold are also open to allow flow through the manifolds without going through any slides Next the wash solution flows
20. bStation and disconnect the power cord before cleaning the instrument DO NOT allow liquid to enter the inside of the power unit Liquid may damage the power unit and present a potential shock hazard Cleaning the Lines After completing a hybridization run a machine clean cycle wash using blank slides and ultrapure water This step is particularly important if the machine will be idle for a few days Note Refer to Section 4 5 Cleaning the Valves and Lines Maintaining the O rings Note It is recommended that the neoprene O rings be after each run as worn O rings will not seal properly and leaking could occur If the O rings are re used ensure that they are cleaned well before the next run is carried out To clean the O rings Remove the O rings from the slide cover Rinse the cover under a stream of water and genily lift an edge of the O ring or use canned air to remove the O ring Place the O rings into a boiling bath of ultrapure water at approximately 80 C for 1 to 2 minutes Remove the O rings from the bath and allow them to air dry To replace the O rings Make sure the channel is free from particulate matter Place the O ring over the channel Gently press the O ring into the groove in the slide lid Do not twist the O ring when replacing it or the slide cover may not seal completely OoGeneTAC HybStation Version 4 0 Issued February 2003 Section 2 4 Basic Maintenance Section 3 Using the HybStation
21. ction 6 Example of a Typical Protocol Example of a Typical Protocol This section shows an example of a typical protocol Step Description 1 Probe Temperature 65 C 2 Temperature Temperature 55 C Time 18 hours Agitate Yes 3 Single Wash Reservoir 1 Waste Bottle 1 Flow Time 10 Seconds Temperature 55 C Temperature Time 20 seconds Cycles 3 4 Single Wash Reservoir 2 Waste Bottle 1 Flow Time 10 Seconds Temperature 25 C Temperature Time 20 seconds Cycles 3 5 Single Wash Reservoir 3 Waste Bottle 1 Flow Time 10 seconds Temperature 25 C Temperature Time 20 seconds Cycles 3 During this typical protocol the reservoirs should contain the following GeneTAC Wash Buffer Solutions Reservoir 1 Medium Stringency Wash Buffer Reservoir 2 High Stringency Wash Buffer Reservoir 3 Post Wash Buffer OoGeneTAC HybStation Version 4 0 Issued February 2003 Section 6 Example of a Typical Protocol
22. d February 2003 GENOMIC SOLUTIONS Section 2 2 2 Using the 21mm Slide Assembly 3 Holding the Insertion Tool in position slide the tool towards 4 With the springs compressed the two Array Slides can be the bottom of the Array Slide Base until it clicks into the insertion dropped into the recesses of the Array Slide Base pasmon Ensure that the slides are properly seated and that the white As the tool slides along the Slide Pad compresses the springs frosted area of each slide is positioned at the bottom of the base until the pad clicks into position When the tool has clicked into facing downwards It is also important to ensure once again that this position the Slide Pad will remain fixed and the tool can be the springs are properly seated flush against the base and the withdrawn edges of the Slide Pads Note It is important to ensure that the springs remain properly seated and that each of the Slide Pads are secure 1 5 To properly position the slides they 6 Using the Insertion Tool carefully slide the Slide Pad need to be pushed towards the top left downwards to bring the bottom of the Slide Pad level with the hand corner of the Array Slide Base bottom of the Array Slide This corner acts as the system datum and Note It is important that the edges of these are aligned and that the slides must always register with this no gap exists between them Failure to do this could result in datum corner when in use
23. dialog box will appear Hew method Hep 3 From the Steps drop down list select the step to be added All available steps will appear in the list New method step Click OK Repeat the above procedures to add additional steps to the protocol 6 From the File menu choose Save The Save As dialog box will then appear allowing the new protocol to be saved Note For additional information refer to the next section Saving a Protocol Section 5 3 Creating a New Protocol GENOMIC T SOLUTIONS Section 5 4 Saving a Protocol Saving a Protocol Changes to a protocol can be saved under the current protocol name or using a new name and create a protocol When you create a new protocol you can save it to any directory under any name 3 Inthe File name field enter a name for the protocol 2 Browse to the directory where the protocol is to be saved Note Because the HybStation does not permit the use of long file names use a name with 8 characters or fewer To save a protocol under a new name 4 Click Save or press the Enter key The software will then save the 1 From the File menu choose Save As The Save As dialog box protocol with a HYB extension appears To save changes to a protocol do one of the following Eare aa e 1 Ba a a a ee eae Bien a Protos EI a On the toolbar click the Save button sis If the HybStation is not networked to a PC a protocol can be saved onto a flopp
24. diting an Existing Protocol Version 4 0 Issued February 2003 2 GENOMIC ie SOLUTIONS Section 3 8 Adding Steps to a Protocol Adding Steps to a Protocol 1 Select a protocol for editing as described on the previous page 2 Add a new step either before a specified step or at the end of a protocol a To add a step before a specified step select the step on the Protocol Definition screen A marker will appear to the right of the step Then press Add at the bottom of the screen a To add a step to the end of the protocol press Add at the bottom of the screen without selecting a step To return to the Protocol screen without adding steps press Finish 3 Press the step to be added Note For a description of all available steps refer to Section 3 11 Repeat steps 2 and 3 to add more steps to your protocol When all required steps have been added press Finish The Protocol screen will then appear 6 On the Protocol screen press Save protocol The Keypad screen will then appear Enter a name for the protocol of up to eight alphanumeric characters using the alphanumeric buttons noting the following Q Q To delete a character press Bkspc To cancel the operation and return to the Protocol screen press Cancel To accept your entry and continue press OK The Main screen will then appear If Finish on the Protocol Definition screen is pressed before the new protocol is saved a warning screen will a
25. e Protocol The Keypad screen will then appear Le GENOMIC SOLUTIONS To save the protocol press No The Protocol screen then appears Press Save Protocol and proceed as described above Deleting a Protocol A protocol can be deleted from either a floppy disk or the internal PC storage 3 Press Floppy Disk or Internal storage A screen then appears To delete a protocol listing all available protocols 1 Onthe Main screen press Edit or create a protocol The Protocol screen will then appear gt GENOMIC sie GENOMIC b SOLUTIONS SOLUTIONS 2 On the Protocol screen press Load or delete stored protocol A 4 Select the protocol to be deleted A marker to the right of the screen then appears requesting the location of the protocol to be protocol will indicate the selection deleted 5 Press Delete The system then removes the protocol gt GENOMIC je SOLUTIONS se ObGeneTAC HybStation Section 3 10 Deleting a Protocol Version 4 0 Issued February 2003 Temperature Multiple ash Drain Section 3 11 The Protocol Steps The Protocol Steps When steps are added to a new protocol or to a saved protocol these steps can consist of the following and as shown in the above window All steps are initiated using the above screen Q Single wash Select a solution to flow through the slide chambers Q Probe Specify where in the protocol the labeled sample is to be added
26. e for the solution The Drain Slides Step This step is used to specify the length of time that each slide is drained To define a drain step 1 From the Steps drop down list choose Drain Slides In the Main window a drain slides step is added on the left with the corresponding tabs on the right 2 On the Drain Slides tab Q Optionally enter a brief description for this step in the protocol by highlighting the current entry and typing a new one The description replaces the name of the step in the step list lt OGeneTAC HybStation Version 4 0 Issued February 2003 Q From the Waste drop down list choose a waste bottle a Specify the length of time that slides are to drain by highlighting the current entry and typing a new one 3 Click the Advanced tab 4 On the Advanced tab select scheduling for this step Section 5 9 5 The Protocol Steps Drain Slides pm i Section 5 9 6 The Protocol Steps GENOMIC SOLUTIONS Creating a Loop is Creating a Loop A loop can be created when a series of steps are repeated in a protocol A Q Enter a name for the loop loop must have a Start Loop step at the beginning and an End Loop step at the end of the series The number of cycles that the series is repeated in defined in the End Loop step Q From the Steps drop down list choose End Loop In the Main window an end loop step is added on the left with the End Loop tab on the right a Add steps t
27. e right hand side Section 5 9 2 The Protocol Steps Introduce Probe 2 On the Probe tab Q Optionally enter a brief description for this step in the protocol by highlighting the current entry and typing a new one The description will replace the name of the step in the step list Q Enter the temperature at which it is required to introduce the labeled sample by highlighting the current entry and typing a new one The Set Temperature Step This step is used to set the temperature for hybridization and the length of time for which the system will cycle at that temperature To set the hybridization temperature 1 From the Steps drop down list choose Set Slide Temperature In the Main window a temperature step is added on the left with the corresponding tabs on the right lt OGeneTAC HybStation Version 4 0 Issued February 2003 On the Temperature tab Q Optionally enter a brief description for this step in your protocol by highlighting the current entry and typing a new one The description replaces the name of the step in the step list Q Enter the desired temperature by highlighting the current entry and typing a new one Q Enter the length of time for the temperature step in hours H minutes Min seconds Sec a Click the Advanced tab 2 Onthe Advanced tab Q To add agitation make sure Enable Agitation is checked The system will then automatically open and close the agitation valves d
28. em Status The HybStation Status screen will then open In this example the HybStation Status screen shows the following Q Ooo A protocol is running on Modules One and Four The protocol has eight steps and the first step is in progress Modules Two Three Five and Six are idle The Progress area shows a progress bar for each active module Modules One through Six correspond to six progress bars from top to bottom To view details of a specific module press the box representing the module A screen will then open showing detailed information This example shows the following information OOoOovood Oo The name of the protocol on this module is DEMO HYB This is Module One The second step of an eight step protocol is currently running The current step is to cycle at 55 C for 12 hours The module is at the set temperature for the current step The current temperature is 55 C the number in parentheses indicates the array element temperature Time Remaining refers to the time remaining for the current step Total Remaining refers to the time remaining for the current protocol To return to the HybStation Status screen press OK To return to the Main screen press Close Screen on the HybStation Status screen OoGeneTAC HybStation Version 4 0 Issued February 2003 Section 3 4 Monitoring a Run Section 3 5 Aborting a Run Aborting a Run If necessary a run can be aborted on all m
29. es as follows Q The HybStation can implement steps with Normal scheduling on all modules at the same time depending on the procedures required by the step This is the most efficient use of the processing time a If Critical or Urgent scheduling is used the current step ties up the HybStation because no other step can run at the same time This is the least efficient use of the processing time but may be necessary for the processes involved Three scheduling options are available as follows Normal Critical This step must not be interrupted Urgent This step will be run as soon as possible When a step finishes processing on any of the modules the HybStation looks to see which step or steps it can start next If a step with Urgent scheduling is ready to start it takes priority followed by steps with Critical scheduling and lastly by steps with Normal scheduling OoGeneTAC HybStation Version 4 0 Issued February 2003 Normal Scheduling Normal is the default scheduling setting The program may interrupt a step on one module to start and perform steps on other modules moving back and forth between modules When Normal scheduling is selected for a wash step for example there is no guarantee that the temperature steps within the wash step will be performed for the exact length of time determined by the protocol Normal scheduling should therefore be applied to steps such as pre conditioning the slide the pre hybridiza
30. etwork more than one HybStation together a communications lead Part No H2001013 is used between the PL2 ports on the connected HybStations Installing the PC Methods Editor Software The software for the PC Editor is available from Genomic Solutions and is installed as follows 1 Install the software by copying the self installing file to the PC and executing it 2 Atthe PC navigate to the folder where the program is installed C ProgramFiles GenomicSolutions HybStationPC 3 Launch the program by double click the icon The Main window will then appear Working in the PC Editor The software is easy to use and is controlled from the Main window The main window comprises Q Q The Menu Bar providing access to functions for working with protocols via menus The Toolbar provides access to functions for working with protocols via buttons As shown on the above figure the first four toolbar buttons are standard Windows program buttons and the next three buttons are used when creating or editing a protocol The Step List area shows a list of all the steps in the current protocol Note To select a step left click on it The Step Properties area shows the properties of a selected step The Network Status area used when networking shows all the Genomic Solutions devices connected to the PC including the instrument type and its status OoGeneTAC HybStation Version 4 0 Issued February 2003 Secti
31. hanges using the same protocol name choose In the step list click on the step to be deleted Save from the File menu 4 Do one of the following e To save the changes using a different protocol name choose Save As from the File menu Q From the Edit menu choose Delete Step Note Always use a file name with 8 characters or less or make the Q On the toolbar click the Delete Step button first 8 characters recognizable A Confirmation dialog box will then appear DigestE ditor EZ AX Are you sure you want to delete this step jw O GeneTAC HybStation Section 5 7 Deleting Steps from a Protocol Version 4 0 Issued February 2003 Er pe vs SOLUTION s Section 5 8 Setting a Method Title is File Name Method Title description of protocol Setting a Method Title The method title is the name that appears in parentheses at the top of the protocol window next to the protocol name The method title is used to add a description of the protocol to the file name To set a method title for a protocol 1 Open the protocol 2 From the File menu choose Set Method Title The Method Title dialog box appears Enter a description of the protocol Method Title 3 Type a description of the protocol 4 Click OK or press the Enter key OoGeneTAC HybStation Version 4 0 Issued February 2003 To change the method title for a protocol 1 Open the protocol 2 From the File menu choo
32. he number of the waste bottle to be used 1 or 2 GENOMIC Note To change the entry press a different number The system e SOLUTONS overrides the current entry with the new one Ca 5 Press OK A screen appears asking for the amount of time the HE selected solution is to flow over the slide HG E GENOMIC a JE IL SOLUTIONS GORE 8 Select the number for the desired temperature To change the entry press Clear and enter a different number 9 Press OK A screen appears prompting for the amount of time the slide is to remain at that temperature GENOMIC 6 Enter the flow time in minutes and or seconds Er re ETN ter 1e Time or This Note To select minutes press Minutes then press the desired number s A small marker will appear next to the Minutes button to indicate it is selected Similarly to select seconds press Seconds then press the desired number s To change an entry press Clear and enter a different number It should also be noted that the details in this note apply to a number of the following steps in this section of the manual 7 Press OK A screen will appear prompting for the temperature at 10 Enter the desired length of time in minutes and or seconds which the wash is to cycle OoGeneTAC HybStation Section 3 12 1 Adding Protocol Steps Version 4 0 Issued February 2003 The Si ngle Wash Step EN Section 3 12 1 Adding Protocol Steps T SOLUTIONS The Single Wash Step
33. ick the Add Step button Scheduling The timing of protocol steps is controlled by scheduling This is set when each step is defined Each module on the HybStation runs independently If all the steps are set to Normal scheduling the GeneTAC HybStation performs the steps concurrently for each module For example if Modules 1 through 4 are selected for a protocol that has three steps the system performs Step 1 on all 4 modules then Step 2 etc But some resources required by the steps use parts of the station exclusively For example the high power input required by the Peltier unit when heating the slides As a result of this only one module can use the resource at a time while the other modules have to wait In some cases the time spent waiting for HybStation resources may not affect the experiment being carried out There are cases however where a wait after a certain step may affect the experiment results For example a wash step flushes solution through the slide and holds it for a given time When the hold time begins the manifold is available for another step to use and might not be available to implement a second wash on the particular slide As a result the wash solution may be held longer than anticipated which may affect the outcome of an experiment To avoid potential problems of this type Critical or Urgent scheduling can be employed If this is used it must be considered how this scheduling will affect the other modul
34. ides The GeneTAC HybStation processes up to 12 slides on six temperature controlled modules by washing fluids over the active surface of each slide It is important to always place and seat slides properly on the instrument Slide Sizes Two types of slide array assembly can be used with the HybStation an 18mm type slide assembly and a 21mm assembly The 18mm type slide assembly has a hybridization area of 18mm x 56mm whereas the 21mm assembly provides a larger hybridization area of 21mm x 68mm as shown in the figure above It must be noted that the two assemblies are quite different and their components are therefore not interchangeable An upgrading kit is now available to enable use of the 21mm assembly on any HybStation Frosted Slides The frosted side of a slide must always be placed face down on the carrier It is essential that hybridization is always carried out on the unfrosted side of a slide The Slide Sealing System To retain the fluids during use a polysulphone cover is fitted over the active surface of the slide A gasket neoprene O ring is integrated in the cover to seal the slide It is critical that the gasket does not overlap the spots on the slide Critical Handling Notes When handling slides follow these recommendations Q Do not touch or label the active surface of the slide Fingerprints labels and pen marks may leach contaminants or prevent sealing by the O rings Q Apply labels to the inact
35. ighlighted Note To deselect a slide press the slide number again To select all slides press Select All at the bottom of the screen The arrows indicate the slide positions selected The system will select positions to ensure even use of all modules Select Start A message screen will then open stating Press Continue when you are ready to start this run Place the slides into the slide holders Note For details of how to place slides onto the HybStation refer to Section 2 2 When the slides have been correctly positioned press Continue The HybStation Status screen will then open The use of this screen for monitoring purposes is described in Section 3 4 Monitoring a Run To exit this screen and return to the Main screen select Close Screen OoGeneTAC HybStation Version 4 0 Issued February 2003 Section 3 2 Running a Protocol Adding a Probe Labeled Sample The HybStation software indicates when to add a labeled sample by displaying the prompt screen To add a labeled sample 1 Atthe screen press the Probe button to add a labeled sample for the slide A check mark will then appear next to the Probe button Note A click will be heard as the valve opens to allow the system to vent This valve must be opened to enable the labeled sample to enter the slide chamber In this example the probe for slide number 1 is selected GE MEWUC SOLUTIONS 2 Inject the labeled sample by pipetting it slowl
36. ions do not exceed 10 of the supply voltage Main Power Lead CbGeneTAC HybStation Section 1 4 Safe Working Practices Version 4 0 Issued February 2003 and Power Connection Section 2 The GeneTAC HybStation 2 gt GENOMIC O GeneTAC HybStation z SOLUTIONS Se amis Faits GENOMIC SOLUTIONS Section 2 1 Introduction to the HybStation WASH BOTTLES ese ia ee fee ue T i uk 116 g GG Gjemt OO 1 2 Ta T4 5 iS a Upper Wan old Oo CO O0 OOOO OO OO F ahii The HybStation System Introduction The GeneTAC HybStation is an automated system for hybridizing and washing microarrays Protocols can be run simultaneously to achieve uniform reproducible results with minimal handling of solutions and slides Each microarray has a port for independent addition of labeled sample The closed environment minimizes evaporation System Overview The HybStation has six Peltier temperature controlled devices with fluidics capabilities For each module two microscope slides are placed array element side facing upwards on the thermally controlled Peltier unit A polysulphone slide cover with chemically inert neoprene O rings and a stainless steel shim is placed over the slides to create the hybridization chamber Fluids enter the hybridization chamber through channels in the slide cover and are controlled by valves mounted inside an
37. ive face of the slide at the end nearest the home position corner Maximum rear face irregularity is 50um that is maximum label thickness is 100um Q Process slides in pairs If it is required to process an odd number of slides use a dummy blank slide in the unused position This should be of the same slide type as the one being hybridized Q Take care to never mark or score the glass slides in any way OoGeneTAC HybStation Version 4 0 Issued February 2003 Section 2 2 Using Slides GENOMIC 2 SOLUTIONS Using the 18mm Slide Assembly A slide carrier is placed under each pair of slides to set the position The home position is 0 0 Placing Slides To place slides on the GeneTAC HybStation 1 Unscrew the black knob that holds the slide cover in position This releases the cover from the thermal module assembly Black Securing Knob 2 Toremove the slide cover gently pull it forward and up The top of the slide cover contains four small red connecting O rings that seal against the reagent manifold There is an indented area at the top center that encloses a small metal guide post that allows the cover to be repositioned Section 2 2 1 Using the 18mm Slide Assembly Check the O rings to make sure they are positioned correctly within the slide cover Place the slides one at a time onto the metal slide holder The metal slide holder is flanged at the top bottom and sides to hold each slide in positi
38. lides press Next at the bottom of the screen The second Valve Screen will then appear listing all three valves for slides 1 through 4 Jr GENOMIC gt SOLUTIONS Select the valve s to be tested A check mark appears next to each selected valve To return to the first Valve screen press Previous To select valves for further slides press Next To close a Valve screen and return to the Maintenance screen press Close To stop testing the valves and return to the Main screen press Finish on the Maintenance screen Note Always ensure that all valves are turned OFF before closing the maintenance screen Testing the Heating Element of a Module The heating element of a module is tested as follows le GENOMIC SOLUTIONS 1 On the Maintenance screen press Temperature The View Modules screen opens GENOMIC aT SOLUTIONS 3 Enter a target temperature that is higher or lower than the current temperature using the keypad on the right hand side of the screen Press Run Observe the temperature increase or decrease Press Stop to enter a new target temperature and use the keypad 2 Select a module on which to test the heating element A to enter the new temperature Temperature screen then opens for the module 7 Press Close to stop the test and return to the Maintenance screen Bus Reset can be pressed to reset data transmission with the module should any communications problem occur
39. m will return to the Protocol Definition screen Continue adding as many steps as necessary for the protocol Review the protocol steps use the Up and Down arrows to scroll through the steps Note To remove one of the steps select the step and press the Remove button de GENOMIC 6 To finish the protocol press the Finish button gt COLLINS Note The top right hand area of the screen will indicate that a protocol has been defined 7 Press Save Protocol The Keypad screen will then appear ObGeneTAC HybStation Section 3 6 Creating a Protocol Version 4 0 Issued February 2003 Section 3 6 Creating a Protocol 8 Atthe Please Enter a File Name for the Protocol screen enter a name for the protocol using up to eight alphanumeric characters To do this use the alphanumeric buttons noting the following a To delete a character press Bkspc Q Tocancel the operation and return to the Protocol screen press Cancel To accept name the entry and continue press OK The Main screen will then appear If Finish on the Protocol Definition screen is pressed before the new protocol is saved a warning screen will appear stating You have not saved this protocol Are you sure you want to lose the changes you have made To save the protocol press No The Protocol screen then appears Press Save Protocol and proceed as described above OrGeneTAC HybStation Section 3 6 Creating a Protocol Version 4 0 Iss
40. o the loop A nested loop is created when a series of steps are repeated within another loop Each nested loop must also include a Start Loop step and an End Loop step To create a loop 1 From the Steps drop down list choose Start Loop In the Main window a start loop step is added on the left with the Loop tab on the right 3 On the tab Q Enter a brief description of the step by highlighting the current entry and typing a new one The description replaces the name of the step in the step list 2 On the tab Q Enter the loop name that was entered on the Start Loop tab Q Enter a brief description of this step by highlighting the current Q Enter the number of cycles that the loop is required to run for entry and typing a new one The description replaces the name of the step in the step list Printing a Protocol An open protocol can be printed out to review the protocol To print a protocol 1 Ensure that the protocol to be printed is open 2 Do one of the following Q From the File menu choose Print Q On the toolbar click the Print button 3 On the Print dialog box click OK Note To see what a printed protocol would look like choose Print Preview 4 Click OK OoGeneTAC HybStation Version 4 0 Issued February 2003 Section 5 10 Printing a Protocol Section 6 Example of a Typical Protocol GENOMIC O GeneTAC HybStation M z SOLUTIONS N SOLUTIONS Se
41. ocol steps OoGeneTAC HybStation Version 4 0 Issued February 2003 Section 3 11 The Protocol Steps Section 3 12 1 Adding Protocol Steps The Single Wash Step Adding a Single Wash Step A wash step has two parts Q Flow Fluid from a reservoir flows over the slide for a set length of time Q Hold The valve closes and the chamber heats to a set temperature for a defined length of time When adding a wash step select the reservoir and waste bottle set flow time and temperature set hold time and temperature determine how many times the wash cycle will run and specify the priority of the wash step It must be remembered that the HybStation can wash only one slide at a time The total wash time is therefore the number of minutes for one wash multiplied by the number of slides Note To return to the Protocol Definition screen without adding a single wash step press Cancel on any of the screens described in the following section On the Protocol Steps screen press Single Wash The Define the Reservoir for this cycle screen then opens 2 GENOMIC SOLUTIONS Press the number of the reservoir bottle to be used 1 5 Note To change the entry press a different number The system overrides the current entry with the new one Press OK The Define the Waste Bottle for this cycle screen opens Select the waste bottle that the wash solution is to be sent to gt GENOMIC SOLUTIONS iG 4 Press t
42. odules or on selected modules To abort the run on all modules 1 Onthe Main screen press System Status The HybStation Status screen appears 2 Press Abort A Confirmation screen will then appear Press Yes The Main screen appears To abort the run on selected modules 1 Onthe Main screen press System Status The HybStation Status screen appears 2 Select the module on which the run is to be aborted The Status screen for the module will appear 3 Atthe upper right hand area of the screen press Abort A Confirmation screen will then appear 4 Press Yes The HybStation Status screen will then appear To abort the run on more modules repeat steps 2 and 3 above To return to the Main screen press Close Screen 3 GENOMIC Hybridisstor Statio amp SOLUTIONS vesion Creating a Protocol Le GEMORC l S SOLUTIONS A new protocol can be created using an external PC and then be run directly or saved on a floppy disk or can be created on the HybStation embedded PC for repeated use The procedure in this section describes in general how to create a protocol To create a new protocol 1 On the Main screen press Edit or create a protocol A new screen will then appear 2 Press Create a new protocol The Protocol Definition screen will then appear 2 GEMOME SOLUTIONS 3 To begin adding steps press Add The Steps screen will then appear When a step has been added the syste
43. on For correct placement ensure that the slide is positioned tightly against the top right hand edge of the flanged carrier plate with the array elements facing upwards Place the slide cover into position over the slides and the flanged carrier plate Ensure that the indentation in the top of the block is resting against the flanged edge at the top of the metal slide holder Note If the system is sealed properly the four red O rings appear as fat 6 Gently place the slide carrier cover assembly onto the module round circles when viewed through the back of the manifold positioning the block assembly against the metal guide pin 8 Re attach the locking mechanism by turning the black knob screw assembly until fingertip tight Note Do not over tighten the knob 9 Continue placing slides on each module as necessary following steps 1 through 8 until all slides are positioned for the run 7 Lower the clamp mechanism into position over the slide cover To ensure a good seal make sure that the slides do not move when positioning the clamp on top of the block ObGeneTAC HybStation Section 2 2 1 Using the 18mm Slide Assembly Version 4 0 Issued February 2003 GENOMIC SOLUTIONS Using the 21mm Slide Assembly The 21mm slide assembly provides a larger hybridization area than the 18mm assembly Note The 21mm assembly is clamped onto the HybStation in a similar way to the 18mm slides so those det
44. on 5 1 Introduction pe Gi MIC pe 4 Sains Section 5 2 Opening a Protocol is Opening a Protocol A protocol is opened through the File menu or by using the toolbar button 1 To open a protocol either Q From the File menu choose Open Q On the tool bar click the Open button 2 The standard Browse dialog box will then open 3 Browse to the location where the protocol is stored This can be the PC hard drive or a floppy disk 4 Select a protocol and click Open The Main window will then open showing the protocol steps At the Main window the step list on the left shows all steps in the protocol and the step properties are shown in the view area on the right To view the properties of any step click on the step To view additional step details of step properties click the Advanced tab Creating a New Protocol When the PC Methods Editor software first opens the main screen has a blank step list Steps are then added to create a new protocol To create a new protocol proceed as follows 1 Start a new file To do this either select New from the File menu or on the toolbar click the New button The Main software window will then appear having a blank step list rer dbi kiim FT haa mal se 2 To add a step to the new protocol select Add Step from the Edit menu or click on the Add Step button on the toolbar ObGeneTAC HybStation Version 4 0 Issued February 2003 The New Method Step
45. or oar ae SOLUTIONS 7 i Hybstation User Manual K GeneTAC HybStation eS GENOMIC 3 SOLUTIONS www genomicsolutions com Genomic Solutions e mail info genomicsolutions com Genomic Solutions Inc Genomic Solutions Ltd Genomic Solutions KK 4355 Varsity Drive 8 Blackstone Road Takanawa Katsurazaka Bldg 1F Ann Arbor Huntingdon 12 24 Takanawa 2 Chome MI 48108 Cambridgeshire PE29 6EF Minato Ku USA United Kingdom Tokyo 108 0074 Japan Phone 1 734 975 4800 Phone 44 0 1480 426700 Phone 81 33 280 0990 Fax 1 734 975 4808 Fax 44 0 1480 426767 Fax 81 33 280 0991 Section 1 Introduction to this User Manual En 2 GENOMIC GeneTAC HybStation EI SOLUTIONS Contents Sectio Introduction to this User Manual n1 1 1 Structure and Contents of this Manual 1 2 Warranty 1 3 Record of Revisions 1 4 Safe Working Practices Section 2 The GeneTAC Hybstation 2 1 Introduction to the HybStation 2 2 Using Slides 2 2 1 Using the 18mm Slide Assembly 2 2 2 Using the 21mm Slide Assembly 2 3 Using Reagents 2 4 Basic Maintenance Section 3 Section 1 1 Contents of this Manual Using the HybStation Initiating the HybStation Running a Protocol Adding a Probe Labeled Sample Monitoring a Run Aborting a Run Creating a Protocol Editing an Existing Protocol Adding Steps to a Protocol Removing Steps from a Protocol Deleting a Protocol The Protocol Ste
46. ort plugs Your Genomic Solutions representative should be contacted for catalog numbers and pricing information Reagent Guidelines Reagents provided by Genomic Solutions can be safely used with the GeneTAC HybStation Use the wash solutions in order of increasing stringency Never use these solutions in the GeneTAC HybStation All acids All bases Organic solvents such as phenol acetone chloroform xylene Chaotropic solutions such as guanidine HCl Ethanol If a precipitate occurs remove the damaged part and soak it in warm ultrapure water overnight If available use a continuous flow waterbath which will aid in dislodging the precipitate Gentle abrasion with a soft brush may help to dislodge the precipitate from the slide cover but take care not to scratch the part The manifolds are not removable The hybridization and wash solutions contain sodium dodecyl sulfate SDS This strong ionic detergent will precipitate out of solution when slightly chilled Inspect solutions before use to assure that precipitation has not occurred SDS will go back into solution upon warming Never use a solution that has a visible precipitate Also medium to high stringency buffers are always recommended for use Basic Maintenance Cleaning the Case Clean the exterior case of the GeneTAC HybStation with a mild detergent and rinse with distilled water Caution Risk of electrical shock can exist Turn OFF power to the GeneTAC Hy
47. ower Connection Safe Working Practices Before operating the HybStation or any associated equipment this User Manual must be read carefully particularly observing all the safety warnings and precautions as stated During normal use the HybStation will not present an electrical hazard to the operator but situations could arise where hazardous conditions may be present The equipment is intended for use by qualified personnel who recognize electrical shock hazards and are familiar with the safety precautions required to avoid possible injury Ensure that the power outlet is properly grounded earthed Each time the equipment is used the integrity of the main power cable must be inspected Be aware that high voltages are an electrical shock hazard For optimum safety do not touch the power cable while power is applied Always switch OFF the power at the mains supply socket before connecting or disconnecting any cables or equipment Replacements for blown fuses must be of the same type and rating as the original Using an incorrect fuse could result in a fire hazard To maintain a safe working environment and protect user personnel at all times the following safe working practices must be adhered to when using the equipment It is also essential that the HybStation be stored and operated within in a properly maintained laboratory environment to achieve optimum long term performance Maintain a well ventilated laboratory
48. p called Start loop xxx where xxx is the name defined for the loop 3 Press Add The Steps screen then appears Add steps until all desired steps are listed on the Protocol Definition screen On the Steps screen press End Loop A Keypad screen then appears prompting for the name of the loop Enter the same name for the loop previously entered in step 2 The system then checks the name to make sure it corresponds with a start loop Note If the correct loop name is not entered a message appears informing that the name is not valid and to please try again To return to the Keypad screen press OK When a valid loop name has been entered a screen appears prompting for the number of times the loop is to be executed GENOMIC SOLUTIONS 8 Enter a number from 1 to 10 The Protocol Definition screen then appears with the loop step listed OoGeneTAC HybStation Version 4 0 Issued February 2003 Section 3 12 6 Adding Protocol Steps Adding a Loop Section 4 Maintaining the System GENOMIC O GeneTAC HybStation EE SOLUTIONS _____ a ae a Om Z Z MIC TIONS Section 4 1 Accessing the Maintenance Screen Accessing the Maintenance Screen All maintenance options are accessed through the Maintenance Choose an Option screen To open the Maintenance screen On the Main screen press Maintenance The Maintenance screen then opens To return to the Main screen
49. ppear stating You have not saved this protocol Are you sure you want to lose the changes you have made To save the protocol press No The Protocol screen then appears Press Save Protocol and proceed as described above OoGeneTAC HybStation Version 4 0 Issued February 2003 Section 3 8 Adding Steps to a Protocol N SOLUTIONS Section 3 9 Removing Steps from a Protocol Removing Steps from a Protocol To remove steps from a protocol 1 Select a protocol for editing as described on the previous pages 6 Enter a name for the protocol of up to eight alphanumeric characters using the alphanumeric buttons noting the following 2 Select the step to be removed A marker to the right of the step indicates the selection made a To delete a character press Bkspc Q Tocancel the operation and return to the Protocol screen press Cancel Q To accept your entry and continue press OK The Main screen will then appear Q If Finish on the Protocol Definition screen is pressed before the new protocol is saved a warning screen will appear stating You have not saved this protocol Are you sure you want to lose the changes you have made 3 Press Remove The program immediately removes the step from the protocol 4 Remove additional steps by repeating the above as required When the required steps have been removed press Finish The Protocol screen will then appear On the Protocol screen press Sav
50. ps Adding Protocol Steps 3 12 1 The Single Wash Step 3 12 2 The Probe Labeled Sample Step 3 12 2 The Temperature Step 3 12 3 The Multiple Wash Step 3 12 4 The Drain Step 3 12 5 Adding a Loop Section 4 Maintaining the System Accessing the Maintenance Screen Checking a Module Temperature Testing the System Valves Testing the Heating Element of a Module Cleaning the Valves and Lines Changing the Network Address Making a Back up Disc Upgrading the HybStation Software Setting the Date and Time OoGeneTAC HybStation Version 4 0 Issued February 2003 Section 5 5 1 5 2 5 3 5 4 5 5 5 6 5 7 5 8 5 9 5 10 Section 4 Appendices Using the PC Methods Editor Software Introduction Opening a Protocol Creating a New Protocol Saving a Protocol Editing a Protocol Inserting Steps into a Protocol Deleting Steps from a Protocol Setting a Method Title The Protocol Steps 5 9 1 Introduction 5 9 2 Introduce Probe Labeled Sample 5 9 3 Set Temperature 5 9 4 Wash Slides 5 9 5 Drain Slides 5 9 6 Creating a Loop Printing a Protocol Example of a Typical Protocol Application and Technical Notes Section 1 1 Contents of this Manual Section 1 2 Warranty Warranty Statement The warranty period for this equipment is as defined in the quotation upon which the order for the equipment was placed The validity of the warranty is conditional upon the product being used strictly in accordance with the informa
51. se Set Method Title The Method Title dialog box appears 3 Inthe text field highlight the current entry then type a new description for the protocol 4 Click OK or press the Enter key Section 5 8 Setting a Method Title Section 5 9 1 The Protocol Steps Introduction The Protocol Steps Introduction Steps can be added to a protocol in the PC Editor by selecting them from the New Method Step drop down list then setting durations temperatures and priorities The Steps drop down list offers the following choices New method step Choose thee type of shen you wand bo adt nboduce Psobe l Wash Sides Dran Sides Start Loop Era Loop Q Introduce Probe Specify the temperature at which the labeled sample is added Set Slide Temperature Specify the temperature of the slides Wash Slides Select the wash solution s temperature and flow time Q Drain Slides Specify the amount of time air should be drawn over the slide to remove a solution Q Start Loop Create a series of steps that is repeated multiple times Q End Loop Select the number of repetitions of the series of steps Additional details about the functions of these steps are provided later in this section To display the Steps drop down list carry out one of the following From the Edit menu choose Insert Step Q From the Edit menu choose Add Step Q On the toolbar click the Insert Step button Q On the toolbar cl
52. temperature the labeled sample is added Note To return to the Protocol Definition screen without adding a Probe step press Cancel on the screen To add a probe step 1 On the Steps screen press Probe The Enter the Temperature To Probe At screen then appears J gt GENOMIC z SOLUTIONS er The T4armrcerst 2 Enter the desired temperature 3 Press OK Section 3 12 2 Adding Protocol Steps The Probe Step Adding a Temperature Step This step is used to enter the temperature for hybridization and the length of time the system holds that temperature The time can be set from 1 second up to 72 hours The temperature step also has an Agitate option If selected the system agitates the fluid on the slides during a temperature step To add a temperature step hybridization step 1 On the Steps screen press Temperature The Enter the Temperature to Cycle At screen appears SEM ns T o 2 Enter the desired temperature Section 3 12 3 Adding Protocol Steps The Temperature Step 3 To add agitation press the Agitate button at the top right of the screen A marker indicates that agitation is selected The system now automatically opens and closes valves during this step allowing the labeled sample to circulate over the entire slide surface for optimal hybridization and to reduce the possibility of local depletion 4 Press OK A screen appears prompting for the length of time for this step
53. tion This option is used to define a temperature at which the unit will cycle and to set a time for the unit to remain at that temperature It is recommended to use this option immediately after the probe insert step to allow proper hybridization of the sample The time can be set from 1 second up to 72 hours The modules are brought to temperature and time countdown starts when a module reaches the specified temperature In this cycle the agitation option can also be actioned When selected this option automatically opens and closes the agitation or pulse valves allowing the labeled sample to circulate over the entire slide surface for optimal hybridization thus reducing the possibility of local depletion The agitation works on a one second open three seconds closed cycle for the duration of the step Every 5 hours during this process the slide s inlet valve and air valve are opened for 1 second to release any pressure built up in the slide module The Multiple Wash Step A multiple wash step consists of several wash steps that are combined as one single step Up to 10 wash steps can be defined under a multiple wash and a multiple wash step can be added several times in a protocol Only one definition of a multiple wash for a protocol can be made When a multiple wash step is defined a screen similar to the Protocol Definition screen appears This provides access to screens enabling the following to be set Q Reservoir bottle
54. tion provided in this User Manual No liability is accepted for loss or damage or consequential loss or damage arising from incorrect use of the equipment The liability of the Company within the guarantee period is limited to repair or replacement of the unit and at the sole discretion of the Company to the refund of the purchase price The HybStation is a complex piece of laboratory equipment Although the equipment and software have been designed for ease of use it is important to read the User Manual carefully If in doubt about any procedures contact Genomic Solutions Only trained personnel should operate the equipment Record of Revisions Version Date of issue Amendments made 4 0 February 2003 Issued to Software Version 3 61 OoGeneTAC HybStation Version 4 0 Issued February 2003 Copyright 2001 Genomic Solutions Inc All rights reserved The information contained in this User Manual is the exclusive property of Genomic Solutions except as otherwise indicated and shall not be reproduced in whole or in part without explicit written consent from Genomic Solutions The distribution of this manual may only occur as authorised in writing by Genomic Solutions GeneTAC is a registered trademark of Genomic Solutions Microsoft is a registered trademark and Windows is a trademark of Microsoft Corporation Section 1 3 Record of Revisions Section 1 4 Safe Working Practices and P
55. tion wash the introduction of a labeled sample or the hybridization period Critical Scheduling Before performing a step with Critical scheduling the HybStation checks that all resources are available before starting the step so it can go through the complete step on one module before proceeding to the next one This is the preferred choice since it guarantees that all wash steps are performed for the exact length of time specified in the protocol Once a step with Critical scheduling has started it ties up the whole station and no other step can run at the same time If several steps are to run consecutively specify those steps with Critical scheduling In that case the HybStation works through all these steps without interruption Urgent Scheduling The program runs an Urgent step as soon as possible and does not interrupt the step once it has started A step with Urgent scheduling interrupts Normal steps that are currently running An Urgent step cannot interrupt a Critical step but can supersede it Section 5 9 1 The Protocol Steps Introduction The Introduce Probe Labeled Sample Step This step is used to specify where in the protocol and at what temperature the labeled sample is added The temperature can range from 1 to 99 C To introduce a labeled sample 1 From the Steps drop down list choose Introduce Probe In the Main window a labeled sample step is added on the left with the corresponding tabs on th
56. twork Address screen appears 2 Use the up arrow and down arrow buttons to change the network address displayed to the left Use 1 for the instrument closest to the controlling computer 3 Press OK to return to the Maintenance screen O GeneTAC HybStation Section 4 6 Changing the Network Address Version 4 0 Issued February 2003 Section 4 7 Making a Back up Disc Making a Back up Disk Make a backup copy of the protocols on a disk using the Make Back up Disk screen To make a backup disk 1 Insert an IBM formatted floppy disk into the disk drive 2 On the Maintenance screen press Make Back up Disk A message screen opens 3 Press Start Upgrading the Hybstation Software Software for the HybStation must be upgraded when a new version is released To upgrade the software 1 Insert the floppy disk that contains the software upgrade 2 Onthe Maintenance screen select Software Upgrade and follow the instructions on the screen Note Be certain to insert the disk before pressing OK on the second screen If the disk is not inserted when OK is pressed turn off the HybStation and repeat the process Cal EN LUE LL Lee TP Wara ObGeneTAC HybStation Section 4 8 Upgrading the Hybstation Software Version 4 0 Issued February 2003 Use the arrows to se Cancel Section 4 9 Setting the Date and Time Setting the Date and Time The date and time for the HybStation at the Set Date and Time screen
57. ued February 2003 UTIONS Section 3 7 Editing an Existing Protocol ir GENOMIC Hytrdisation Star aie SOLUTIONS ers 7 GENOMIC gt GENOMIC a SOLUTIONS SOLUTIONS GENOMIC Mere is the protocol shored Editing an Existing Protocol An existing protocol can be edited and saved under the same or a new name for repeated use Editing a protocol effectively means adding or removing steps Note It is only possible to edit a protocol that was created with HybStation software This is done using the touch screen Selecting a Protocol for Editing A protocol must be loaded before it can be edited To select a protocol for editing proceed as follows 1 Onthe Main screen press Edit or Create a Protocol The Protocol screen will then appear 2 On the Protocol screen press Load or Delete Stored Protocol A screen appears prompting Where is the Protocol Stored 3 Select Floppy Disk or Internal Storage A list with available protocols will appear 4 From the list select the protocol to be edited A marker to the right hand of the protocol name indicates the selection 5 Press Load The Protocol screen appears indicating at the top right hand area that a protocol is defined On the Protocol screen press Edit or review protocol The Protocol Definition screen appears listing the steps in the protocol This can then be edited as described on the following pages O GeneTAC HybStation Section 3 7 E
58. uring this step allowing the labeled sample to circulate over the entire slide surface for optimal hybridization and to reduce the possibility of local depletion a Select the required scheduling for this step Section 5 9 3 The Protocol Steps Set Temperature Section 5 9 4 The Protocol Steps GENOMIC SOLUTIONS Wash Slides TassT The Wash Slides Step This step is used to select a solution from one of the five available a Define a temperature by highlighting the current entry and reservoirs to flow through the slide chambers for a specified period of time typing a new one at a specified temperature a Define a flow time and a hold time by highlighting the current To define a Wash Slides step entries and typing in new ones 1 From the Steps drop down list choose Wash Slides In the Main Q Click the Advanced tab window a wash slides step is added on the left with the corresponding tabs on the right 2 On the Wash Slides tab Q Optionally enter a brief description for this step in the protocol 3 Om he Advanced tag by highlighting the current entry and typing a new one The a Set the number of times you want the wash to cycle by description replaces the name of the step in the step list highlighting the current entry and typing a new one Q From the Source drop down list select one of the five a Select the scheduling for this step reservoirs Q From the Waste drop down list select a waste bottl
59. y disc and transferred to the HybStation m pa MMM Save sce Acie Peak FB Cree Editing a Protocol A protocol can by edited by adding inserting or deleting steps Note It must be noted that a protocol created using the methods editor software on the HybStation cannot be edited using this program Adding Steps to a Protocol When a step is added to a protocol PC Methods Editor software places the steps at the end of the protocol To add a step to an existing protocol 1 Open a protocol The Main window will then appear showing the steps for the protocol 2 Do one of the following e From the Edit menu choose Add Step e On the toolbar click the Add Step button The New Method Step dialog box will then appear Choose the ippa of shep pou vasmi bo mit A tres _ 3 From the Steps drop down list select the step to be added All available steps are shown in the list New method step Ghose thet hype of shep you wan bo add 4 Click OK Repeat Steps 2 through 4 to add additional steps to the protocol 6 Save the changes to the protocol e To save the changes using the same protocol name choose Save from the File menu e To save the changes using a different protocol name choose Save As from the File menu Note Always use a file name with 8 characters or less or make the first 8 characters recognizable OrGeneTAC HybStation Version 4 0 Issued February 2003 Section
60. y into the port using a standard 200ml pipette If using the 18mm slide assembly it is recommended that 100ul to 110ul is used This should be increased to approximately 140 150ul when using the 21mm slide assembly Section 3 3 Adding a Probe The probe port is located above a diffusion channel machined into the slide cover There is also a complimentary diffusion channel at the top of the slide cavity Capillary action tends to draw the labeled sample out of the first diffusion channel during insertion The labeled sample must fill up to the top diffusion channel This area accommodates thermal expansion and contraction of the fluid and fluid displacement due to minor thermal expansion of the slide cover 3 When the labeled sample has been added insert the labeled sample plug 4 Press the Finished button related to the slide where the labeled sample was added The check mark on the screen will then disappear 5 To add labeled sample to the second slide position repeat steps 1 to 4 6 When labeled sample has been added to the last slide press Finished at the bottom of the screen The system will then continue with the defined protocol Monitoring a Run A hybridization run is monitored at the HybStation Status screen This screen identifies the modules and shows the current status Q Q Q Q Module number Temperature Current step Total steps in the protocol To monitor a run On the Main screen press Syst

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