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AB 3130/3130xl GA Maintenance, TS, and Ref Guide 4352716E

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1. Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide a Chapter 5 Reference Tables Sequencing Summary Tables KB Basecaller Basecaller and DyeSet Primer Files Using KB Basecalling Table 3130 3130xI Genetic Analyzer Basecaller and DyeSet Primer Files Used with BigDye Terminator Chemistry and KB Basecalling DNA Sequencing KB Basecalling Run Chemistry Polymer Module DyeSet Primer Basecaller BigDye Terminator v1 1 POP 4 UltraSeq36_POP4 KB_3130_POP4_BDTv1 mob KB bcp Cycle Sequencing Kit StdSeq50_POP4 LongSeq80_POP4 POP 6 RapidSeq36_POP6 KB_3130_POP6_BDTv1 mob StdSeq50_POP6 POP 7 UltraSeq36_POP7 KB_3130_POP7_BDTv1 mob RapidSeq36_POP7 FastSeq50_POP7 StdSeq50_POP7 LongSeq80_POP7 BigDye Terminator v3 1 POP 4 UltraSeq36_POP4 KB_3130_POP4_BDTv3_ mob Cycle Sequencing Kit StdSeq50_POP4 LongSeq80_POP4 POP 6 RapidSeq36_POP6 KB_3130_POP6_BDTv3 mob StdSeq50_POP6 POP 7 UltraSeq36_POP7 KB_3130_POP7_BDTv3 mob RapidSeq36_POP7 FastSeq50_POP7 StdSeq50_POP7 LongSeq80_POP7 78 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide ABI Basecaller Table and Dye Chemistry Terminator Kits Chapter 5 Reference Tables Sequencing Summary Tables Basecaller and DyeSet Primer Files Using ABI Basecalling with Dye Terminator
2. Clear rows Shift Delete Fill Down Special Alt D 4dd Sample Run Shift 4 7 Click GK to save the plate record 66 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 4 Data Collection Software Advanced Functions Edit gt Fill Down Special Option for Plate Records Examples of Fill Down Special Examples of completed plate records and run scheduling for the 3130 and 3130x instruments and 96 and 384 well plates are shown below Plate Narne Plate Sealing Septa z Operator b ap bap SeqSarmples Owner Well Sample Name Comment Priority Results Group 1 Instrument Protocol Analysis Protocol 1 D01 LRS 100 SeqA_50cm Seq_50cm_POP6 3130POP6_BDTv3 KB De a E01 LRS 100 SeqA_50cm Seq_50cm_POP6 3130POP6_BDTv3 KB De F0 LRS 100 SeqA_50cm Seq_50cm_POP6 3130POP6_BDTv3 KB De GO1 LRS 100 Seq4_50cm Seq_50cm_POP6 3130POP6_BDTv3 KB De H01 LRS 100 SeqA_50cm Seq_50cm_POP6 3130POP6_BDTv3 KB De 402 LRS 100 SeqA_50cm Seq_50cm_POP6 3130POP6_BDTv3 KB De B02 LRS 100 SeqA_50cm Seq_50cm_POP6 3130POP6_BDTv3 KB De c02 LRS 100 SeqA_50cm Seq_50cm_POP6 3130POP6_BDTv3 KB De u ioj xi D02 LRS 100 SeqA_50cm Seq_50cm_POP6 3130POP6_BDTv3 KB De E02 LRS 100 SeqA_50cm Seq_50cm_POP6 3130POP6_BDTv3 KB De F02 LRS 100 SeqA_50cm Seq_50cm_POP6 313
3. DANGER Class 2 ll laser radiation present when open and interlock defeated Do not stare directly into the beam DANGER de Class 2 ll rayonnement laser en cas d ouverture et d une neutralisation des dispositifs de securite Eviter toute exposition directe avec le faisceau DANGER Class 2 ll laser radiation present when open Do not stare directly into the beam DANGER de Class 2 ll rayonnement laser en cas d ouverture Eviter toute exposition directe avec le faisceau DANGER Class 2 ll LED when open and interlock defeated Do not stare directly into the beam DANGER de Class 2 ll LED en cas d ouverture et d une neutralisation des dispositifs de securite Eviter toute exposition directe avec le faisceau DANGER Class 2 II LED when open Do not stare directly into the beam DANGER de Class 2 ll LED en cas d ouverture Eviter toute exposition directe avec le faisceau CAUTION Moving pars ATTENTION Parties mobiles General Instrument Safety Nore PHYSICAL INJURY HAZARD Use this product only as specified in this document Using this instrument in a manner not specified by Applied Biosystems may result in personal injury or damage to the instrument Moving and Nexen PHYSICAL INJURY HAZARD The instrument is to be moved Lifting the and positioned only by the personnel or vendor specified in the applicable site Instrument preparation guide If you decide to lift or move the instrument
4. No User is logged in Plate Name SeqA_2 Plate Sealing Septa GA Instruments GA Instruments ga3130xl DavidPT4 Run Scheduler Run View i LE Results Group Well Sample Name Comment Res f Database Manager 1 DO1 LRS Seq Elga3130x Module e HE E01 LRS Seq lene al a Module M 2 LS ti f oo 4 Run_David PT4_20 G01 LRS Seq H E DavidPT4 5 Run_David PT4_20 Regular Validated B I TRS Seq G Efinstrument Status 6 Run_David PT4_20 Regular Validated je e BJJEPT Chart A02 LRS Seq of Event Log B02 LRS Se i Hil Spatial Run Scheduler t q Run Scheduler co2 LRS Seq i Plate View Run view BIE i ii Seq i E capillaries Viewer E02 LRS Seq onara Viewer a F Spectral Viewer F02 LRS Seq F Ah Manual Control E Service Log Description System Status gt No Current Run Plate SeqA_2 has been linked to Bay 0 User defined run priority schedule samples in wells A01 H02 are now scheduled as Run 2 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 4 Data Collection Software Advanced Functions Edit gt Fill Down Special Option for Plate Records Edit gt Fill Down Special Option for Plate Records Using Fill Dow
5. 4 gt System Status Clear Errors Semero No Current Run Status light Disk drive full error message Runs can not start until data is removed from the drive and or database is cleaned up Cleaning Drives _ Ensure that you have sufficient drive space by regularly e Archiving data e Deleting unneeded files e Emptying the trash e Defragmenting the drives 29 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 2 Computer Maintenance Hard Disk and Database Status Hard Disk and Database Status Manually Checking Available Disk Space on Drive E 1 In the tree pane of the Data Collection software click GA Instruments gt Database Check the Database Status section Foundation Data Collection Version 3 0 No User is logged in Manager to open the Database Manager Some BS 7 Aca erumei lt GA Instruments gt Database Manager 2 Check the Database Status section The Data ice ance s e E jga3130x1 Mai t 7 Run Status Collection software will prompt you when it is 70 75 full At 78 full the software will not Start a run Free Disk Space Status Disk Drive Free Disk Space MB 3 Ifthere is insufficient space c oss 54790 agg99 a Archive the sample files to a CD RW see heat lo page 31 or another volume b Delete the sample file data from the drive E and
6. Basecaller and DyeSet Primer Files Used with BigDye Terminator Chemistry and ABI Basecalling oe ABI Basecalling Run Sequencing Polymer Basecaller DyeSet Primer Module Chemistry BigDye POP 4 UltraSeq36_POP4 Basecaller DT3130POP4LR BD v1 Terminator v1 1 3130POP4UR bcp mob i LongSeq80_POP4 Basecaller 3130POP4_80cmv3 bcp POP 6 RapidSeq36_POP6 Basecaller DT3130POP6 BD v2 3130POP6RRv2 bcp mob StdSeq50_POP6 Basecaller 3130POP6SR bcp BigDye POP 4 UltraSeq36_POP4 Basecaller DT3130POP4 BDv3 v1 Terminator v3 1 3130POP4UR bcp mob Cycle LongSeq80_POP4 Basecaller Sedenemg ih 3130POP4_80cmv3 bcp POP 6 RapidSeq36_POP6 Basecaller DT3130POP6 BDv3 v1 3130POP6RRv2 bcp mob StdSeq50_POP6 Basecaller 3130POP6SRv2 bcp ABI Prism POP 4 UltraSeq36_POP4 Basecaller DT3130POP4 dRhod v2 dRhodamine 3130APOP4UR bcp mob alee LongSeq80_POP4 Basecaller Sequencing 3130POP4_80cmv3 bcp Ready Reaction POP 6 RapidSeq36_POP6 Basecaller DT3130POP6 dRhod v2 Kit 3130POP6RRv2 bcp mob StdSeq50_POP6 Basecaller 3130POP6SR bcp Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 19 ABI Basecaller Chapter 5 Reference Tables Sequencing Summary Tables Table and Dye Chemistry Primer Kits 3130x Basecaller and DyeSet Primer Files Used for Dye Primer Chemistry Basecaller and DyeSet Primer Files Using ABI Basecalling with Dye Prim
7. Instrument er bes e Received instructions in both general safety practices for laboratories and specific safety practices for the instrument e Read and understood all applicable Material Safety Data Sheets MSDSs See About MSDSs on page xii Chemical Safety Chemical Hazard Nee CHEMICAL HAZARD Before handling any chemicals refer to Warning the Material Safety Data Sheet MSDS provided by the manufacturer and observe all relevant precautions Nr CHEMICAL HAZARD All chemicals in the instrument including liquid in the lines are potentially hazardous Always determine what chemicals have been used in the instrument before changing reagents or instrument components Wear appropriate eyewear protective clothing and gloves when working on the instrument About MSDSs_ Chemical manufacturers supply current Material Safety Data Sheets MSDSs with shipments of hazardous chemicals to new customers They also provide MSDSs with the first shipment of a hazardous chemical to a customer after an MSDS has been updated MSDSs provide the safety information you need to store handle transport and dispose of the chemicals safely Each time you receive a new MSDS packaged with a hazardous chemical be sure to replace the appropriate MSDS in your files Obtaining MSDSs You can obtain from Applied Biosystems the MSDS for any chemical supplied by Applied Biosystems This service is free and available 24 hours a day xii Appl
8. 1 0 0 ene ee eee nes 1X Safety Labels on Instruments 0 0 ee een ees X General Instrument Safety 62 lt ctsaceocedted ea wt hiwee cuss Ea E a Re E xi Chemical a Noar eer e E 2g Go Ga ER xii Chemical Waste Safety sssasiresendras derit iE 2604835 84454 Tarana eENA do xiii Perel oae ea a toned e ar ea a e a a XIV Nea CE SALClY were Gas cee ees ote tu Sowa bees E E eeces i aeoeredae XV WOEKS AUOM SaICIY 4 6 2 405040 58 665 ode ara bed oe he dae erR wee abe debe ae xvi Safety and Electromagnetic Compatibility EMC Standards xvii Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide vii Safety Safety Conventions Used in This Document Safety Conventions Used in This Document viii Safety Alert Words Four safety alert words appear in Applied Biosystems user documentation at points in the document where you need to be aware of relevant hazards Each alert word IMPORTANT CAUTION WARNING DANGER implies a particular level of observation or action as defined below Definitions IMPORTANT Indicates information that is necessary for proper instrument operation accurate chemistry kit use or safe use of a chemical N oF eel Indicates a potentially hazardous situation that if not avoided may result in minor or moderate injury It may also be used to alert against unsafe practices Nore Indicates a potentially hazardous situation that
9. Terminator Cycle Sequencing Ready Reaction Kit table of dye set and standards 77 ABI PrisM dGTP BigDye Terminator v 3 0 Cycle Sequencing Ready Reaction Kit table of dye set and standards 77 ABI PrisM dRhodamine Terminator Cycle Sequencing Kit table of information 77 account password see password AmpFISTR kits matrix standard 83 table of dye sets filter modules 83 array port illustration of 2 autosampler 10 calibrating 23 controlling See manual control commands non optimal calibration 51 will not move forward 38 Autosampler Calibration Wizard calibration autosampler 23 B basecaller and DyeSet Primer files 78 basecaller files 78 79 80 basecaller and ABI basecalling 79 BigDye Terminator chemistry information tables 78 BigDye Terminator v3 1 Cycle Sequencing Kit table dye set and standard 77 Bubble Remove Wizard 22 bubbles clearing 22 buffer fill line 2 buffer jar illustration of 2 buffer valve pin illustration of 2 buffer making and storing 15 Index C calibration standards types fragment analysis 83 capillary array care 20 failing 44 illustration of 2 manually filling 8 poor performance 55 storing off the instrument 21 storing on the instrument 21 when to change 18 capillary array knob and tip illustration of 2 cathode bar 18 CD creating a data 31 Change Polymer Type Wizard 17 check valve diagram of 2 claims processing 90 cleaning instrument routine 5 Cleanup Da
10. 15 18 16 15 18 16 15 18 16 15 18 15 15 18 15 arama Publisher SpectralRun iDey iDey iDey iDey iDey iDey iDey iDey m Description System Status Postprocessing Spectral calibration has completed Number of caps passed in spectral calibration 0 Finished saving spectral calibration data Saving spectral calibration data Capillary 4 failed calibration due to bad data Capillary 3 failed calibration due to bad data Capillary 2 failed calibration due to bad data Capillary 1 failed calibration due to bad data Insufficient numk Insufficient numk Insufficient numk Insufficient numk Run_iDev_2003 09 15_15 15 0002 status has changed to Ex gt Type Error Dye Set Date 09 15 03 Time 15 18 18 ES list at alih stiaes fee Coss Cat _ Publisher iDey Description Number of caps passed in spectral calibration 0 PThu Sep 25 12433 25 POT 2003 T Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 45 Chapter 3 Troubleshooting Spectral Calibration Troubleshooting failing capillaries continued The window is updated with the information from the failed E5 spectral calibration My Blo GA Instruments gt ga3130 gt iDey gt Spectral Viewer No spectral gt profile 0 50 10 Intensity vs Pixel Number 0 Raw data gt 0 200 400 600 800 1000 120
11. Genotypes capillary injection b 1bp resolution at 99 99 accuracy Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 81 Chapter 5 Reference Tables Fragment Analysis Summary Tables Kits and Run Fragment Analysis Kits Run Modules and Dye Sets Modules Module xt xt xt CO N Q Q Oo Q Q A Q O O O O O O O x a a a a a a O A 8 P 2 2 2 B O O at D D D D o a D a a D D D D D TA 2 co gt gt gt ee o Ke T Application Kit A a amp amp amp Z Z u c E T 2 09 ep D D D D D D I z O O O O O O O reas g m a a a a a ia Q I SNaPshot Multiplex System E5 E5 Custom oligos D F D F D F D F D F D F G5 G5 G5 G5 G5 G5 Linkage Mapping Set human D G5 D G 5 D G5 D G D G 5 D G5 v2 5 ABI PriSM Mouse Mapping Set D G5 D G5 D G5 gt D G5 D G5 D G5 v1 0 4 Dye Stockmarks kits bovine F and canine 5 Dye Stockmarks kit equine G5 AFLP kits F 4 Dye AmpF STR kits F 5 Dye AmpF STR kits G5 82 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 5 Reference Tables Fragment Analysis Summary Tables AmpFZSTR Kit Kits Run Modules and Dye Sets Table HIDFragmentAnalysis 36_POP4 AmpF STR COfiler Kit F AmpF
12. Standards c UL us Canadian EMC Standard European Safety and EMC Standards CE Australian EMC Standards Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide This section provides information on e U S and Canadian Safety Standards e Canadian EMC Standard e European Safety and EMC Standards e Australian EMC Standards This instrument has been tested to and complies with standard UL 3101 1 Safety Requirements for Electrical Equipment for Laboratory Use Part 1 General Requirements This instrument has been tested to and complies with standard CSA 1010 1 Safety Requirements for Electrical Equipment for Measurement Control and Laboratory Use Part 1 General Requirements This instrument has been tested to and complies with ICES 001 Issue 3 Industrial Scientific and Medical Radio Frequency Generators Safety This instrument meets European requirements for safety Low Voltage Directive 73 23 EEC This instrument has been tested to and complies with standards EN 61010 1 2001 Safety Requirements for Electrical Equipment for Measurement Control and Laboratory Use Part 1 General Requirements and EN 61010 2 010 Particular Requirements for Laboratory Equipment for the Heating of Materials EMC This instrument meets European requirements for emission and immunity EMC Directive 89 336 EEC This instrument has been tested to and compl
13. Up to 650 ME 74 minute CDO or 700 ME 80 minute CD of files and folders can be added to a data CD project 5 Click Record recod The Record CD Setup dialog box appears 6 Click Start Recording See Also e Working with Files and Folders in the Data CD Project Making a Data CD from a CD Image Instructions for creating a data CD 32 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 2 Computer Maintenance Defragmenting the Computer Hard Drive Defragmenting the Computer Hard Drive The fragmentation of files decreases the performance of both the Data Collection software and the computer operating system Programs take a longer time to access files by performing multiple search operations of the fragments When to Defragment the Computer Hard Drive Defragment the computer hard drive e At least once every month e Before fragmentation reaches 10 Defragmenting the Drives 1 In the Windows desktop right click My Computer then select Manage In the tree tab of the Computer Management dialog box click Computer Management Local gt Disk Fragmenter Select the E drive Click Defragment The computer displays the Defragmentation Complete dialog box after completing the defragmentation In the Defragmentation Complete dialog box click Close In the Computer Management dialog box click XJ Open Tompuker Explore Sea
14. instrument to move the autosampler to the forward position IMPORTANT Never use organic solvents to clean the instrument 3 Wipe off any liquid on or around the autosampler using a lint free tissue 4 Clean off any polymer build up crystals on the instrument including the capillary tips and the stripper plate with deionized water and lint free tissue 5 Clean the array port knob plug or opening threads of these parts with moistened lab wipes 6 Clean out the drip trays with deionized water and lint free tissue Resetting the Instrument Reset the instrument when e A fatal error as indicated by the red status light e The instrument does not respond to the 3130 3130x Data Collection software Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 5 Chapter 1 Maintenance Resetting the Instrument Two procedures can reset the instrument e Press the reset button through the pin hole on the front of the instrument to dump and reload the firmware and to reset the electronics Try this method first e Shut down and restart the computer and the instrument Resetting With the Reset Button 1 Close the instrument doors 2 Using a long narrow implement such as a straightened paper clip press the reset button on the front of the instrument Reset button Resetting by Powering Down 1 Close the instrument doors 2 Power off the instrument by pressing
15. 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 1 Chapter 1 Maintenance Polymer Delivery Pump Polymer Delivery Pump Syringe fitting Components of the polymer delivery pump PDP are identified in the drawing below Mounting pin PDP motor PDP motor cover Water seal Waste fitting Water trap Mounting pin Capillary array tip Capillary array Capillary array knob Piston Pump chamber Pump block Check valve Double tapered ferrule 2olymer supply tube Polymer supply bottle cap with hole Polymer Array port Interconnect tube Buffer valve pin Lower polymer block Mounting pin Mounting pin Overflow hole Buffer fill line supply bottle Electrode Buffer jar 16 mL anode reservoir GR2459 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 1 Maintenance Performing Maintenance Tasks Performing Maintenance Tasks Overview This section lists common tasks required to maintain your Applied Biosystems 3130 3 130x Genetic Analyzers in good working condition The tasks are divided into tables based on how often you should perform each task ANITY Wear appropriate protection including gloves laboratory goggles and coat whenever you work with the fluids used on this instrument or parts
16. 58 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Data Collection Software Advanced Functions Overview This chapter covers the following topics Customizine Run Modules 2 lt i2sisd bdwdeteees Sneed een deen wth eee bees ba 56 Run Priority Scheduling 2 0 cc cee nes 58 Edit gt Fill Down Special Option for Plate Records 0 cee ee eee 61 Multi application Mixed Plate Record ccc nes 65 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 59 Chapter 4 Data Collection Software Advanced Functions Customizing Run Modules Customizing Run Modules You can modify default run modules to suit your particular needs 1 Click GA Instruments gt E ga3130x or ga3130 gt instrument name gt Module Manager 2 Click New The Run Module Editor dialog Run Modine en z box opens Run Module Description _ Marne 3 Complete the Run Module Editor dialog box Type a Enter a name for your new module Template iit heim ate aa b In the Type drop down list select the type of module Regular Spatial or Spectral Description c In the Template drop down list select a template module as a basis for the new module Note You cannot edit a default module installed ee ae ce with the 3130 3130x Genetic Analyzer Name Value Range Data Colle
17. BB capiArray Viewer F M Spectral viewer F Ah Manual Control Se Service Log 0 Spectral Spects0_POP6_1 Validated U 96 well plate on a 3130 genetic analyzer M spectral Calibration Plate Editor x File Edit Plate Name Spectral _Z_384 Operator bap Plate Sealing Septa zj Owner bap Well Sample Name Comment Priority Instrument Protocol 1 401 MtxStd 100 Spectral_Z_50cm zj B0 co MtxStd 100 Spectral_Z_50crn po E0 MtxStd 100 Spectral_Z_50crm Fa Got MtxStd 100 Spectral_Z_50cm sy ee m Jm Kot o x Description Ok Cancel gt iDev gt Run Scheduler Run View po RuniD Run Type Module i i 7 esus Group E Database Manager gas130 E Plate Manager i T Protocol Manager F ls Module Manager Run History Pidey EAinstrument Status Hil Spatial Run Schedule E Run Scheduler BY Plate View 1 Spectral Spects0_POP6_1 Validated B Spectral_ _ 384 E capillaries Viewer F HB capiArray Viewer F M Spectral viewer Ah Manual Control Service Log 384 well plate on a 3130 genetic analyzer 68 Applied Biosystems 3130 3130x Genetic Analyzers Mainten
18. Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 49 Chapter 3 Troubleshooting Run Performance Troubleshooting run performance Observation Possible Cause Recommended Action No peaks in any sample file Bubbles in the system Visually inspect the polymer block for bubbles No sample injection Remove bubbles using the Bubble Remove Wizard 1 If bubbles persist select the Water Wash Wizard 2 If necessary select the Replenish Polymer Wizard to install fresh polymer CHEMICAL HAZARD POP 4 POP 6 and POP 7 polymer causes eye skin and respiratory tract irritation Read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves Possible contaminant in the polymer Select the Water Wash Wizard path Possible contaminant or crystal deposits Bring the polymer to room temperature swirl to in the polymer bottle dissolve any deposits Replace the polymer if it has expired CHEMICAL HAZARD POP 4 POP 6 and POP 7 polymer cause eye skin and respiratory tract irritation Read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves Green Start button is Communication failure between the Data Install Software Patch CE_DC_300 002 To disabled Collection Software and Sequencing download the patch go to Instrument http www appliedbiosystems com then click the link for Suppo
19. Chapter 1 Maintenance Fluids and Waste Polymer Storing Polymer Store any remaining POP polymer at 2 to 8 C until the expiration date printed on the jar Note Excessively hot environments may shorten the working life of the polymer When to Change the Polymer Changi the polymer weekly The polymer is good at POP 4 or POP 6 Polymer 25 C for about 7 days Storage Conditions SuM TWThF S 20 C to 25 C 7 days Before Using the Polymer 1 Remove the polymer from 4 C storage 2 Loosen the cap and bring the polymer to room temperature 3 To dissolve deposits tighten the cap and gently swirl the polymer Replenishing the Polymer Neer CHEMICAL HAZARD POP Polymers causes eye skin and respiratory tract irritation Read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves IMPORTANT Wear gloves when you handle the polymer gF 16 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 1 Maintenance Fluids and Waste 1 Click Wizards gt Replenish Polymer Wizard TEREE Help Install Array Wizard Change Polymer Type Wizard Replenish Polymer Wizard Bubble Remove wizard Water Wash Wizard Instrument Shutdown wizard Sutosanpler Calibration Wizard Update Cap Array Info 2 Follow the directions given in the wizar
20. Push the Tray button on the outside of the instrument The autosampler will move forward automatically 2 Open the instrument doors and remove all plate assemblies and fluid reservoirs on the autosampler 3 Close the instrument doors The autosampler will move to the return position automatically 4 hen the autosampler stops moving click i Initialize to setup the autosampler for calibration When the autosampler stops moving click Next Cancel Finish Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 23 Chapter 1 Maintenance Manual Control Manual Control Note Manual control is active only if the oven and instrument doors are closed Table of Commands The following table displays the manual control options in the Data Collection software autosampler Bring autosampler to forward position Initialize and return to previous position Move autosampler up down Command Function Command Options Value Electrophoresis Turn On Off power e On supply e Off Set voltage A number between 0 0 and 15 kV Read voltage N A Read current Laser Set laser state e idle e On e Off Set laser power A number between 0 and 25 mW Read laser power N A setting Read laser power Read laser current Open Close shutter Open e Closed Oven Set state e On e Off Set temperature A number between 18 and 65 C Autosample
21. Restart the computer launch Console did not start properly It takes several minutes before data collection software opens Computer screen is frozen Communication error There will be no loss of data However if the instrument is in the middle of a run wait for the run to stop Then exit the Data Collection software and restart as described above Autosampler does not move to Possible communication error Restart the system and then press the Tray button the forward position Oven or instrument door is not 1 Close and lock the oven door closed 2 Close the instrument doors 3 Press the Tray button Instrument does not respond to Autosampler reinitializes its Wait for the autosampler to home before commands immediately after location continuing closing the doors 38 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 3 Troubleshooting Instrument Status Instrument Status Troubleshooting instrument status see also Instrument Startup on page 38 Observation Possible Cause Recommended Action The yellow light in the LED panel A Power override is enabled Cycle power on the system in the following order on the bottom left hand corner of the instrument remains solid yellow a Boot Reboot the computer workstation b Log in to the computer workstation c Ensure that the buffer water and waste reservoirs are in their appropri
22. Run samples KB Type of Run Length Module Time 7 Basecaller cm Type min 3130 3130x QV LOR Genetic Genetic Analyzer Analyzer Ultra rapid 36 POP 4 UltraSeq36_POP4 40 144 576 400 POP 7 UltraSeq36_POP7 35 164 656 500 Rapid 36 POP 6 RapidSeq36_POP6 60 96 384 500 POP 7 RapidSeq36_POP7 96 384 600 Fast 50 POP 7 FastSeq50_POP7 60 96 384 700 Standard 50 POP 4 StdSeq50_POP4 100 56 224 600 POP 6 StdSeq50_POP6 150 36 144 600 POP 7 StdSeq50_POP7 120 48 192 850 Long read 80 POP 4 LongSeq80_POP4 210 24 96 700 POP 7 LongSeq80_POP7 170 32 128 950 a Length of Read LOR is the usable range of high quality or high accuracy bases determined by Quality Values QV generated by KB Basecaller v1 2 The LOR is determined by using a sliding window of 20 bases which has an average QV gt 20 b 98 5 basecalling accuracy less than 2 Ns 76 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 5 Reference Tables Sequencing Summary Tables Calibration Sequencing Dye Sets Calibration Standards and Chemistry File Standard Table Sequencing Chemistry Dye Set Spectral Calibration Standard Chemistry File e BigDye Terminator v3 1 Cycle Z_BigDyeV3 BigDye v3 1 Matrix Standards Matrix Standard menial me a BigDye v3 1 Terminator Sequence Standard e ABI PRISM dGTP BigDye Sequencing Standard Terminator v 3 0 Cycle Sequencing Ready Reaction Kit e
23. STR Profiler Plus Kit AmpF STR Profiler Plus D Kit AmpF STR SGM Plus Kit Other 4 Dye AmpF STR Kits AmpF STR SEfiler Kit G5 AmpF STR Identifiler Kit AmpF STR Yfiler Kit Other 5 Dye AmpF STR Kits Kits Calibration Fragment Analysis Dye Sets Calibration Standards and Chemistry File Standards Table Fragment Analysis Chemistry Dye Set Spectral Calibration Standard Chemistry File Custom oligos D DS 30 Matrix Standards Matrix Standard e ABI PRISM Mouse Mapping Set v1 0 D DS 31 Matrix Standards e Custom oligos e AFLP kits F DS 32 Matrix Standards e Stockmarks Kits 4 dye bovine and canine e AmpF STR COfiler Kit e AmpF STR Profiler Plus Kit e AmpF STR Profiler Plus D Kit e AmpFLSTR SGM Plus Kit e Other 4 Dye AmpF STR Kits ABI Prism SNaPshot Multiplex System E5 DS 02 Matrix Standards e ABI PRiSM Linkage Mapping Set v2 5 G5 DS 33 Matrix Standards e Stockmarks Kit 5 dye equine e Custom Oligos e AmpF STR Identifiler Kit e AmpF STR SEfiler Kit e AmpFLSTR Yfiler Kit e Other 5 Dye AmpFLSTR Kits Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 83 Chapter 5 Reference Tables Run Modules Run Modules Spectral Run Modules pi Peep an Run Module ype cm POP 4 22 Spect22_POP4 36 Spe
24. after it has been installed do not attempt to lift or move the instrument without the assistance of others the use of appropriate moving equipment and proper lifting techniques Improper lifting can cause painful and permanent back injury Depending on the weight moving or lifting an instrument may require two or more persons Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide XI Safety Chemical Safety Moving and Neer Do not attempt to lift or move the computer or the monitor without Lifting Stand the assistance of others Depending on the weight of the computer and or the monitor Alone Computers moving them may require two or more people and Monitors Things to consider before lifting the computer and or the monitor e Make sure that you have a secure comfortable grip on the computer or the monitor when lifting e Make sure that the path from where the object is to where it is being moved is clear of obstructions e Do not lift an object and twist your torso at the same time e Keep your spine in a good neutral position while lifting with your legs e Participants should coordinate lift and move intentions with each other before lifting and carrying e Instead of lifting the object from the packing box carefully tilt the box on its side and hold it stationary while someone slides the contents out of the box Operating the Ensure that anyone who operates the instrument has
25. and Reference Guide Run Performance Chapter 3 Troubleshooting Run Performance Troubleshooting using Run validation tests Run Validation All validation tests must pass before the run starts The Test checks The capillary array length and or polymer type in the Instrument Protocol against the capillary array length and or polymer type in the database The available space in the database and drive E If a different length capillary array was installed and the appropriate active spectral calibration was not selected or does not exist Look For 1 System Status changes from green to red System Status gt Sy Stern Status 2 View the error messages in the Event Log Corrective Action Correct the Instrument Protocol or 1 Use the wizards to update the information in the database 2 Set or create an active spectral calibration 3 Relink the plate then click b To correct 1 See H1a Heading1_anywhere Hard Disk and Database Status on page 30 to access information on databases and sample data storage 2 Make more space 3 Click p To correct 1 In the Spectral Calibration Viewer set the active spectral calibration for the dye set and array length you are using 2 If one does not exist create a new spectral calibration for the dye set and array length you are using then set as the active spectral calibration 3 Click E Applied
26. by using the Database Manager See Deleting Processed Frame Data on page 34 Select the Plate Manager view Select a spectral plate that you want to delete Click Delete Ye amp P Repeat steps 3 and 4 as needed Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 35 Chapter 2 Computer Maintenance Deleting Records from the Database Option two Delete a spectral plate after deleting its associated processed plates manually Note Use this option if you are trying to delete one or two spectral plates and you do not want to delete all the processed plates in the database 1 Select the Plate Manager view 2 Search for and select a processed plate associated with the spectral calibration you are trying delete 3 Click Delete to delete the processed plate 4 Repeat steps 2 and 3 until all associated processed plates are deleted 5 Search for and select the spectral plate that you want to delete 6 Click Delete 36 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Troubleshooting Overview This chapter includes troubleshooting the following topics TGSHUMICHE IANO an gece hide eess hehe ohana ase A 38 Instrument Status io dot ee On ee ewe d oe Heke wo ea eee Sake eee eerie 39 Spatial Calibration gwen sds ene bk eee nee nie ee Adee see we ows 41 Special CADNO hand aoa s aoe ou es a eee RA S 42 Pla
27. dry especially in the center o e GR1573 Ko N E Oo 3130 xl capillary array 3130 capillary array Installing Removing or Replacing a Capillary Array IMPORTANT Wear gloves when you handle the polymer blocks Z Nem CHEMICAL HAZARD POP polymer causes eye skin and respiratory tract irritation Read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves 1 Close the oven and instrument doors and then press the Tray button 18 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 1 Maintenance Capillary Array 2 Select Wizards gt Install Array Wizard TEREE Help IMPORTANT The capillary array length defined Install Array Wizard in the wizard must match the array length you are using Replenish Polymer Wizard Bubble Remove Wizard Water Wash Wizard Instrument Shutdown Wizard Change Polymer Type Wizard 3 Open instrument and oven doors 4 Follow the directions given in the wizard to 4utosampler Calibration wizard install or replace an array Update Cap Array Info 5 Click Finish when done 6 Close and lock the oven door then close the instrument doors IMPORTANT If you installed or replaced an array that is a different length than the one you were using you must reset the active spectral calibration or create a new spectral calibrati
28. empty the contents of the Recycle Bin Check disk space status here 30 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Archiving Data A basic version of Roxio Easy CD Creator 5 software is loaded on your Dell computer Use this software to archive data to a CD The software is also part of the CD set you received with your Dell computer Creating a Data CD 1 Select Start gt All Programs gt Roxio Easy CD Creator 5 gt Applications gt Easy CD Creator The Untitled Easy CD Creator dialog box opens Optional For help creating a data CD select Help Topics gt Contents tab 2 In the left tree pane select Making Data CDs for Archiving and Sharing gt Making a Data CD Chapter 2 Computer Maintenance Archiving Data Untitled Data CD Project Easy CD Creator E s loj x File Edit view CD Tools Track Internet Help Select source files ova J oe 5 Apps D v fs ce rT Easy CDCreator 5 gt Name Size Type Modified a Adobe File Folder 7 3 2001 10 21 4M C ppliedBio File Folder 3 4 2002 3 04 PM bap stuff File Folder 9 21 2001 11 02 4M J Forms File Folder 4 20 2001 12 11 PM CI FrameMaker Tem File Folder 4 20 2001 12 01 PM gt f P ee E Pee PENI ae IN Add Remove data B gt Ga project 7 ra preview transitions 020711_2143 Project Size O bytes Estimated free space 650
29. from Hitachi Ltd as part of a strategic partnership between Applied Biosystems and Hitachi Ltd as well as patented technology of Applied Biosystems Trademarks AB Design Applera Applied Biosystems AFLP AmpFISTR BigDye Cofiler GeneMapper Identifiler Profiler Profiler Plus SeqScape SGM Plus SNaPshot StockMarks and Yfiler are registered trademarks and Hi Di POP POP 4 POP 6 POP 7 and SEfiler are trademarks of Applied Biosystems or its subsidiaries in the U S and or certain other countries Dell is a registered trademark of Dell Computer Corporation Microsoft Windows and Windows XP are registered trademarks of the Microsoft Corporation in the United States and other countries Oracle is a registered trademark of the Oracle Corporation All other trademarks are the sole property of their respective owners Part Number 4352716 Rev E 06 2010 Contents Preface V How to Use This Guide i440 024 anaana aaa V How to Obtain More Information 0 00 cee ees vi How to Obtain Support anaana naaa aaea eee et tees vi Safety vii Safety Conventions Used in This Document 2 000 ee viii Symbols on Instruments anana aana Ix Safety Labels on Instruments 000 ccc eee ene X General Instrument Safety a na nananana xi Chemical Salely csser iee eres et beet ende Tee aa Ea T a E a a xii Chemical Waste Safety a na nanana aa XIV El ctrical Safely f 40nGes Gale bee ees ETETE eed eu ee ENE
30. if not avoided could result in death or serious injury N aeda Indicates an imminently hazardous situation that if not avoided will result in death or serious injury This signal word is to be limited to the most extreme situations Except for IMPORTANTS each safety alert word in an Applied Biosystems document appears with an open triangle figure that contains a hazard symbol These hazard symbols are identical to the hazard icons that are affixed to Applied Biosystems instruments see Safety Symbols on page x Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Safety Symbols on Instruments Examples The following examples show the use of safety alert words IMPORTANT You must create a separate Sample Entry Spreadsheet for each 96 well microtiter plate AN oF Wael The lamp is extremely hot Do not touch the lamp until it has cooled to room temperature Nore CHEMICAL HAZARD Formamide Exposure causes eye skin and respiratory tract irritation It is a possible developmental and birth defect hazard Read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves JN aedis ELECTRICAL HAZARD Failure to ground the instrument properly can lead to an electrical shock Ground the instrument according to the provided instructions Symbols on Instruments Electrical Symbols on Instruments The following
31. knob interconnecting tube nuts and Daily check valve Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 1 Maintenance Performing Maintenance Tasks Weekly Tasks Perform these tasks at least once per week Maintenance Task Frequency Replace the polymer using the Replenish Polymer Wizard Weekly or as needed Flush the water trap See Flushing and Filling the Water Trap on Weekly page 13 Check the storage conditions of the used arrays Weekly Restart the computer and instrument Weekly Monthly Tasks Perform these tasks at least once per month Maintenance Task Frequency Run the Water Wash Wizard Monthly or as needed Flush the array port during this wizard whether or not bubbles are present in the array port Defragment the hard drive Monthly As Needed Tasks Perform these tasks as needed Maintenance Task Frequency Clean the drip tray As needed Change the array As needed Remove any dried polymer from the capillary tips Use a lint free wipe As needed moistened with deionized water 4 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 1 Maintenance Routine Cleaning Routine Cleaning General Cleaning 1 Ensure the oven and instrument doors are closed 2 Press the Tray button on the front of the Tray button
32. l E Plate Manager 1 Run David PT4_20 Regular StdSeq50_POP6_1_ Validated a t T Protocol Manager 2 Run_David PT4_20 Regular StdS5Seq50_POP6_1 Validated Hije Module Manager 16 Run History PdaviaPT4 A SeqSamples AMGEneamnises E EAinstrument Status noa E E D CR A Ka e a aA ADD EJS HHA a 2 E Evert Log Bil Snatial Run Scheduler A HHHHHHHHE 384 well plate on a 3130x genetic analyzer 67 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 4 Data Collection Software Advanced Functions Edit gt Fill Down Special Option for Plate Records MA spectral Calibration Plate Editor E x File Edit Plate Name Spectral_Z Operator bap Plate Sealing Septa x Owner bap Sample Name Comment Priority Instrument Protocol 1 100 Spectral_Z_50crn Spectral_Z_50crn c01 LRS 100 Spectral_Z_50crn D01 LRS 100 Spectral_Z_50cm E01 F01 G01 H01 402 B02 co2 H 2r is logged in a Ale x Description Ok Cancel 6130 gt iDev Run Scheduler Run View Database Manager A a E Ega3130 Run RunD RunType Module Status EE Plate Manager 1 i T Protocol Manager Gs Module Manager R Snortral Run History a a e aA Divev EEEE E Instrument Status j Hil Spatial Run Schedule ED Run Scheduler Plate View i Run View E capillaries Viewer
33. n appropriate application H12 Application E SeqScape_IDEVRT C None E GeneMapper Generic E SequencingAnalysis E GeneMapper IDEVRT SeqScape_IDEVRT c Repeat the process for additional samples and applications Set Application H12 Application GeneMapper Generic EE None GB GeneMapper Generic E SequencingAnalysis GS GeneMapper IDEVRT GS SeqScape_IDEVRT Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 11 Chapter 4 Data Collection Software Advanced Functions Multi application Mixed Plate Record 5 Create the Sequencing sample sheets plate record Set ea 5a a On the plate map click a well position that represents a sequencing sample b Click Sample Sheet my Application C SequencingAnalysis Sb Done DO E07 Fo G07 The Sequencing Analysis Plate editor Mle eat opens m Raa E EEA c Complete the plate record wW Note The well column contains only those on DE wells that were designated as sequencing samples on the plate map d Click _SK_ You are automatically returned to the Integrated Plate dialog box Description Ok Cancel 72 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 4 Data Collection Software Advanced Functions Multi application Mixed Plate Record 6 Create t
34. planning your runs Correct the files and rerun the calibration Check for broken capillaries and refill the capillary array Check the expiration date and storage conditions of the matrix standards and or reagents If necessary replace with a fresh lot Rerun the spectral standards and if necessary increase the amount of spectral standard added Replace the polymer with a fresh lot using the Replenish Polymer Wizard CHEMICAL HAZARD POP 4 polymer POP 6 polymer and POP 7 polymer cause eye skin and respiratory tract irritation Read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves Select the Bubble Remove Wizard to clear the bubbles Properly bring the polymer to room temperature do not heat to thaw rapidly Swirl to dissolve any solids Replace the polymer if it has expired Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 43 Chapter 3 Troubleshooting Spectral Calibration Troubleshooting failing capillaries Failing Capillary assigned a spectral profile Manually Overriding a Spectral Profile To override a spectral calibration profile 1 Review the data 2 In the plate diagram select the capillary spectral profile you want to override 3 Click Override Spectral The Override Spectral dialog box opens 5 Click OK 6 Click Save 7 In Save the modified
35. ramp step Applied Biosystems recommends that you do not change this value Voltage_Step_Interval Time from the start of separation to Data_Delay_Time 1 3600 sec the start of data collection Run_Time 300 14000 sec Duration data is collected after Data_Delay_Time 6 Click OK Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 61 Run Priority Scheduling Priority Values Chapter 4 Data Collection Software Advanced Functions Run Priority Scheduling The user definable run priority scheduling function allows you to schedule runs in custom order providing flexibility when scheduling runs A default value of 100 is assigned to each sample in the plate record Changing the value to a smaller number causes that set of 16 or 4 samples to run before the others in the injection list Scheduling Examples Default Run Scheduling Using a 96 well Plate and 16 Capillary Array In this example 100 1s the priority value for all samples in the plate record and the default run priority schedule is used see table below Samples AO7 H08 called out on the plate record correspond to Run 4 as displayed in the Run Scheduler gt Run View window Well Numbers Run Num
36. that may come into contact with these fluids Daily Tasks Perform these tasks at least once per day Maintenance Task Frequency Ensure adequate levels of buffer and water in reservoirs Before each run Ensure the plate assemblies are properly assembled Before each run IMPORTANT The holes in the plate retainer must align with the holes in the septa or the capillary tips will be damaged Ensure the plate assemblies are positioned on the plate deck properly Before each run Plates should sit snugly on the deck IMPORTANT Never use warped plates Check the level of buffer in the buffer jar Ensure that the overflow hole Before each run faces the front of the instrument and is not occluded Replace the water and 1X run buffer in the reservoirs on the instrument Every 48 hours and make sure that the outside of the assemblies are dry Check for bubbles in the pump block lower polymer block Daily or before each interconnect tube polymer supply tube and channels run Remove all bubbles with the Bubble Remove wizard Check the loading end header to ensure the capillary tips are not Daily or before each crushed or damaged run Check the level of polymer in the bottle to ensure sufficient volume for Daily or before each runs run Check the pump block and the lower polymer block to ensure they fit Daily securely on the instrument Clean the instrument surfaces Daily Check for leaks around the array
37. the Bubble Remove Wizard to clear detected appears The run bubbles aborts Leak in the polymer system Check for evidence of leaks Tighten the tubing connectors and array knob Buffer valve leakage Check the buffer valve pin and see if it closes correctly Buffer jar overflows very Bubbles in the polymer path Check for bubbles and remove if present quickly with polymer Overuse of the Bubble Remove Wizard 56 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 3 Troubleshooting Run Performance Troubleshooting run performance continued Observation Possible Cause Recommended Action Detection cell comes out Improperly placed detection cell Loosen the array knob Close the detection while replacing the capillary block door Retighten the array knob array Replacing the cell in the correct orientation is difficult Detection cell stuck It is To loosen the detection cell SiC Unto A wel 1 Undo the array knob and pull the polymer changing the capillary array block towards you to first notch 2 Hold both sides of the capillary array around the detection cell area and apply gentle pressure equally on both sides 3 Remove the capillary comb from the holder in oven 4 Release Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 5 Chapter 3 Troubleshooting Run Performance
38. the on off button on the front of the instrument 3 Restart the computer a Select Start gt Turn off Computer On Off button b In the dialog box select Restart then click OK IMPORTANT Wait until the computer has completely restarted before proceeding 4 Turn on the instrument then wait for the solid green light 5 Launch the Data Collection software Service Console applications start automatically 6 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 1 Maintenance Moving and Leveling the Instrument Moving and Leveling the Instrument N or Veale PHYSICAL INJURY HAZARD Do not attempt to lift the instrument or any other heavy objects unless you have received related training Incorrect lifting can cause painful and sometimes permanent back injury Use proper lifting techniques when lifting or moving the instrument Two or three people are required to lift the instrument depending upon instrument weight 1 Remove the following components from the instrument e Any plate assemblies from the autosampler e Water and buffer reservoirs from the autosampler e Capillary array by selecting Instrument Shutdown Wizard See Performing a Long Term Shutdown on page 10 e Anode buffer reservoir 2 Switch off the breaker on the back of the instrument 3 Disconnect the power cord and the Ethernet cable IMPORTANT While moving
39. 0 1400 1600 1800 2000 2200 2400 2600 Intensity vs Scan Number Capillary Data i Dye Set E5 z Failed gt y Active Calibration for Dye Set C api ari es Matrix used for Capillary Condition Q Value List of Calibrations for Dye Set PThu Sep 25 12 33 25 PDT 2003 z Rename H12 teaches Noa Current Run 6 Use the list of questions below when reviewing the raw data to determine the cause of the failure How many peaks Any extraneous peaks Peak order Peak shape and signal strength Negative peaks Additional peaks positive or negative under the main color peak Note It is helpful to magnify the raw data for the review process see THL TableHeadLeft Tip Magnifying the Spectral Profile or Raw Data on page 42 Magnified raw data Raw data 46 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 3 Troubleshooting Plate Linking Plate Linking Troubleshooting plate linking Plate does not link Spatial calibration was not performed 1 Perform a spatial calibration 2 Relink the plate s in the Run Scheduler The plates in the Run Scheduler A wizard was used after linking a plate but Relink the plate s in the Run were linked but now are before starting a run automatically unlinking Scheduler unlinked the plate warning hl AN Plate s unlinked Applied Biosystems 3130 3130x Genetic
40. 0POP6_BDTv3 KB De G02 LRS 100 SeqA_50cm Seq_50cm_POP6 3130POP6_BDTv3 KB De H02 LRS 100 SeqA_ 50cm Seq_50cm_POP6 3130POP6_BDTv3 KB De p a j A403 B03 1 Validated Sii i 2 B SeqSamples2 Description _o Cancel PH Ld 4 F DB F Hil Spatial Run Scheduler Run Scheduler Plate View gt Run View F E capillaries viewer F E capiArray viewer F M Spectral viewer F Ah Manual Control Service Log oe NOP amp we N 96 well plate on a 3130x genetic analyzer SequencingAnalysis Plate Editor xj gt Edit Plate Name SeqSamples2 Operator bp o Plate Sealing Septa 7 Owner fe ap Well Sample Name Comment Priority Results Group 1 Instrument Protocol 1 Analysis Protocol 1 Seq4 amp _50cm Seq_50cm_POP6 3130POP6_BDTv3 KB De p B01 co1 LRS 100 SeqA_50cm Seq_50cm_POP6 3130POP6_BDTv3 KB De D01 E01 LRS 100 SeqA_50cm Seq_50cm_POP6 3130POP6_BDTv3 KB De F01 GO1 LRS 100 SeqA_5O0cm Seq_50cm_POP6 3130POP6_BDTv3 KB De H01 101 LRS 100 SeqA_50cm Seq_5O0cm_POP6 3130POP6_BDTv3 KB De Jot logged in 0 x KO1 LRS 100 Seq amp _5Ocm Seq_SO0cm_POP6 3130POP6_BDTv3 KB De L01 x scription Ok Cancel J gt DavidPT4 Run Scheduler gt Run view ss _ Run Type Module Status 15
41. 4 MB on a 74 min CD 703 12 MB on an 80 min CD 74 00 80 00 l0 objects DataCD Joliet Track At Once Help Topics Back KL Contents B Index hh Search ag Overview E Making Custom Music CDs a jee meede at t an bese a5 Making a Data CD from a CO jee i Ey Working with Files and Folder beeen i Ey Validating a CD Project E Advanced Data CD Topics a Copying CDs E Troubleshooting a CO Creator Reference Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 31 Chapter 2 Computer Maintenance Archiving Data 3 Follow the instructions to create the CD With Easy CD Creator you can make a data CD to store computer data such as the files and folders on your hard disk This is especially useful for archiving your important files or sharing them with your colleagues Unlike a music CD a data CD is used for data storage only and cannot be played on your home or car stereo CD player To make a data CD 1 Start a new data CD project From the File menu point ta New CD Project then select Data CD 3 In the Select Source Files drop down list box select the folder where your filles are located a list of all files in the folder appears in the Source window 4 Select the file hold down the Ctrl or Shift key to select multiple Add files in the Source window and then click Add The file is added to the data CD project Mote
42. Analyzers Maintenance Troubleshooting and Reference Guide 4 Chapter 3 Troubleshooting Plate Linking Troubleshooting plate linking continued The plate links but System A different length capillary array was installed Status changes from green to and the appropriate active spectral calibration red was not selected or does not exists System Status p Sy stern Status The capillary array length and or polymer type selected in the Instrument Protocol does not match capillary array length and or polymer type stored in the database The database and or drive E is full 1 View the error messages in the Event Log 2 Inthe Spectral Calibration Viewer set the active spectral calibration for the dye set and array length 3 If one does not exist create a new spectral calibration for the dye set and array length you are using then set it as the active spectral calibration 4 Relink the plate s in the Run Scheduler Correct the Instrument Protocol or 1 Use the wizards to update the information in the database 2 Set or create an active spectral calibration 3 Relink the plate To check the available space 1 View the error messages in the Event Log 2 Proceed to H1a Heading1_anywhere Hard Disk and Database Status on page 30 3 Make more space 4 Relink the plate s in the Run Scheduler 48 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting
43. Applied Applied Biosystems 3130 3130x Genetic Analyzers AB Bee ystems HITACHI Maintenance E Troubleshooting and aReference Guide Instrument Maintenance Computer Maintenance Troubleshooting Data Collection Software Advanced Functions Reference Tables me f AT l Ni i NN i uh A Copyright 2007 2010 Applied Biosystems All rights reserved Information in this document is subject to change without notice Applied Biosystems assumes no responsibility for any errors that may appear in this document This document is believed to be complete and accurate at the time of publication In no event shall Applied Biosystems be liable for incidental special multiple or consequential damages in connection with or arising from the use of this document NOTICE TO PURCHASER This instrument is Authorized for use in DNA sequencing and fragment analysis This authorization is included in the purchase price of this instrument and corresponds to the up front fee component of a license under process claims of U S patent claims and under all process claims for DNA sequence and fragment analysis of U S patents now or hereafter owned or licensable by Applied Biosystems for which an Authorization is required and under corresponding process claims in foreign counterparts of the foregoing for which an Authorization is required The running royalty component of licenses may be purchased from Applied Bi
44. BigDye Terminator v1 1 Cycle E BigDyeVi DS 01 Matrix Standards Matrix Standard Perene a BigDye v1 1 Terminator Sequence Standard e ABI PRISM BigDye Primer Cycle Sequencing Standard Sequencing Kits e ABI PRISM dGTP BigDye Terminator Cycle Sequencing Kit ABI PRISM dRhodamine Dye dRhodamine Matrix Standards Kit Matrix Standard Terminator Cycle Sequencing Ready Reaction Kit a dGTP kits are not supported on capillary electrophoresis instruments due to compressions on certain sequence context regions you can run the kits if you do not care about the compression issues Dye Set and Run Sequencing Kits Dye Sets Polymer Type and Run Modules Modules POP 4 POP 6 Polymer Polymer pons Polymer o o 8 8 o 8 8 o o 8 7 8 g 3g 8 8 amp 8 g Sequencing Chemistry Dye Set 9 A g B N g 7 3 A 5 8 c 2 8B 5S OQ 8 B c 5 S g 5 g tools BigDye Terminator v3 1 Cycle Sequencing Kit Z BigDye v J J J J J J J J J V3 ABI PRISM dGTP BigDye Terminator v3 0 Cycle Sequencing Ready Reaction Kit S S S S S BigDye Terminator v1 1 Cycle Sequencing Kit E_BigDye V A A J J ABI PRISM dGTP BigDye Terminator Cycle wi Sequencing Kit ABI PRISM dRhodamine Dye Terminator lf ie 12 1 te le le ie t fea Cycle Sequencing Ready Reaction Kit ABI PRISM BigDye Primer Cycle Sequencing ls le r xz Pee ee je dae J Kits
45. ELECTRICAL SHOCK HAZARD Severe electrical shock can result from operating the Applied Biosystems 3130 3130x Genetic Analyzers without its instrument panels in place Do not remove instrument panels High voltage contacts are exposed when instrument panels are removed from the instrument Power JN pyleiaagg ELECTRICAL HAZARD Grounding circuit continuity is vital for the safe operation of equipment Never operate equipment with the grounding conductor disconnected gt DUIS ELECTRICAL HAZARD Use properly configured and approved line cords for the voltage supply in your facility JN aedis ELECTRICAL HAZARD Plug the system into a properly grounded receptacle with adequate current capacity Overvoltage The Applied Biosystems 3130 3130x Genetic Analyzers system have an installation Rating overvoltage category of II and is classified as portable equipment Physical Hazard Safety AT ee oS Moving Parts _ gt PHYSICAL INJURY HAZARD Moving parts can crush and cut Keep hands clear of moving parts while operating the instrument Disconnect power before servicing the instrument Laser Safety Laser The Applied Biosystems 3130 3130x Genetic Analyzers use an Argon laser Under Classification normal operating conditions the instrument laser is categorized as a Class I laser When safety interlocks are disabled during certain servicing procedures the laser can cause permanent eye damage and therefore is classified under those co
46. F USE LOSS OF DATA FAILURE OR INTERRUPTION IN THE OPERATION OF ANY EQUIPMENT OR SOFTWARE DELAY IN REPAIR OR REPLACEMENT OR FOR LOSS OF REVENUE OR PROFITS LOSS OF GOOD WILL LOSS OF BUSINESS OR OTHER FINANCIAL LOSS OR PERSONAL INJURY OR PROPERTY DAMAGE NO AGENT EMPLOYEE OR REPRESENTATIVE OF Applied Biosystems HAS ANY AUTHORITY TO MODIFY THE TERMS OF THIS LIMITED WARRANTY STATEMENT OR TO BIND APPLIED BIOSYSTEMS TO ANY AFFIRMATION REPRESENTATION OR WARRANTY CONCERNING THE PRODUCT THAT IS NOT CONTAINED IN THIS LIMITED WARRANTY STATEMENT AND ANY SUCH MODIFICATION AFFIRMATION REPRESENTATION OR WARRANTY MADE BY ANY AGENT EMPLOYEE OR REPRESENTATIVE OF APPLIED BIOSYSTEMS WILL NOT BE BINDING ON APPLIED BIOSYSTEMS UNLESS IN A WRITING SIGNED BY AN EXECUTIVE OFFICER OF APPLIED BIOSYSTEMS THIS WARRANTY IS LIMITED TO THE BUYER OF THE PRODUCT FROM APPLIED BIOSYSTEMS AND IS NOT TRANSFERABLE Some countries or jurisdictions limit the scope of or preclude limitations or exclusion of warranties of liability such as liability for gross negligence or wilful misconduct or of remedies or damages as or to the extent set forth above In such countries and jurisdictions the limitation or exclusion of warranties liability remedies or damages set forth above shall apply to the fullest extent permitted by law and shall not apply to the extent prohibited by law Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Ref
47. ance Troubleshooting and Reference Guide Chapter 4 Data Collection Software Advanced Functions Multi application Mixed Plate Record Multi application Mixed Plate Record Protocols fora To run a mixed plate containing sequencing SeqScape software and or fragment Mixed Plate analysis samples the following files are required Record e Sequencing analysis Results Group Instrument Protocol Analysis Protocol e SeqScape software analysis Results Group Instrument Protocol Analysis Protocol Files created in SeqScape software e Fragment analysis Results Group Instrument Protocol Files created in GeneMapper software Creating Spectral For every dye set and capillary array length combination you use a separate spectral Calibrations calibration must be created Setting the Active If you changed the capillary array length to run multi application samples you must set Spectral the active spectral calibration for each dye set used See the Applied Biosystems Calibration 3 30 3130xl Genetic Analyzers Getting Started Guide on how to set the active calibrations once calibrations are performed for each dye set on each capillary length Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 69 Chapter 4 Data Collection Software Advanced Functions Multi application Mixed Plate Record Creating and Completing a Mixed Plate Record 1 In
48. anels Wear proper eye protection and post a laser warning sign at the entrance to the laboratory if the top or front panels are removed for service ANS LASER BURN HAZARD An overheated laser can cause severe burns if it comes in contact with the skin DO NOT operate the laser when it cannot be cooled by its cooling fan Always wear appropriate laser safety goggles Workstation Safety Correct ergonomic configuration of your workstation can reduce or prevent effects such as fatigue pain and strain Minimize or eliminate these effects by configuring your workstation to promote neutral or relaxed working positions NIN MUSCULOSKELETAL AND REPETITIVE MOTION HAZARD These hazards are caused by potential risk factors that include but are not limited to repetitive motion awkward posture forceful exertion holding static unhealthy positions contact pressure and other workstation environmental factors To minimize musculoskeletal and repetitive motion risks e Use equipment that comfortably supports you in neutral working positions and allows adequate accessibility to the keyboard monitor and mouse e Position the keyboard mouse and monitor to promote relaxed body and head postures XVI Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Safety Safety and Electromagnetic Compatibility EMC Standards Safety and Electromagnetic Compatibility EMC Standards U S and Canadian Safety
49. are fresh Hi Di formamide and re prepare samples CHEMICAL HAZARD Formamide causes eye skin and respiratory tract irritation It is a possible reproductive and birth defect hazard Read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves Use a recommended protocol for salt removal Dilute salts with water Refill the capillary array and look for polymer leakage If problem persists contact Technical Support Re inject the same samples Check the sample preparation Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 53 Run Performance Chapter 3 Troubleshooting Troubleshooting run performance continued Observation No current Elevated current Fluctuating current Possible Cause Water placed in buffer reservoir position 1 Not enough buffer in anode reservoir Buffer too dilute Bubble s present in the lower polymer block and or the array and or tubing Degraded polymer Incorrect buffer dilution Arcing in the lower polymer block Bubble in polymer block A slow leak may be present in the system Recommended Action Replace with fresh 1X running buffer Add buffer up to the fill line Prepare 1X running buffer Add 3 mL 10X Genetic Analyzer Buffer with EDTA to 27 mL deionized water CHEMICAL HAZARD 10X Genetic Analyzer Buffer with EDTA may cause eye s
50. ate stations Close the oven door Close the stacker drawer Close the instrument doors Q gt O0 Q Cycle power on the Applied Biosystems 3130 Series Genetic Analyzer The account password for User 1 Boot Reboot the instrument and computer name 3130User has changed workstation or has been entered with the wrong case the user name and password are case sensitive 2 Log in taking care to type 3130User with the capitalization shown here The account password for User Start up in the following sequence name 3130User is expired or 1 Log out of the computer and turn off the corrupt instrument 2 Boot up the computer 3 After the computer has booted completely turn the instrument on Wait for the green status light to come on IMPORTANT Do not launch the Data Collection software 4 Reset the account password a Right click My Computer b Click Manage c In the Computer Management window click Local Users and Groups then click User d On the right side of the window right click 3130User then select Set Password e Set the password to 3130User confirm the password entry then click OK f In the Computer Management window right click 3130User and select Properties g Confirm User cannot change password and Password never expires are selected Click OK then exit out of the Computer Management windo
51. ation of chemicals Do not leave chemical containers open Use only with adequate ventilation for example fume hood For additional safety guidelines consult the MSDS e Check regularly for chemical leaks or spills If a leak or spill occurs follow the manufacturer s cleanup procedures as recommended on the MSDS e Comply with all local state provincial or national laws and regulations related to chemical storage handling and disposal Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide xili Safety Chemical Waste Safety Chemical Waste Safety Chemical Waste N AON HAZARDOUS WASTE Refer to Material Safety Data Sheets and Hazard _ local regulations for handling and disposal Nem CHEMICAL WASTE HAZARD Wastes produced by Applied Biosystems instruments are potentially hazardous and can cause injury illness or death Chemical Waste To minimize the hazards of chemical waste Safety Guidelines y e Read and understand the Material Safety Data Sheets MSDSs provided by the manufacturers of the chemicals in the waste container before you store handle or dispose of chemical waste e Provide primary and secondary waste containers A primary waste container holds the immediate waste A secondary container contains spills or leaks from the primary container Both containers must be compatible with the waste material and meet federal state and local requirements for container storag
52. ber Priority Well Numbers Run Number Priority fii SequencingAnalysis Plate Editor 4 x File Edit Plate Name M Foundation Data Collection Yersion 3 0 No EA in SS 5 x File View Instrument Service Tools Wizards Help Plate Sealing gt BBP I A E J GA Instruments i Well Sample Name Comment PAN Resi ff Resuts Group GA Instruments gt ga3130 gt DavidPT4 Run Scheduler gt Run View B07 CRS seq i a R aes manors RuniD Module Status ue 1 coy LRS seq EPlate Manager 1 Run_David PT4_20 Regular StdSeq50_POP6_1 Validated a Do LRS Seq arroa Manet 2 Run_David PT4_20 Regular StdSeq50_POP6_1 Validated rT ttf i Mi d M J mMuNLVaYUT i _2u owMmocyvu_Tvru_i yYanualcu 16 2 E07 LRS Seq Bl gt ai Run_David PT4_20 Regular StdSeq50_POP6_1 Validated DevidPT4 Sap Eee ESGlLi Ea e es A Seqa_2 B FO LRS Seq See weed Status Run David PT4_20 Regular StdSeq50_POP6_1 Validated QF ELD CGC BA GO7 LRS Seq BYEPT Chart 7 7 7 Ho7 LRS Seq E evert Log TTT rs fll Spatial Run Schedijler Lib A08 LRS Seq E Run Scheduler I fs B08 LRS Seq Eon 7 kun view cos LRS Seq Z capillaries Viewer f TT aE HBB Cap Array Viewer DOS LRS Seq fi Spectral Viewer i Manual Control s H Service Log Description Default run priority schedule samples in wells A07 H08 are scheduled as Run 4 62 Applied Bios
53. ble Remove wizard electrophoresis current path Absence of bubbles Water wash Wizard in the current path is important for problem free ee daie electrophoresis a l Autosampler Calibration Wizard Update Cap Array Info 2 Replace the buffer if excess polymer is expelled into the anode buffer jar during bubble removal 22 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Autosampler Calibration When to Calibrate the Autosampler Calibrate the autosampler only as needed Symptoms of autosampler alignment problems may include e Poor injection for a small number of capillaries e Low signal strength e No evidence of sample Calibrating the Autosampler 1 Close the oven and instrument doors 2 Select Wizards gt Autosampler Calibration Wizard 3 If plates are linked in the Run Scheduler the plates automatically are unlinked In the Warning dialog box click HK 4 Follow the directions given in the wizard to calibrate the autosampler 5 Click Finish and turn the instrument power off for 10 sec then on Chapter 1 Maintenance Autosampler Calibration ieee Help Install Array Wizard Change Polymer Type Wizard Replenish Polymer Wizard Bubble Remove Wizard Water Wash Wizard Instrument Shutdown Wizard Autosampler Calibration Wizard Update Cap Array Info Autosampler Calibration Wizard Step 1 Clear and Initialize Autosampler 1
54. ct36_POP4 SpectSQ36_POP4 50 Spect50_POP4 80 Spect80_POP4 POP 6 36 Spect36_POP6 50 Spect50_POP6 POP 7 36 Spect36_POP7 50 Spect50_POP7 80 Spect80_POP7 Sequencing Run Modules Capillary Polymer Array Length Module cm POP 4 36 UltraSeq36_POP4 50 StdSeq50_POP4 80 LongSeq80_POP4 POP 6 36 RapidSeq36_POP6 50 StdSeq50_POP6 POP 7 36 UltraSeq36_POP7 RapidSeq36_POP7 50 FastSeq50_POP7 StdSeq50_POP7 80 LongSeq80_POP7 Fragment Analysis Run Modules See Fragment Analysis Resolution Performance and Specifications on page 81 and Kits and Run Modules on page 82 for available fragment analysis run modules 84 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Capillary Arrays Reagents and Standards Parts List Description Part Number 3130 Genetic Analyzer 22 cm capillary array 4333463 36 cm capillary array 4333464 50 cm capillary array 4333466 80 cm capillary array 4333465 3130x Genetic Analyzer 22 cm capillary array 4319898 36 cm capillary array 4319531 50 cm capillary array 4315930 80 cm capillary array 4319899 Description Part Number 10X Genetic Analyzer Buffer with EDTA 402824 3100 3130 BigDye Terminator v3 1 Matrix standard 4336974 BigDye Terminator v3 1 Cycle Sequencing Ready Reaction 4337455 Kit 100 Reactions BigDye Terminator v3 1 Sequencing Standa
55. ction software 50 18 65069 x PreRun_Voltage 12 2 0 15 k volts Pre_Run_Time J 180 1 1000 sec 4 Optional Enter a description of your new run seta 10 y 1 15 Kvols 7 Injection_Time 22 1 600 sec module Woltage_Number_Of_Steps 10 1 100nk i Voltage _Step_ Interval E BO 1 60 sec Data_Delay_Time 1200 1 3600 sec Run_ oltaqe E 12 2 0 15 k volts z Run_Time S500 300 14000 SEC 4 af E Ok Cancel 60 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 4 Data Collection Software Advanced Functions Customizing Run Modules 5 Change to the desired module parameters using allowable ranges shown in the table below Name Range Comment Oven_Temperature 18 65 C Poly_Fill_Vol variable to 38000 counts Current_Stability 0 2000 Amp PreRun_Voltage 0 15 kV Injection_Voltage 0 15 kV Run_Voltage 0 15 kV Voltage_Number_Of_S 0 100 steps teps Temperature setting for main oven throughout run Check for amount of polymer available in the PDP Maximum current variation during electrophoresis Pre run voltage setting before sample injection Prerun voltage time Injection voltage setting for sample injection Sample injection time Number of voltage ramp steps to reach Run_Voltage Applied Biosystems recommends that you do not change this value Final run voltage 0 60 sec Dwell time at each voltage
56. d to load fresh polymer on the instrument 3 Relink plate s if applicable Changing to a Different Polymer Type ANITY CHEMICAL HAZARD POP Polymers causes eye skin and respiratory tract irritation Read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves IMPORTANT Wear gloves when you handle the polymer 1 Click Wizards gt Change Polymer Type TEEN Hep Wizard Install Array Wizard 2 Follow the wizard prompts Change Polymer Type Wizard Replenish Polymer Wizard Bubble Remove Wizard Water Wash Wizard Instrument Shutdown wizard Autosampler Calibration Wizard Update Cap Array Info Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 17 Chapter 1 Maintenance Capillary Array Capillary Array When to Change A capillary array should last approximately 100 runs Cap IAG AMAY The following problems may indicate that a new capillary array is required e Poor sizing precision or allele calling e Poor resolution and or decreased signal intensity Checking the Nee ELECTRICAL SHOCK FIRE HAZARD Do not leave liquid on Cathode Bar _ the cathode header This can lead to electric shock or even fire if not properly maintained When placing a used array back on the instrument be sure that the cathode bar is dry see figure below A wet bar could lead to arcing Back view Ensure the cathode header is
57. e e Minimize contact with chemicals Wear appropriate personal protective equipment when handling chemicals for example safety glasses gloves or protective clothing For additional safety guidelines consult the MSDS e Minimize the inhalation of chemicals Do not leave chemical containers open Use only with adequate ventilation for example fume hood For additional safety guidelines consult the MSDS e Handle chemical wastes in a fume hood e After emptying the waste container seal it with the cap provided e Dispose of the contents of the waste tray and waste bottle in accordance with good laboratory practices and local state provincial or national environmental and health regulations Waste Disposal If potentially hazardous waste is generated when you operate the instrument you must e Characterize by analysis if necessary the waste generated by the particular applications reagents and substrates used in your laboratory e Ensure the health and safety of all personnel in your laboratory e Ensure that the instrument waste is stored transferred transported and disposed of according to all local state provincial and or national regulations IMPORTANT Radioactive or biohazardous materials may require special handling and disposal limitations may apply XIV Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Safety Flectrical Safety Electrical Safety JN aUl dis
58. e Publisher Description Protocol Manager 08 22 03 19 42 42 David PT5 Run_David PT5_ 2003 08 22 16 56_0520 status has changed to Compl a Module Manager 08 22 03 19 39 37 System Status Ready P pa eA 08 22 03 19 39 37 System Status Idle E Event Log 08 22 03 19 39 36 Run completed instrument Protocol 08 22 03 19 39 35 David PT5 The number of runs has changed to 0 fifi Spatial Calibration Viewer 08 22 03 19 39 35 System Status Post Batch E Capillary Viewer 08 22 03 19 39 35 Sample Plate Unloaded oo Baray Viewer 08 22 03 19 39 35 System Status Postprocessing p M Spectral Calibration Viewer i jS Reextraction David PTS E4 Instrument Status YEPT Chart a ae Event Log pe Hi Spatial Run Scheduler Run Scheduler Error Messages p E capillary Viewer BB Array Viewer Type Date Time Publisher Description Error M Spectral Viewer a Manual Control 08 22 03 08 22 03 19 39 35 19 39 05 Disk drive E for sample files is full Please clean up the disk then try again Disk drive E for sample files is full Please clean up the disk then try again Error mi service Log Error 08 22 03 19 38 33 Disk drive E for sample files is full Please clean up the disk then try again a ADNA Anaona Miel Ariun C far carnia filas ia foll Dlanan alaan nn tha dial than tu ananin Error 08 22 03 19 37 27 Disk drive E for sample files is full Please clean up the disk then try again
59. e of defects in materials and workmanship under normal use If there is a defect in the media covered by the above warranty and the media is returned to Applied Biosystems within the ninety 90 day warranty period Applied Biosystems will replace the defective media Applied Biosystems does not warrant that the operation of the instrument or its operating software will be uninterrupted or error free Any applicable warranty period under these sections begins on the earlier of the date of installation or ninety 90 days from the date of shipment for hardware and software installed by Applied Biosystems personnel For all hardware and software installed by the buyer or anyone other than Applied Biosystems and for all other products the applicable warranty period begins the date the product is delivered to the buyer Warranty claims must be made within the applicable warranty period or for chemicals or other consumable products within thirty 30 days after receipt by the buyer The above warranties do not apply to defects resulting from misuse neglect or accident including without limitation operation with incompatible solvents or samples in the system operation outside of the environmental or use specifications or not in conformance with the instructions for the instrument system software or accessories improper or inadequate maintenance by the user installation of software or interfacing or use in combination with software or product
60. e protocol To remove any suspected contaminants in the PDP To remove persistent bubbles followed by the Bubble Remove Wizard if needed To replace old polymer in the PDP Instrument Prepare the instrument for a period of disuse of greater than one week Shutdown Autosampler Calibrate the autosampler positions Calibration Update Cap Array e Update the capillary array information and the serial number Info e Correct an entry mistake after using a wizard a The eu polymer block is cleaned on the instrument using this wizard and should not be removed 12 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Flushing and Filling the Water Trap Overview The PDP water trap should be flushed with either distilled or deionized water at least once per week to wash out any diluted polymer and to clear bubbles Leave the trap filled with either distilled or deionized water To flush the water seal trap 1 Fill the supplied 20 mL all plastic Luer lock syringe in the PDP Cleaning kit PN 4359572 with distilled or deionized water Expel any bubbles from the syringe Do not use a syringe smaller than 20 mL Doing so may generate excessive pressure within the trap Attach the syringe to the forward facing Luer fitting at the top of the pump block Hold the fitting with one hand while threading the syringe onto the fitting with the other hand Op
61. eaches 150 countries on six continents For sales office locations and technical support please call our local office or refer to our Web site at www appliedbiosystems com Applied Biosystems is committed to providing the world s leading technology and information for life scientists s 850 Lincoln Centre Drive Foster City CA 94404 USA Phone 1 650 638 5800 Toll Free In North America 1 800 345 5224 Fax 1 650 638 5884 06 2010 Applied Biosystems Part Number 4352716 Rev E
62. eaction Optimize reaction conditions resulting in uneven signal distribution Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 51 Chapter 3 Troubleshooting Run Performance Troubleshooting run performance continued Observation Possible Cause Recommended Action Low signal strength Degraded formamide Use a fresh aliquot of Hi Di formamide CHEMICAL HAZARD Formamide causes eye skin and respiratory tract irritation It is a possible reproductive and birth defect hazard Read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves Pipetting error not enough sample Increase the amount of DNA added Recalibrate the pipets Sample has high salt concentration Dilute with distilled or deionized water Desalt using a column purification method Insufficient mixing Vortex the sample thoroughly and then centrifuge the tube to condense the sample to the bottom of the tube Autosampler out of calibration Check the injection with 20 uL samples If the 20 uL samples have adequate signal levels then recalibrate the autosampler using the Autosampler Calibration Wizard Power off and on the instrument to use the new calibration values Weak amplification of DNA Reamplify the DNA Check DNA quality Elevated baseline Possible contaminant in the polymer Select the Water Wash Wizard path Possible contamina
63. ection V ersion 3 0 File View Service Tools Wizards Help gt Heb il BGA Instruments i Results Group 2 Database Manager S 3130 E2 Plate Manager Ta Protocol Manager ls Module Manager E Run History ibev E Instrument Status fi Spatial Run Schedule E Run Scheduler E capillaries Viewer BB Cap Array Viewer Spectral Viewer H Service Log No User is logged in Mak AS GA Instruments ga 3130xl iDey Manual Control Manual Control Send Defined Command For Command Name Value Range Comments K E System Status gt No Event Received No Current Run 2 Inthe Send Defined Command For drop down list select a function 3 In the Command Name drop down list select a command and enter a value if required Note The command names are filtered based the function selected in step 2 4 Click 26 Send Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Computer Maintenance Overview This chapter covers the following topics Computer Task EISS 2 424454 54505 60 eter ge eae nee e ee te ee enka eee s xe 28 Working With Drives 2 cence ene ees 28 Hard Disk and Database Status ow eee nnn 30 AE A WA 545 ace ase twee are sd ae ae Oe ee ee eae ee eae ewes eee ee 31 Defragmenting the Computer Hard Drive 0 eee 33 Deleting Records from the Database nee 34 Applied Biosystem
64. ee eee 90 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Preface How to Use This Guide Purpose of This Guide Audience Assumptions Text Conventions User Attention Words The Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide provides instructions for maintaining the Applied Biosystems 3130 3130x Genetic Analyzers It includes how to troubleshoot hardware software and chemistry issues This manual also includes reference information This manual is written for principle investigators and laboratory staff who are planning to operate and maintain the Applied Biosystems 3130 3130x Genetic Analyzers This guide assumes the following background Familiarity with Microsoft Windows XP operating system Knowledge of general techniques for handling DNA samples and preparing them for electrophoresis A general understanding of hard drives and data storage file transfers and copying and pasting If you want to integrate the 3130 3130x genetic analyzers into your existing laboratory data flow system you need networking experience This guide uses the following conventions Bold indicates user action For example Type 0 then press Enter for each of the remaining fields e Italic text indicates new or important words and is also used for emphasis For example Before analyzing always prepare fresh matrix A
65. eee ees Pe os XV Physical Hazard Safety 0 0 ccc eee tenes XV Laser Safety ned ceecuascmhaehee Sew ebws BEA REESE Re EES Cbs eee Re eed XV WorkStallon Saiely 224 4 ive cu i eewdencaw howd em teed ee ees ce eee bes Ee xvi Safety and Electromagnetic Compatibility EMC Standards xvii Maintenance 1 Polymer Delivery PUMP 222 26 otene anamannan 2 Performing Maintenance Tasks 2 000 cee eee eee eee 3 Routine Cleaning 0 ee eee eee eee 5 Resetting the Instrument 0 0 ccc eee tenes 5 Moving and Leveling the Instrument 0 00 eee T Shutting Down the Instrument 0 0 0 eens 8 WIZAIOS foo Bete ee bebe ce Been howe e oe A a ee ewe eke cane 11 Flushing and Filling the Water Trap 2 0 ces 13 FIGS and Wase tonnes oh Uae ee hee eee eee NEOR oho eee DES eas eee ee 15 Capillary Array 2202 once e620 dees bee yew Gee eee ewe ous eee en ees 18 Storing Capillary ArrayS 1 0 eee eee ene 21 Autosampler Calibration 0 0 0 eee eens 23 Manual COMO cates sche eehucae bones bees Enpi ehetes sh eee oe eat 24 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide iii Computer Maintenance 27 Computer Task LISTS iridaceae aa wot el eee ew Bsa ed we ete ee led ee ca 28 Working With Drives goscs bse cece eh ete ee bo eee ae ed eal dee hoa e ee a 28 Hard Disk and Database Status 0 0 0 cece ee ees 30 ACANDO 246 erase waive ae
66. electrodes do get bent follow the procedure Storing Capillary Arrays on page 21 IMPORTANT Never use organic solvents to clean the instrument Filling the See Fill the Capillary With Fresh Polymer Using Manual Control on page 8 Capillary Array Using Manual Control 20 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 1 Maintenance Storing Capillary Arrays Storing Capillary Arrays Storing a Capillary Array on the Instrument Store the capillary array on the instrument only when the capillary array will be unused for less than week To store the capillary array on the instrument follow the instructions to perform a short term shutdown described on page 8 Storing a Capillary Array off the Instrument Store the capillary array off of the instrument when the capillary array will be unused for longer than 1 week IMPORTANT Before storing the capillary array for long periods fill the capillaries with fresh polymer IMPORTANT Wear gloves while performing the following procedure and any other time you handle the capillary array septa or buffer reservoirs Nee CHEMICAL HAZARD POP Polymer causes eye skin and respiratory tract irritation Read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves 1 Remove the capillary array from the instrument TEREE Help by selecting Install Arra
67. en the Luer fitting by grasping the body of the fitting and turning it and the attached syringe approximately one half turn counterclockwise Open the exit fitting at the top left side of the pump block by turning it approximately one half turn counterclockwise Flushing and Filling the Water Trap Chapter 1 Maintenance e amp O Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 13 Chapter 1 Maintenance Flushing and Filling the Water Trap 6 Hold an empty tube or beaker under the exit fitting to receive approximately 5 mL of waste Flush the trap by pushing steadily on the syringe plunger IMPORTANT DO NOT USE EXCESSIVE FORCE when you push the syringe plunger as this may damage the trap seals Take approximately 30 seconds to flush 5 mL of either distilled or deionized water through the trap Note Because the water trap volume is approximately 325 uL a relatively small volume of water is adequate for complete flushing However a larger volume only improves flushing as long as force and flow rate are kept within the limits given above 7 Close the fittings in this order by turning each clockwise until the fittings seal against the block a Luer fitting b Exit fitting IMPORTANT Do not over tighten the fittings Very little pressure develops within the trap during pump operation so the fittings require only enough tightening to p
68. er DNA Sequencing Chemistry ABI Prism BigDye Primer Cycle Sequencing Kit Polymer POP 6 ABI Basecalling Run Module Basecaller DyeSet Primer RapidSeq36_POP6 Basecaller DP3130POP6 BD 3130POP6RRv2 bcp 21M13 v1 mob StdSeq50_POP6 Basecaller DP3130POP6 BD 3130POP6SR bcp 21M13Rev v1 mob 80 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 5 Reference Tables Fragment Analysis Summary Tables Fragment Analysis Summary Tables Performance Fragment Analysis Resolution Performance and Specifications Table l 24 hr Throughput GT Capillary Polymer Run Resolution Specification Run Modules Length Time Type min s ene bp ji cm Analyzer Analyzer High Throughput Small Size Fragment Analysis FragmentAnalysis22 22 POP 4 20 5 760 23 040 400 0 15 _POP4 SNP22_POP4 22 20 5 760 23 040 120 0 50 Standard Fragment Analysis FragmentAnalysis36 36 POP 4 45 2 560 10 240 500 0 15 _POP4 HIDFragmentAnalysis 45 2 560 10 240 500 0 15 36_POP4 SNP36_POP4 30 3 840 15 360 120 0 50 FragmentAnalysis36 POP 7 35 3 290 13 170 500 0 15 _POP7 FragmentAnalysis50 50 POP 4 65 1 760 7 040 500 0 15 _POP4 FragmentAnalysis50 POP 6 90 1 200 4 800 500 0 15 _POP6 FragmentAnalysis50 POP 7 50 2 300 9 220 500 0 15 _POP7 a 20 GT
69. erence Guide 89 Appendix B Instrument Warranty Information Damages Claims and Returns Damages Claims and Returns 90 Damages Claims Returns If shipping damage to the product is discovered contact the shipping carrier and request inspection by a local agent Secure a written report of the findings to support any claim Do not return damaged goods to Applied Biosystems without first securing an inspection report and contacting Applied Biosystems Technical Support for a Return Authorization RA number After a damage inspection report is received by Applied Biosystems Applied Biosystems will process the claim unless other instructions are provided Do not return any material without prior notification and authorization If for any reason it becomes necessary to return material to Applied Biosystems contact Applied Biosystems Technical Support or your nearest Applied Biosystems subsidiary or distributor for a return authorization RA number and forwarding address Place the RA number in a prominent location on the outside of the shipping container and return the material to the address designated by the Applied Biosystems representative Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Numerics 3130 basecaller and DyeSet Primer files 3130calib ini 40 79 80 A ABI PrisM BigDye Primer Cycle Sequencing Kits table dye sets and standards 77 ABI PrisM dGTP BigDye
70. eshooting 42 spectral calibration standard types 77 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 93 T technical support for computers with altered configuration 87 tests validation 49 troubleshooting failing capillaries 44 instrument startup 38 39 instrument status 39 leaks 56 password 39 plate linking 47 power override 39 run performance 50 spatial calibration 41 spectral calibration 42 using validation tests 49 yellow status light instrument 39 U Update Cap Array Info wizard 20 W warranty damages claims returns 90 exceptions 88 for computers with altered configuration 87 limitations 88 period 87 warranty claims 88 warranty exceptions 88 warranty period effective date 88 water seal illustration of 2 water trap filling 13 flushing and filling 13 illustration of 2 wizards accessing and overview 11 Autosampler Calibration 23 Bubble Remove Wizard 22 Change Polymer Type Wizard 17 Install Array Wizard 19 Instrument Shutdown 10 Replenish Polymer Wizard 17 Update Cap Array Info 20 Y yellow status light instrument 39 Z Z dye set sequencing kit table 77 94 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide www appliedbiosystems com Worldwide Sales and Support Applied Biosystems vast distribution and service network composed of highly trained support and applications personnel r
71. for or impose extra charges for supporting nonstandard computer configurations or components that have not been supplied or recommended by Applied Biosystems Applied Biosystems also reserves the right to require that computer hardware and software be restored to the standard configuration prior to providing service or technical support For systems that have built in computers or processing units installing unauthorized hardware or software may void the Warranty or Service Plan Limited Product Warranty Limited Warranty Applied Biosystems warrants that all standard components of its Applied Biosystems 3130 and 3130x Genetic Analyzers will be free of defects in materials and workmanship for a period of one 1 year from the date the warranty period begins Applied Biosystems will repair or replace at its discretion all defective components during this warranty period After this warranty period repairs and replacement components may be purchased from Applied Biosystems at its published rates Applied Biosystems also provides service agreements for post warranty coverage Applied Biosystems reserves the right to use new repaired or refurbished instruments or components for warranty and post warranty service agreement replacements Repair or replacement of products or components that are under warranty does not extend the original warranty period Applied Biosystems warrants that all optional accessories supplied with its Applied Biosystem
72. for the administrator maintaining the computer system and software files of the Applied Biosystems 3130 3 130x Genetic Analyzers e Applied Biosystems 3130 3130xl Genetic Analyzers Quick Reference Card P N 4362825 Contains a flowchart on how to run your samples and instrument a table of maintenance tasks and a Data Collection software reference guide Send Us Your Applied Biosystems welcomes your comments and suggestions for improving its user Comments documents You can e mail your comments to techpubs appliedbiosystems com How to Obtain Support For the latest services and support information for all locations go to http www appliedbiosystems com then click the link for Support At the Support page you can e Search through frequently asked questions FAQs e Submit a question directly to Technical Support e Order Applied Biosystems user documents MSDSs certificates of analysis and other related documents e Download PDF documents e Obtain information about customer training e Download software updates and patches In addition the Support page provides access to worldwide telephone and fax numbers to contact Applied Biosystems Technical Support and Sales facilities vi Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide This section covers the following topics Safety Conventions Used in This Document 0000 cee eee eee Vill Symbols on Instruments
73. h appropriate caution Indicates the presence of an electrical shock hazard and to proceed with appropriate caution Indicates the presence of a hot surface or other high temperature hazard and to proceed with appropriate caution Indicates the presence of a laser inside the instrument and to proceed with appropriate caution gt b B gt gt Indicates the presence of moving parts and to proceed with appropriate caution Safety Labels on Instruments The following CAUTION WARNING and DANGER statements may be displayed on Applied Biosystems instruments in combination with the safety symbols described in the preceding section English Francais CAUTION Hazardous chemicals Read the Material Safety Data Sheets MSDSs before handling ATTENTION Produits chimiques dangeureux Lire les fiches techniques de s ret de mat riels avant la manipulation des produits CAUTION Hazardous waste Read the waste profile if any in the site preparation guide for this instrument before handling or disposal ATTENTION D chets dangereux Lire les renseignements sur les d chets avant de les manipuler ou de les liminer CAUTION Hazardous waste Refer to MSDS s and local regulations for handling and disposal WARNING Hot lamp ATTENTION D chets dangereux Lire les fiches techniques de s ret de mat riels et la regulation locale associ es a la manipulation et l limination des d c
74. he GeneMapper software sample sheet plate record Set Application a On the plate map click a well position that represents a GeneMapper software sample b Click Sample Sheet to open the GeneMapper software Plate editor c Complete the plate record d Click OK T Create the SeqScape software sample sheet plate record a On the plate map click a well position that represents a sequencing sample b Click Sample Sheet to open the SeqScape software Plate editor c Complete the plate record d Click OK 8 Click Done Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 13 Chapter 4 Data Collection Software Advanced Functions Multi application Mixed Plate Record 14 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Reference Tables Overview This chapter covers the following topics Sequencing Summary Tables 0500000 sita cence ee eeses a e 12 Fragment Analysis Summary Tables ene I7 Run Modus Guesou en eente ereen ree a e E E E 80 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 15 Chapter 5 Reference Tables Sequencing Summary Tables Sequencing Summary Tables Performance Sequencing Resolution Performance and Specification Table 24 hr Throughput number of Capillary Polymer
75. hets AVERTISSEMENT Lampe br lante WARNING Hot Replace lamp with an Applied Biosystems lamp AVERTISSEMENT Composants br lants Remplacer la lampe par une lampe Applied Biosystems CAUTION Hot surface ATTENTION Surface br lante DANGER High voltage DANGER Haute tension X Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Safety General Instrument Safety English Francais WARNING To reduce the chance of electrical shock do not remove covers that require tool access No user serviceable parts are inside Refer servicing to Applied Biosystems qualified service personnel AVERTISSEMENT Pour viter les risques d lectrocution ne pas retirer les capots dont l ouverture n cessite l utilisation d outils L instrument ne contient aucune piece r parable par l utilisateur Toute intervention doit tre effectu e par le personnel de service qualifi de Applied Biosystems DANGER Class 3B laser radiation present when open and interlock defeated Avoid direct exposure to laser beam DANGER Class 3B laser radiation when open Avoid direct exposure to laser beam DANGER Class 3B rayonnement laser en cas d ouverture et d une neutralisation des dispositifs de s curit Eviter toute exposition directe avec le faisceau DANGER Class 3B rayonnement laser en cas d ouverture Eviter toute exposition directe avec le faisceau
76. ied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Safety Chemical Safety To obtain MSDSs 1 Go to https docs appliedbiosystems com msdssearch html 2 In the Search field type in the chemical name part number or other information that appears in the MSDS of interest Select the language of your choice then click Search 3 Find the document of interest right click the document title then select any of the following e Open To view the document e Print Target To print the document e Save Target As To download a PDF version of the document to a destination that you choose 4 To have a copy of a document sent by fax or e mail select Fax or Email to the left of the document title in the Search Results page then click RETRIEVE DOCUMENTS at the end of the document list 5 After you enter the required information click View Deliver Selected Documents Now Chemical Safety To minimize the hazards of chemicals Guidelines e Read and understand the Material Safety Data Sheets MSDS provided by the chemical manufacturer before you store handle or work with any chemicals or hazardous materials See About MSDSs on page xii e Minimize contact with chemicals Wear appropriate personal protective equipment when handling chemicals for example safety glasses gloves or protective clothing For additional safety guidelines consult the MSDS e Minimize the inhal
77. ies with standard EN 61326 Class B Electrical Equipment for Measurement Control and Laboratory Use EMC Requirements This instrument has been tested to and complies with standard AS NZS 2064 Limits and Methods Measurement of Electromagnetic Disturbance Characteristics of Industrial Scientific and Medical ISM Radio frequency Equipment XVII Safety Safety and Electromagnetic Compatibility EMC Standards xviii Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Maintenance Overview This chapter covers the following topics Pohmer Delivery PUMP o054540046 50 odadves e uveses4 beceenteweedune ees 2 Performing Maintenance Tasks 2 eens 3 Routine Cleaning 4 2522 6 ceeneeto hee es ede ee eee GA oH ee Beare ea head oan 5 Resetun p ihe ASIMMICH odtha arte aes ge eos ae we ewes eee ees cee 5 Moving and Leveling the Instrument 0 0 0 ccc eee 7 Shutting Down the Instrument 2 2 eee ees 8 WEZanGS sb ee eek aoe eed boone eh bee bbe eee whens See tee eee 11 Flushing and Filling the Water Trap 6 ees 13 PINS and Waste g4 0noseecu nad oursn IEN EEAS a deew as odds 15 Capilaty Alay wskeaveas oy we genes erates ete eee deca hwo nee es E 18 Storing Capillary Arrays 60 eee eee e eens 21 Autosampler Calibration lt 4 icace ds scadacdvavsdod bees s eed eee bcos eeGbeaes 23 Manoa COn senro eee hooded eee aoe edu eeeeeaenee bute nc 24 Applied Biosystems 3130
78. ion software guide you through several maintenance procedures nieee Help Install Array Wizard Change Polymer Type Wizard Replenish Polymer Wizard Bubble Remove Wizard Water Wash wizard Instrument Shutdown wizard Autosampler Calibration Wizard Update Cap Array Info If plates are linked in the Run Scheduler and you complete a wizard the plates automatically unlink You will get a warning dialog box Click mk and then relink the plate if applicable AN Plate s unlinked The following table lists the wizards and when to use them Wizard Use to Install Array e Install a capillary array On a new instrument To reactivate an instrument that has been shut down e Replace an installed capillary array with another capillary array Change Polymer e Change to a different polymer type than the one presently being Type used Replenish Polymer Replenish the polymer supply e Replace the polymer in the PDP with polymer of the same or different lot e Enter polymer information when Data Collection software is installed or upgraded Bubble Remove Remove bubbles in the PDP chamber channels and tubing Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 11 Chapter 1 Maintenance Wizards Wizard Use to Water Wash e Wash the PDP chamber lower polymer block channels and tubing with water As part of a monthly maintenanc
79. kin and respiratory tract irritation Read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves Pause run and inspect for bubbles hidden in the tubing connectors Select the Bubble Remove Wizard to remove the bubbles Open fresh supply of polymer and use Replenish Polymer Wizard Prepare 1X running buffer Add 3 mL 10X Genetic Analyzer Buffer with EDTA to 27 mL deionized water CHEMICAL HAZARD 10X Genetic Analyzer Buffer with EDTA may cause eye skin and respiratory tract irritation Read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves Inspect the lower polymer block for discoloration or damage Replace the lower polymer block if necessary Pause run and inspect for bubbles hidden in the tubing connectors Select Bubble Remove Wizard to remove the bubbles Check polymer blocks for leaks Tighten all fittings 54 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Troubleshooting run performance continued Observation Poor performance of capillary array used for fewer than 100 runs Migration time becomes progressively slower Migration time becomes progressively faster Possible Cause Incorrect buffer concentration Not enough buffer in anode reservoir Arcing Poor quality samples possible cleanup problems Poor qualit
80. leshooting 39 interconnect tube 2 K KB basecalling run modules 78 L laser controlling See manual control commands leaks troubleshooting 56 LED instrument status 39 length of read definition 76 leveling after moving instrument 7 LOR definition 76 loss of resolution 53 low signal strength 52 lower polymer block illustration of 2 Luer fitting illustration of 2 M maintenance tasks 3 computer 28 routine 5 manual control accessing 26 filling capillary array 8 options table 24 manual control commands 24 manually filling capillary array 8 matrix standard fragment analysis 83 migration time too fast or too slow 55 modules 60 fragment analysis 81 82 KB basecalling 78 run module tables 84 run parameters 61 sequencing 76 mounting pin illustration of 2 moving the instrument 7 N No candidate spectral files found 43 O O ring illustration of 2 oven controlling See manual control commands overflow hole illustration of 2 92 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide gt password case sensitive 39 changing 39 expired or corrupt 39 troubleshooting 39 PDP motor cover illustration of 2 peaks troubleshooting 56 piston illustration of 2 plate linking relinking 47 plate record creating multi application 69 fill down special option 65 polymer cleaning off 5 storing 16 polymer blocks bubbles 22 polymer delivery
81. n History 4 Run_David PT4_20 Regular StdSeq50_POP6_1 Validated Fo LRS E E DavidPT4 5 Run_David PT4_20 Regular StdSeq50_POP6_1 Validated E Ef instrument Status 6 Run_David PT4_20 Regular StdSeq50_POP6_1 Validated mee LR BRYEPT Chart HO LRS n E Event Log A Hil Spatial Run Scheduler A08 LRS Bj Run Scheduler Bos LRS Plate View cos LRS a E capillaries viewer pos LRS A BB capiArray Viewer i M Spectral viewer Ah Manual Control i Service Log Description System Status gt Plate SeqA_2 has been linked to Bay 0 A Seqa_2 lt a F EJ O CGC BA 1 2 3 4 s i DNAN N es ee ee ee 1 1 12 No Current Run User defined run priority schedule samples in wells A07 H08 are scheduled as Run 1 due to G07 sample assigned a value of 80 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 63 Chapter 4 Data Collection Software Advanced Functions Run Priority Scheduling The rest of the samples are run after the samples in wells AO7 H08 Samples in wells A01 H02 are now scheduled as Run 2 M SequencingAnalysis Plate Editor File Edit J Foundation Data Collection ersion 3 0 File View Instrument Service Tools Wizards Help gt E E gt A
82. n Scheduler Error 08 26 03 08 33 37 Database is full Please go to Database Manager panel to clea E Run Scheduler Error 08 26 03 08 32 57 Database is full Please go to Database Manager panel to clea S capillary Viewer Error 08 26 03 08 32 12 Database is full Please go to Database Manager panel to clea BB array TENS Error 08 26 03 08 31 10 Database is full Please go to Database Manager panel to clea a ra Error 08 26 03 08 30 23 Database is full Please go to Database Manager panel to clea E Service Log Error 08 26 03 08 29 29 Database is full Please go to Database Manager panel to clea Error 08 26 03 08 29 23 Database is full Please go to Database Manager panel to cle IEC ea Clear Errors Database full error message 28 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 2 Computer Maintenance Working With Drives Disk Drive Full Error To view the error messages click A GA Instruments gt E ga3130 or ga3130xl1 gt g instrument name gt E Instrument Status gt EJ Event Log fi Foundation Data Collection ersion 3 0 File View Service Tools Wizards Help gt BB B A GA Instruments 18 x Administrator user is logged in GA Instruments ga3130 DavidPTS Instrument Status Event Log W Resutts Group t Database Manager Event Messages BE ga3130x1 22 Plate Manager Date Tim
83. n Special Option Based on your plate type 96 or 384 well and capillary array 16 or 4 capillaries the software automatically fills in the appropriate well positions for a single run The Fill Down Special option works with all plate records Spectral Sequencing Analysis SeqScape software GeneMapper software and Mixed plates Creating and Completing the Plate Record 1 In the tree pane of the Data Collection software click GA Instruments gt E ga3130 or ga3130xl gt 22 Plate Manager 2 Click New to open the New Plate Dialog dialog box 3 Complete the information in the New Plate Dialog box then click Ok to open the Plate Editor 4 Complete the columns for a single well position Note You can start at any well position the software automatically fills up or down based on the default run scheduling patterns 5 Highlight the entire row MA spectral Calibration Plate Editor File Edit Operator ba s S Owner ba s S ell Sample Name Comment Priority Instrument Protocol 1 Plate Name Plate Sealing Septa 100 poy a _z_50cm KO1 xi Description Ok Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 65 Chapter 4 Data Collection Software Advanced Functions Edit gt Fill Down Special Option for Plate Records 6 Select Edit gt Fill Down Special Edit Fill Down Ctrl D Copy Ckrl Z Paste Ctrl
84. nalyzers Maintenance Troubleshooting and Reference Guide 9 Chapter 1 Maintenance Shutting Down the Instrument 7 Place the reservoirs into position on the autosampler as shown below 8 Close the instrument doors Note Closing the doors returns the autosampler to the home position placing the tips of the capillaries in buffer 9 Shut down the computer and turn off the instrument Performing a Long Term Shutdown Select Instrument Shutdown Wizard and follow the prompts IMPORTANT Make sure all parts are completely dry before long term storage ee ee Water reservoir Water reservoir waste i rinse eS aani an amn ana an a an i a an a a ai T T Cathode reservoir 1X running buffer D e e e e e e l i i i ee Ma Home position niee Help Install Array Wizard Change Polymer Type Wizard Replenish Polymer Wizard Bubble Remove Wizard Water Wash wizard Instrument Shutdown Wizard Autosampler Calibration Wizard Update Cap Array Info 10 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Wizards Accessing Wizards General Use Guidelines Chapter 1 Maintenance Wizards In the tree pane of the Data Collection software click GA Instruments gt E ga3130 or ga3130x gt amp instrument name or any topic name below instrument name to see Wizards in the menu bar The wizards in the Data Collect
85. nd then repeat the run 44 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Troubleshooting failing capillaries continued If All Capillaries Fail Viewing the Raw Data for a Failed Spectral Calibration 1 In the tree pane of the Data Collection software click amp GA Instruments gt ga3130 or ga3130x gt 3 instrument name gt ii Spectral Viewer then review the spectral data You observe The window displays data from the previous passing spectral calibration This System Status is blinking red 2 Click EJ Instrument Status gt Event Log to view the Event and Errors messages 3 Click fi Spectral Viewer 4 In the Dye Set drop down list select the dye set for the failed calibration 5 In the List of Calibrations drop down list select the failing run The failing run has a asterisk next to its name Chapter 3 Troubleshooting Spectral Calibration System Status Event Messages lf all capillaries fail no spectral profiles are created However the raw data can still be viewed System failure check Event Log Type W Info Info Error Info into Info Info Info Info into _ Error Messages Date 09 1 5 03 09 15 03 09 1 5 03 09 15 03 09 1 5 03 09 15 03 09 1 5 03 09 15 03 09 15 03 09 1 5 03 ami minm Time 15 18 19 15 18 19 16 18 18 15 18 18 16 18 16
86. nditions as a Class 3B laser The Applied Biosystems 3130 3130x Genetic Analyzers has been tested to and complies with 21 CFR 1040 10 and 1040 11 as applicable The 3130 3130x Genetic Analyzers have been tested to and complies with standard EN60825 1 Radiation Safety of Laser Products Equipment Classification Requirements and User s Guide Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide XV Safety Workstation Safety Laser Safety Requirements Additional Laser Safety Information To ensure safe laser operation e The system must be installed and maintained by an Applied Biosystems Technical Representative e All instrument panels must be in place on the instrument while the instrument is operating When all panels are installed there is no detectable radiation present If any panel is removed when the laser is operating during service with safety interlocks disabled you may be exposed to laser emissions in excess of the Class 3B rating e Do not remove safety labels or disable safety interlocks Refer to the user documentation provided with the laser for additional information on government and industry safety regulations ASIII LASER HAZARD Lasers can burn the retina causing permanent blind spots Never look directly into the laser beam Remove jewelry and other items that can reflect the beam into your eyes Do not remove the instrument top or front p
87. nt or crystal deposits Bring the polymer to room temperature swirl to in the polymer dissolve any deposits Replace the polymer if it has expired CHEMICAL HAZARD POP 4 POP 6 and POP 7 polymer cause eye skin and respiratory tract irritation Read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves Poor spectral calibration Perform new spectral calibration 52 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Troubleshooting run performance continued Observation Possible Cause Loss of resolution Too much sample injected Poor quality water Poor quality or dilute running buffer Degraded polymer Capillary array used for more than 100 injections Degraded formamide High salt concentration in samples Poor resolution in some Insufficient filling of capillary array capillaries Poor quality samples Chapter 3 Troubleshooting Run Performance Recommended Action Dilute the sample and re inject Use distilled or deionized water Prepare fresh running buffer from 10X 3130 buffer with EDTA CHEMICAL HAZARD 10X Genetic Analyzer Buffer with EDTA may cause eye skin and respiratory tract irritation Read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves Use a fresh supply of polymer Replace with new capillary array Prep
88. ollow the handling instructions Wear appropriate protective eyewear clothing and gloves No signal Incorrect preparation of sample Bubbles in sample tray Autosampler not correctly aligned The capillary tips may be hitting the bottom of the wells or they may not be touching the samples Centrifuge samples to remove bubbles Check the autosampler calibration If necessary recalibrate the autosampler using the Autosampler Calibration Wizard 42 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Troubleshooting spectral calibration continued Observation If the spectral calibration fails or if a message displays No candidate spectral files found Data Error One or more peaks fall below the minimum required amplitude of 750 Spikes in the data or Bad dye order detected error message Possible Cause Blocked capillary Incorrect chemistry file dye set and or run module selected Insufficient filling of array Expired matrix standards or old reagents One or more peaks fall below the minimum required amplitude of 750 Expired polymer Bubbles in the polymer system Possible contaminant or crystal deposits in the polymer Chapter 3 Troubleshooting Spectral Calibration Recommended Action Refill capillary array You may have to install a fresh array or consider that capillary non usable for purposes of
89. on for the dye set and array length combination see Activating a Spectral Calibration in the Applied Biosystems 3130 3 130xl Genetic Analyzers Getting Started Guide T Relink plate s if applicable Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 19 Capillary Array Chapter 1 Maintenance Updating Use the Update Cap Array Info wizard to Capillary Array Information Update the capillary array length and serial number information into the database Correct an entry error after using another wizard IMPORTANT The capillary array length defined in the wizard must match the array length you are using Caring for the Follow these guidelines to properly care for the capillary array and area Capillary Array and Work Area Wear gloves and handle the capillary array gently Do not touch the detection cell Keep the ends of the capillary array wet at all times Do not overtighten the capillary array knob Clean off any polymer buildup crystals on the instrument including the capillary electrodes and the stripper plate with deionized water and lint free tissue Nore CHEMICAL HAZARD POP polymer causes eye skin and respiratory tract irritation Read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves Note When cleaning the capillary electrodes be careful not to bend them out of position If the
90. osystems or obtained by using Authorized reagents purchased from Authorized suppliers in accordance with the label rights accompanying such reagents Purchase of this instrument does not itself convey to the purchaser a complete license or right to perform the above processes This instrument is also licensed under U S patent claims and apparatus and system claims in foreign counterparts thereof No rights are granted expressly by implication or by estoppel under composition claims or under other process or system claims owned or licensable by Applied Biosystems For more information regarding licenses please contact the Director of Licensing at Applied Biosystems 850 Lincoln Centre Drive Foster City California 94404 USA Applied Biosystems 3130 and 3130x Genetic Analyzers Covered by one or more of U S Pats Nos RE37 606 RE37 941 NOTICE TO PURCHASER The purchase price of this Applied Biosystems 3130 3130x Genetic Analyzer includes a grant of a limited non transferable license under U S patent claims and method claims of its foreign counterparts and element claims of its foreign counterparts to use this particular instrument for electrophoresis methods employing fluorescence as a means of detection No other licenses or rights are hereby conveyed either expressly by implication or estoppel including but not limited to any claims to a composition The Applied Biosystems 3130 3130x Genetic Analyzers include patented technology licensed
91. pump PDP illustration 2 water trap 13 polymer supply bottle cap with hole illustration of 2 polymer supply bottle illustration of 2 polymer supply tube illustration of 2 power override enabled 39 triggers 39 troubleshooting 39 priority scheduling 62 pump block illustration of 2 pump chamber illustration of 2 R RA number 90 RA number See return authorization number red status light 38 removing bubbles 22 Replenish Polymer Wizard 17 reporting damages 90 reservoirs cleaning 10 positions on the autosampler 10 resetting the instrument 5 resolution fragment analysis 81 resolution loss 53 return authorization RA number 90 returning damaged items 90 returns 90 Roxio Easy CD accessing 31 elevated baseline 52 elevated current 54 fast migration time 55 fluctuating current 54 high signal 51 loss of resolution 53 low signal 52 no current 54 no signal 51 parameter ranges 61 priority scheduling 62 slow migration time 55 run module 84 customizing 60 tables 84 run time fragment analysis 81 Run validation tests 49 S scheduling run priority 62 sequencing run modules 84 specifications 76 shut down 8 shutdown 10 signal too high 51 spatial calibration persistently bad results 41 troubleshooting 41 unusual peaks 41 specifications fragment analysis 81 sequencing 76 spectral calibration deleting a 35 if a capillary fails 44 if all capillaries fail 45 no signal 42 override capillaries 44 troubl
92. r Initialize N A A number between 500 and 500 steps Move autosampler to site e Buffer left front for 1X running buffer home position e Water left rear for deionized water e Water right front for deionized water e Waste right rear for deionized water 24 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 1 Maintenance Manual Control Command Function Command Options Value Polymer Deliver Pump Initialize polymer delivery pump Home piston Read piston position Move piston down N A 1 to 38000 counts Move piston up 1 to 38000 counts Fill capillary array 1 to 38000 counts Buffer Valve Close Open buffer e Close valve e Open Detection Cell Heater Turn On Off e On detection cell e Off heater Read detection cell N A heater temperature Oven Turn On Off oven e On e Off Set oven A number between 18 and 70 C temperature Read oven N A temperature Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 25 Manual Chapter 1 Maintenance Control Using Manual Control Note Manual control functions cannot be used during a run 1 In the tree pane of the Data Collection software click GA Instruments gt E ga3130 or ga3130x gt J instrument name gt Manual Control Foundation Data Coll
93. ra r Grate ears ee ata ee Barra eae eee ae 31 Defragmenting the Computer Hard Drive 0 0 00 eee 33 Deleting Records from the Database 2 0 ccc es 34 Troubleshooting 37 mstrument SLANG DS aiaa paai aa a edule XB wha ated ak ey ae WA elec we ea a 38 ISCHMIM Cit StatUS mirare Tee ack seaaea ce hacen Gat asians kota a oo TANA 39 Spatial Calibration rrai sass G ocas ce AEA ad See we Gee Sean RA 41 Spectral Calibration srr dea eae atin a Paar de eae AA 42 PAG LIKING crore ast Bate ease Seater ee tees Uae WS Ae ee ee ae ee 47 RUMPErOrmMaNCE sik tina iyi Yd nl tare sy Rep hata tod ane deed er ied Ge wh Bae aye ey 49 Data Collection Software Advanced Functions 59 Customizing Run Modules c2 0 4 sen 22g Seah oe ta ooo WENGER ee ees 60 R n Priority Scheduling sisisrscers bo eb Stee weed edad ooo es Mee ee eee eo 62 Edit gt Fill Down Special Option for Plate Records 2 0 0 c eee eae 65 Multi application Mixed Plate Record 0 0 cee ee ees 69 Reference Tables 75 Sequencing Summary Tables 0 00 ee ees 76 Fragment Analysis Summary Tables 0000 cece eee eee 81 PALI MOOUGS gees 22 veer Seed cence tee ps es ee Ae oes Ba eee Sh ae Bee a 84 Parts List 85 Instrument Warranty Information 87 Computer Configuration resim sanra eran han REEE E Ee eee ew ek Eee ee as 87 Limited Product Waranty ecto wars cS Pisranaid odri ene eee Re hes Eee Gara wae 87 Damages Claims and Returns 0 0 ccc
94. ration fails again 1 Fill the capillaries with polymer 2 Repeat the spatial calibration Check for a broken capillary particularly in the detection cell area If necessary replace the capillary array using the Install Array Wizard Replace the capillary array and then repeat the calibration Call Technical Support if the results do not improve Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 41 Chapter 3 Troubleshooting Spectral Calibration Spectral Calibration Tip Magnifying the Spectral Profile or Raw Data 1 In the tree pane of the Data Collection software click 1 0 GA Instruments gt E ga3130x or 0 8 ga3130 gt J instrument 0 6 name gt Spectral Viewer 0 4 2 In the spectral profile or raw data display ue click drag the cursor to create a box Hus around the area of interest fensity vs Pixel Number 3 Release the mouse button The Data Collection software displays the selected region 4 Press the r key to reset the view pou Pixel Number Magnified area of that spectral profile Troubleshooting spectral calibration Observation Possible Cause Recommended Action Replace samples with fresh samples prepared with fresh Hi Di formamide CHEMICAL HAZARD Formamide causes eye skin and respiratory tract irritation It is a possible reproductive and birth defect hazard Read the MSDS and f
95. rch Map Network Drive Disconnect Network Drive Create Shorkcut Rename Properties gt ve Wia Drives Aahe i Bepa y volume Session Status File System Capacity Free Space Free Space 6 001 ME 4 640 ME 10308 52 543 MB _55 003MB 42 504 MB 76 59 435 MB 32 039 MB D Fragmented fies M Contiguous files E System fies Free space Defragmentation Complete E 2 x Defragmentation is complete For DC E View Report Close Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 33 Chapter 2 Computer Maintenance Deleting Records from the Database Deleting Records from the Database Deleting Processed Frame Data N or Neale The Cleanup Database utility deletes all run data and plate records in the database Before running the utility be sure that all runs have been extracted from the database 1 In the tree pane of the Data Collection software click GA Instruments gt j Database Manager to view the Database Manager Foundation Data Collection Version 3 0 No User is logged in me View Help AS BGA Instruments LE Results Group Database Manager E ga3130xl GA Instruments Database Manager Database Status Run Status Database is 0 full Cleanup Processed Plate There are 3 runs in the database Free Disk Space S
96. rd 4336935 GeneScan 120 LIZ Size Standard 4324287 GeneScan 500 LIZ Size Standard 4322682 GeneScan 500 ROX Size Standard 401734 GeneScan HD400 ROX Size Standard 402985 Hi Di Formamide 4311320 Matrix Standard DS 01 4315974 Matrix Standard DS 02 4323014 Matrix Standard DS 30 4345827 Matrix Standard DS 31 4345829 Matrix Standard DS 32 4345831 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 85 86 Appendix A Parts List Spare Parts Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Description Part Number Matrix Standard DS 33 4345833 Performance Optimized Polymer 4 POP 4 Polymer 4316355 Performance Optimized Polymer 6 POP 6 Polymer 4352757 Performance Optimized Polymer 7 POP 7 Polymer 4352759 Description Part Number Array comb holders 628 0164 Array port plug 628 3776 Buffer reservoir 16 mL 4358351 Buffer water waste reservoir 628 0163 Ferrule knob 628 3730 Ferrule sleeves 628 0165 Polymer bottle 4362387 Polymer tubing assembly 628 3732 Septa strip buffer reservoir 4315932 Instrument Warranty Information Computer Configuration Applied Biosystems supplies or recommends certain configurations of computer hardware software and peripherals for use with its instrumentation Applied Biosystems reserves the right to decline support
97. revent water leaks Excessive tightening can damage the fittings c Remove the syringe from the Luer fitting Hold the fitting with one hand while turning the syringe counterclockwise with the other hand 14 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Fluids and Waste When to Change the Buffer Nem CHEMICAL HAZARD 10X Genetic Analyzer Buffer with EDTA may cause eye skin and respiratory tract irritation Read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves Change the buffer before each batch of runs or at least every 24 hours Making Buffer for a Single Run To prepare 50 mL of 1X running buffer 1 Add 5 mL of 10X Genetic Analyzer buffer into a graduated cylinder 2 Add deionized water to bring the total volume up to 50 mL 3 Mix well Storing the Buffer The 1X running buffer can be stored at e 2 to 8 C for up to 1 month e Room temperature for 1 week Chapter 1 Maintenance Fluids and Waste 50 mL graduated cylinder Buffer Storage Conditions 45 mL DI H O 5 mL 10X Genetic Analyzer buffer Option A Option B 2 C to 20 C to 8 C 25 C SuM TWThF S SuM TWThF S S 1 month 7 days Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 15
98. right arrow bracket gt separates successive commands you select from a drop down or shortcut menu For example Select File gt Open gt Spot Set Right click the sample row then select View Filter gt View All Runs Two user attention words appear in Applied Biosystems user documentation Each word implies a particular level of observation or action as described below Note Provides information that may be of interest or help but is not critical to the use of the product IMPORTANT Provides information that is necessary for proper instrument operation accurate chemistry kit use or safe use of a chemical Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide V Preface How to Obtain More Information How to Obtain More Information Related The following related document is shipped with the system Documentation e Applied Biosystems 3130 3130xl Genetic Analyzers Getting Started Guide P N 4352715 Contains procedures and information to start a run using the instrument system e Applied Biosystems 3130 3130xl Genetic Analyzers Site Preparation Guide P N 4352717 Contains the space environmental and electrical requirements to support the 3130 3130xI Genetic Analyzer system e Applied Biosystems 3730 3730xl DNA Analyzers and Applied Biosystems 3130 3130x Genetic Analyzers AB Navigator Software Administrator Guide P N 4359472 Provides information and procedures
99. rt then Software Downloads then Applied Biosystems 3130 3130xI Genetic Analyzer then Updaters and Patches To install the patch follow the instructions in the Read Me pdf file 50 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 3 Troubleshooting Run Performance Troubleshooting run performance continued Observation Possible Cause Recommended Action No signal Autosampler calibration is not optimal Check the injection with 20 uL samples e fthe 20 uL samples have adequate signal level then recalibrate the autosampler using the Autosampler Calibration Wizard IMPORTANT You must power on the instrument to use the new values e fthe 20 uL samples still have no signal then check the other possible causes Bubble at bottom of sample tube Centrifuge the sample tubes Bent capillary array tips Replace the capillary array and recalibrate the autosampler using the Autosampler Calibration Wizard Failed reaction Repeat reaction Cracked or broken capillary Visually inspect the capillary array including the detector window area for signs of breakage No signal Blocked capillary Refill capillary array You may have to install a fresh array or consider that capillary non usable for purposes of planning your runs Signal too high Sample concentration is too high Dilute the sample Decrease the injection time Too much DNA added to the r
100. s not supplied or authorized by Applied Biosystems and modification or repair of the product not authorized by Applied Biosystems THE FOREGOING PROVISIONS SET FORTH Applied Biosystems SOLE AND EXCLUSIVE REPRESENTATIONS WARRANTIES AND OBLIGATIONS WITH RESPECT TO ITS PRODUCTS AND APPLIED BIOSYSTEMS MAKES NO OTHER WARRANTY OF ANY KIND WHATSOEVER EXPRESSED OR IMPLIED INCLUDING WITHOUT LIMITATION WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE WHETHER ARISING FROM A STATUTE OR OTHERWISE IN LAW OR FROM A COURSE OF DEALING OR USAGE OF TRADE ALL OF WHICH ARE EXPRESSLY DISCLAIMED THE REMEDIES PROVIDED HEREIN ARE THE BUYER S SOLE AND EXCLUSIVE REMEDIES WITHOUT LIMITING THE GENERALITY OF THE FOREGOING IN NO EVENT SHALL APPLIED BIOSYSTEMS BE LIABLE WHETHER IN CONTRACT TORT WARRANTY OR UNDER ANY STATUTE INCLUDING WITHOUT LIMITATION ANY TRADE PRACTICE UNFAIR COMPETITION OR OTHER STATUTE OF SIMILAR IMPORT OR ON ANY OTHER BASIS FOR DIRECT INDIRECT PUNITIVE INCIDENTAL MULTIPLE Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Appendix B Instrument Warranty Information Limited Product Warranty CONSEQUENTIAL OR SPECIAL DAMAGES SUSTAINED BY THE BUYER OR ANY OTHER PERSON OR ENTITY WHETHER OR NOT FORESEEABLE AND WHETHER OR NOT APPLIED BIOSYSTEMS IS ADVISED OF THE POSSIBILITY OF SUCH DAMAGES INCLUDING WITHOUT LIMITATION DAMAGES ARISING FROM OR RELATED TO LOSS O
101. s 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 2 Chapter 2 Computer Maintenance Computer Task Lists Computer Task Lists Weekly Tasks Perform this task at least once per week Maintenance Task Frequency Check database space Weekly Delete plate records from the instrument database and archive sample files Restart the computer and instrument Working With Drives Checking Before a run or batch of runs the Data Collection software checks the space on drives C Available Space D E and F to ensure that there is sufficient space to store the newly created database and on All Drives sample file data The Data Collection software sends a warning message e Remove data the drive is getting full e Clean up the database when the database is getting full 70 to 75 of capacity View the Errors pane s Instrument Status window for generated errors and in the Event Log window Also check the status light in the bottom left hand corner of the data collection window to see if it flashes red Full Database To view the error messages click GA Instruments gt E ga3130 or ga3130x gt Error instrument name gt EA Instrument Status gt Event Log re eee s 3 6 3130 Error Messages EI gat ie Type Date Time Publisher Description ET Error 08 26 03 08 34 11 Database is full Please go to Database Manager panel to clea fifi Spatial Ru
102. s 3130 and 3130x Genetic Analyzers such as peripherals printers and special monitors will be free of defects in materials and workmanship for a period of ninety 90 days from the date the warranty begins Applied Biosystems will repair or replace at its discretion defective accessories during this warranty period After this warranty period Applied Biosystems will pass on to the buyer to the extent that it is permitted to do so the warranty of the original manufacturer for such accessories With the exception of consumable and maintenance items replaceable products or components used on or in the instrument are themselves warranted to be free of defects in materials and workmanship for a period of ninety 90 days Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 87 Appendix B Instrument Warranty Information Limited Product Warranty Warranty Period Effective Date Warranty Claims 88 Warranty Exceptions Warranty Limitations Applied Biosystems warrants that chemicals and other consumable products will be free of defects in materials and workmanship when received by the buyer but not thereafter unless otherwise specified in documentation accompanying the product Applied Biosystems warrants that for a period of ninety 90 days from the date the warranty period begins the tapes diskettes or other media bearing the operating software of the product if any will be fre
103. spectral calibration dialog box enter a new name then click Save 8 Select the just saved spectral calibration and click Set to activate the spectral calibration When a Calibration Fails following e Verify the freshness of the reagents used 4 Select a new capillary value from the drop down list If a capillary fails it is automatically assigned the spectral profile of its nearest passing capillary For applications where pull up and pull down peaks cause critical errors repeat the spectral calibration and use a unique spectral for each capillary array length and polymer type AQ Dye Set z Bigdyev3 z Matrix used tor Capillary 10 10 yt Condition 3 673966 Poma _ Capillary 10 G Value 0 977386 selected Poot lo Override Spectral D H12 fi override Spectral x Matrix used for Capillary 10 10 Ahat capillary do you want to override with Capillary Data Wed Dye Set Z BigDyeV3 Matrix used for Capillary 10 9 Active Calibration for Dye Set Z BigDye V3 wed Jun 04 14 28 16 PDT 2003 Condition 3 652025 List of Calibrations for Dye Set Z BigDye V3 wed Jun 04 14 28 16 PDT 2003 r Q Value 0 976264 Please enter a unique name to save n If the spectral calibration failed or if you do not like the appearance of the passed calibration try one or more of the e Verify that the correct chemistry and run module were selected If not correct a
104. tabase utility 34 communication cable must be original 40 replacing 40 computer checking hard drive space 30 configuration requirement 87 frozen 38 technical support for altered configuration 87 current troubleshooting 54 customizing 60 D damage reporting 90 damaged items returning 90 data archiving 31 none in capillaries 50 Data Collection software will not launch 38 Data Explorer software 3130calib ini file 40 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 91 database checking disk space 30 deleting records 34 error messages 28 defragmenting hard drive 33 double tapered ferrule illustration of 2 drive checking available space 28 cleaning 29 defragmenting 33 dye primer chemistry information table 80 dye set fragment analysis 83 Dye Terminator chemistry files 78 79 DyeSet Primer files 78 79 80 E E dye set sequencing kit table 77 electrode illustration of 2 elevated baseline 52 error messages 28 viewing 29 event log accessing 29 event viewer blank 38 F failing capillaries 44 fill down special option 65 filter set fragment analysis 82 flushing water trap 13 fragment analysis filter set 82 kit types 82 run modules 84 H hard drive space checking 30 hard drive defragmenting 33 Install Array Wizard 19 instrument cleaning routine 5 moving and leveling 7 resetting 5 shutdown 8 instrument status troub
105. table describes the electrical symbols that may be displayed on Applied Biosystems instruments Symbol Description Indicates the On position of the main power switch Indicates the Off position of the main power switch Indicates the On Off position of a push push main power switch Indicates a terminal that may be connected to the signal ground reference of another instrument This is not a protected ground terminal Indicates a protective grounding terminal that must be connected to earth ground before any other electrical connections are made to the instrument Indicates a terminal that can receive or supply alternating current or voltage Indicates a terminal that can receive or supply alternating or direct current or voltage Iil D OO Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Ix Safety Safety Labels on Instruments Safety Symbols The following table describes the safety symbols that may be displayed on Applied Biosystems instruments Each symbol may appear by itself or in combination with text that explains the relevant hazard see Safety Labels on Instruments on page x These safety symbols may also appear next to DANGERS WARNINGS and CAUTIONS that occur in the text of this and other product support documents Symbol Description Indicates that you should consult the manual for further information and to proceed wit
106. tatus Disk Drive Free Disk Space MB 1059 D 54790 lE 49999 F 40217 G lo 2 Click Cleanup Processed Plates The following dialog box opens Cleanup Database m xj 2 The cleanup will delete all the regular processed plates and the associate run records from the database This action cannot be undone Cancel 3 Click oK Note The spatial and spectral calibrations are not deleted Note It may take several minutes to clean up the database 1f it contains a lot of data or is full 34 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 2 Computer Maintenance Deleting Records from the Database Deleting a Spectral Calibration e Spectral calibrations can be deleted by deleting the spectral plate associated with the spectral calibration only after deleting all processed plates associated with the spectral plate Processed plates are associated with a spectral plate if the plates used the spectral plate s calibration as the active calibration when it was processed e Delete spectral plates that are not associated with any processed plates directly in the Plate Manager Option one Delete a spectral plate after performing the Cleanup processed plate procedure Note Use this option if you want to delete many spectral plates and you don t mind deleting all processed plate data from the database 1 Clean up all processed plates
107. te Linking gee heeh he da ene e ned hee cndephee 2650s HE de REE See Ee Ses 47 R n Pemommance ssgrcaeass weno ds ev eeaceeu os aoe eos nee aeeeseaeenes 49 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 37 Chapter 3 Troubleshooting Instrument Startup Instrument Startup Troubleshooting instrument startup see also Instrument Status on page 39 Observation Possible Cause Recommended Action No communication between the Incorrect Ethernet configuration Check the configuration of the IP address instrument and the computer 1 Select Start gt All Programs gt Accessories gt The event viewer is blank a g Command Prompt 2 At the CA prompt type IPconfig all 3 Press Enter The command prompt window displays information on the network 4 Ensure the IP address for Ethernet adapter 1 is set for the machine i e the motherboard Ethernet connection The correct IP address is 192 168 0 1 Note The local IT group should use Adapter 2 for networking Instrument red light is blinking Incorrect start up procedure Start up in the following sequence 1 Log out of the computer 2 Turn off the instrument 3 Boot up the computer 4 After the computer has booted completely turn the instrument on Wait for the green status light to come on 5 Launch the Data Collection software Data Collection software will not Applications in the Service
108. the Applied Biosystems 3130 Genetic Analyzer Software v2 0 and v3 0 look in C AppliedBiosystems Firmware If the problems persists contact Applied Biosystems Technical Support or Technical Assistance Center 40 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Spatial Calibration Troubleshooting spatial calibration Observation Start Spatial Calibration button is disabled Unusual peaks or a flat line for the spatial calibration Persistently bad spatial calibration results Possible Cause Communication failure between the Data Collection Software and Sequencing Instrument The instrument may need more time to reach stability An unstable instrument can cause a flat line with no peaks in the spatial view Improper installation of the detection cell Broken capillary resulting in a bad array fill Bad capillary array Chapter 3 Troubleshooting Spatial Calibration Recommended Action Install Software Patch CE_DC_300 002 To download the patch go to http www appliedbiosystems com then click the link for Support then Software Downloads then Applied Biosystems 3130 3130xl Genetic Analyzer then Updaters and Patches To install the patch follow the instructions in the Read Me pdf file Repeat the spatial calibration Reinstall the detection cell to reposition and make sure it fits in the proper position If the calib
109. the instrument avoid any shock or vibration 4 Move the instrument 5 Place the bubble level on the autosampler deck 6 Turn the instrument legs to level the instrument i To move the Turn the leg instrument corner up right clockwise down left counterclockwise Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide T Chapter 1 Maintenance Shutting Down the Instrument Shutting Down the Instrument Perform the appropriate shutdown procedure based on the information in the following table If the instrument will be unattended for Perform this shutdown procedure no more than 1 week with a full Short term puneligsen Ol IMPORTANT The key to a successful short term shutdown is keeping the capillary array in 1X running buffer This prevents the polymer from drying in the capillaries for more than 1 week Long term Performing a Short Term Shutdown Fill the Capillary With Fresh Polymer Using Manual Control 1 Ensure the oven and instrument doors are closed 2 Collect polymer waste a Click A GA Instruments gt E ga3130 or ga3130x J instrument name gt Manual Control b In the Send Defined Command drop down menu select Autosampler c In the Command Name drop down menu select Move autosampler to site d In the Value menu select Waste e Click Send Command Wait for the autosampler to stop mo
110. the tree pane of the Data Collection software Ei gh GA Instruments click GA Instruments gt E ga3130 or ove Resutts Group ga3130x gt 3 Plate Manager Coe sa ee Plate Manager n Ty Protocol Manager j Hj Module Manager E E Run History H E David PTS 2 Click _New The New Plate Dialog dialog box opens 3 Complete the information in the New Plate Dialog a Type a name for the plate b Type a description for the plate optional New Plate Dialog i R Marne c Select Mixed in the Application drop down m oe list 3b d Select 96 well or 384 well in the Plate Type drop down list Application none l 3c e Type a name for the owner and operator ao EZ 3d f Click OF Owner Marne o 3e Operator Mame D Sf OK Cancel The Integrated Plate Dialog box opens integrated Plate Dialog xl _ l a ae Owner Name bp t lt sCS Operator Name bp tst lt sCS H12 Application Onne sf Sample Sheet Done 70 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 4 Data Collection Software Advanced Functions Multi application Mixed Plate Record 4 Inthe Set Application pane Set Application 4 a a On the plate map click a well position The ADI run of 16 or 4 capillaries is outlined oo ll b In the Application drop down list select the BERR e eY e
111. ving and Send Command becomes active before proceeding 3 Fill the capillaries a In the Send Defined Command for drop down menu select Polymer Delivery Pump 8 Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide Chapter 1 Maintenance Shutting Down the Instrument b In the Command Name select the appropriate Fill lt length gt cm capillary array length c Click Send Command The array fill is finished when Send Command becomes active d Return the buffer reservoir to the capillaries Cleaning the Reservoirs 1 Press the Tray button to move the autosampler forward 2 Open the doors then remove the e Plates e Cathode buffer reservoir and water reservoirs 3 Dispose of remaining fluids and rinse out the reservoirs with deionized water Note Follow your company s waste disposal practices for appropriate disposal procedures 4 Rinse the cathode reservoir with 1X running TT buffer and then fill to the line with 1X running buffer about 16 mL Fill line 5 Fill the three water reservoirs to the line with quality deionized water about 16 mL N o7 Be sure that the septa fit snugly and flush on the tops of the reservoirs in order to prevent damaging the capillary tips 6 Place a clean reservoir septa on each reservoir and dry the outside of the reservoirs using a lint free wipe Applied Biosystems 3130 3130x Genetic A
112. w Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 39 Chapter 3 Troubleshooting Instrument Status Troubleshooting instrument status see also Instrument Startup on page 38 continued Observation Possible Cause Recommended Action The yellow light in the LED panel The original communication e Only the communication cable shipped with the on the bottom left hand corner cable is loose has been instrument can be used as it is specifically of the instrument remains solid replaced with a standard cable designed for the instrument yellow continued or is improperly attached e Confirm that the original communication cable is attached snugly with the computer labeled end attached to computer and instrument labeled end attached to instrument Computer network configuration Confirm the following are unchanged otate Nast nanged e The name of the computer workstation e The firewall antiviral software on the computer workstation e The original IP address of the computer network card e The computer configuration for network access e The Operating System Service Pack The instrument software can not Confirm that the Instrument Data Collection find the 3130calib ini file Software 3130calib ini file is in the appropriate location e For the Applied Biosystems 3130 Genetic Analyzer Software v1 0 look in C 3130 Firmware e For
113. y Wizard Install Array Wizard 2 Select Store Array and follow the prompts Change Polymer Type Wizard Replenish Polymer Wizard 3 Replace the cover over the detection cell Bubble Remove wizard Water Wash Wizard 4 Fill a buffer reservoir with fresh 1X running ipeeramene shutdnaniiisard buffer and cover with a septa strip Insert the aaa Autosampler Calibration wizard capillary tips into the buffer Update Cap Array Info 5 Fill the shipping vial with fresh 1X running buffer and insert the detection end of the capillary array Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 21 Chapter 1 Maintenance Storing Capillary Arrays 6 Store the capillary array upright Check the 1X running buffer level in the reservoir and tube weekly and replenish the buffer as needed Removing Bubbles from the Polymer Blocks Bubbles may be found in the polymer system especially after a polymer change or array installation Remove the bubbles from all parts of the polymer system including the pump chamber the pump block channel polymer supply and interconnect tubing and the lower polymer block channel To clear bubbles 1 Select Wizards gt Bubble Remove Wizard to clear bubbles Install Array Wizard IMPORTANT Remove bubbles from the G interconnect tubing and the channel of the lower Replenish Polymer Wizard polymer block These areas are part of the Bub
114. y formamide Incorrect buffer Leak in system Improper filling of the system with polymer Expired polymer Water in polymer system resulting in diluted polymer Buffer valve leakage Chapter 3 Troubleshooting Run Performance Recommended Action Prepare 1X running buffer Add 3 mL 10X Genetic Analyzer Buffer with EDTA to 27 mL deionized water CHEMICAL HAZARD 10X Genetic Analyzer Buffer with EDTA may cause eye skin and respiratory tract irritation Read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves Add buffer up to the fill line Check for moisture in and around the septa the reservoirs the oven and the autosampler Desalt samples using a recommended purification protocol Prepare fresh Hi Di formamide and re prepare samples CHEMICAL HAZARD Formamide causes eye skin and respiratory tract irritation It is a possible reproductive and birth defect hazard Read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves Use 10X Genetic Analyzer Buffer with EDTA to prepare 1X running buffer CHEMICAL HAZARD 10X Genetic Analyzer Buffer with EDTA may cause eye skin and respiratory tract irritation Read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves Tighten the tubing connectors and array knob Polymer delivery pump ma
115. y need to be serviced Call a service representative Check expiration of polymer If necessary change the lot Use Bubble Remove Wizard to add polymer to system Check the buffer valve pin and see if it closes correctly Applied Biosystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide 55 Chapter 3 Troubleshooting Run Performance Troubleshooting run performance continued Observation Possible Cause Recommended Action Extra peaks in the Data off scale Dilute the sample and re inject the sample electropherogram Possible contaminant in sample Re amplify the DNA Sample renaturation Heat denature the sample in good quality formamide and immediately place on ice CHEMICAL HAZARD Formamide causes eye skin and respiratory tract irritation It is a possible reproductive and birth defect hazard Read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves Peaks exhibit a shoulder in Sample renaturation Heat denature the sample in good quality GeneMapper software formamide and immediately place on ice appease AGNI CHEMICAL HAZARD Formamide causes eye skin and respiratory tract irritation It is a possible reproductive and birth defect hazard Read the MSDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves Error message Leak Bubbles in the polymer system Select
116. ystems 3130 3130x Genetic Analyzers Maintenance Troubleshooting and Reference Guide User definable Run Priority Scheduling fil SequencingAnalysis Plate Editor Chapter 4 Data Collection Software Advanced Functions Run Priority Scheduling In this example the priority value for sample G07 is arbitrarily set to 80 a lower number than 100 forcing the software to give the sample a higher run priority All other samples remain 100 Sample well G07 is contained in the AO7 H08 injection set All 16 samples now correspond to Run 1 as displayed in the Run Scheduler gt Run View window The table below shows the change in the run priority schedule Well Numbers Run Number Priority A07 H08 A01 H02 A03 H04 A05 H06 A09 H10 A11 H12 MO oa AIO N File Edit Plate Name M Foundation Data Collection ersion 3 0 No User is logged in File View Instrument Service Tools Wizards Help Plate Sealing gt BEEP A Aca Instruments h 5 GA Insti nt 3130x David PT4 Run Schedul Run vi _ Well Sample Ne Name i Resuts Group nsiruments gt ga xi gt Davi gt Run Scheduler RUN view Bus LRS 2 Database Manager S E HHHH 5 1 co7 LRS Elga3130x Pe ear rarer ETT veep 22 Plate Manager 1 Run SUELE DO LRS i Ta Protocol Manager e Mu 14 2U oyulal omMocysu_rvru_i p EO LRS i Sija Module Manager 3 Run_David PT4_20 Regular StdSeq50_POP6_1 Validated H QiilRu

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