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Agilent 2100 Bioanalyzer Troubleshooting and

1. 120 o1 Oo Si TS ia a al i ae ee ee ie eT i a oe So oe a D pS a a on a 6 6 7 5 80 8 90 95 Time seconds Show me how to solve Peaks Migrating Late Back to Symptoms Contents A 100 V Index Peaks Migrating Late Most Probable Causes Solution Vortex speed too high Vortex at lower medium speed For chips use only the IKA vortexer Probable Causes Solution Vortex adapter not connected tightly Press vortex adapter tightly on mount vortex adapter must not rock Replace vortex adapter p n 5022 2190 if necessary Back to Symptoms Contents A 101 V Index Late Migration and Peak Broadening 45 40 35 30 25 20 Fluorescence 25 30 35 40 s so ss 60 65 70 75 30 35 a0 Time seconds Show me how to solve Late Migration and Peak Broadening Back to Symptoms Contents A 102 V Index Late Migration and Peak Broadening Most Probable Causes Solution Genomic DNA or high molecular weight DNA in Perform additional enzymatic digestion with the following sample well e g uncompletely sample digested Lambda DNA Back to Symptoms Contents A 103 V Index Bend Ladder Baseline at Ss Spy fe se Ea We Ue es Pe ea I I Lo fan ive LO gousosaion 4 110 105 100 95 90 85 el 60 shi 75 Ol 70 6
2. rtridge Metal lever J Contents A 259 V Index Removing the Pin Set of the 16 Pin Cartridge 1 Remove the 16 pin cartridge as described above 2 Open the bayonet socket of the pin set by turning the plastic lever to the left as described in Figure below Figure 6 Opening the Bayonet Socket of the Pin Set Plastic lever 3 Remove the cover of the bayonet socket by gently pulling the plastic lever as shown in Figure 6 The pin set may stick to the electrode base Remove it by carefully pulling it off See Figure 7 Contents A 260 V Index Figure 7 Releasing the Pin Set Electrode base Bayonet Cover NOTE For hints on how to clean the pin set refer to Cleaning the Pin Set of the 16 pin Cartridge 267 Contents A 261 V7 Index Inserting the Pin Set of the 16 Pin Cartridge WARNING Make sure that the pin set is completely dry before placing it back into the electrode base Even small amounts of liquid on the pin set can damage the high voltage power supply 1 Put the pin set on the cartridge base and the bayonet cover on the pin set See Figure 8 Contents A 262 V Index Figure 8 Inserting the Pin Set Electrode base Pin set Bayonet Cover Contents A 263 V Index 2 Lock the pin set to the e
3. Most Probable Causes Solution Laser defective Check laser using the Hardware Diagnostics 48 If the laser is defective call Agilent Technologies Gel dye mix was loaded in the destain well instead of destaining solution Discard chip and prepare new chip according to protocol Probable Causes Solution Autofocus failure Check autofocus using the Hardware Diagnostics 48 If autofocus fails call Agilent Technologies Least Probable Causes Solution High voltage power supply defective Check high voltage power supply using the Hardware Diagnostics 48 If the power supply is defective call Agilent Technologies Fingerprint on focusing lens Clean lens like decribed in Lens Maintenance 270 Back to Symptoms Contents A 208 V Index Spikes MUUVI CSC ErNLCE 15 20 25 30 35 Time seconds Show me how to solve Spikes Back to Symptoms Contents A 209 V Index Spikes Most Probable Causes Solution Chip gel dye mix destaining solution contaminated Prepare new chip with new gel dye mix and new destaining solution Wear powder free gloves only Don t touch the underside of the chip Don t touch the wells of the chip Clean the electrodes Load the chip immediately after taking it out of its sealed bag Gel dye mix destaining solution not properly prepared Refer to the Reagent Kit Guide for proper preparation
4. je rm jadi Agilent 2100 Bioanalyzer Troubleshooting and Maintenance Guide for Molecular Assays Edition March 01 Agilent Technologies WARNING For details of safety see the Site Preparation and Safety Manual for the Agilent 2100 Bioanalyzer The Agilent 2100 Bioanalyzer is marked with this symbol when the user should refer to the Site Preparation and Safety Manual in order to protect the Agilent 2100 Bioanalyzer against damage 00o 00o XIJ LabChip and the LabChip logo are registered trademarks of Caliper Ad Technologies Corp in the US and other countries Welcome Welcome to the Agilent 2100 Bioanalyzer Maintenance and Troubleshooting Guide This online manual provides novice and advanced users with information needed to successfully run assays with the Agilent 2100 Bioanalyzer A quick look at How to Use This Guide on page 4 explains how easy it is to use this online manual and helps you to get started Contents A3V Index How to Use This Guide Use the interactive bookmarks in this frame to choose your desired topic Use Acrobat Reader s navigation bar to move around within a topic see Navigating within Acrobat Reader Acrobat Reader Users Guide_pdf File Edit View Tools Window Help ET ujal oi lt gt Djam al C0 welome bO Howto Use This Guide C Contents C Quick Step Overview O Starting the Software lt Preparing and Running an Assay Ci Reagent Kits Ci Proced
5. 2 Press the Add button to add a new Network Adapter Contents A32V Index 3 Inthe following dialog choose the Have Disk Button to load the RocketPort PCl Quad driver Select Network Adapler 24 x Click the Network Acapter that matcres you hardware and then H click OK If pou have an installation disk for this component click Hi Have Disk Network Adapter E3 3Com 3C508 ISA 16 bit Ethernet Adapter E4 3Com Etherlink II Adapter falso 11 6 and 16 TPI EEE E 3Com Etherlink Ill ISA PCHCIA Adapter E3 3Com EtherLink III PCI Bus Maste Adapter 30590 3 3Com Ethelink16 ZtherLirk16 TP Adapter FMI ann Cant Ctharl inl OCI AN MM OMDACE T SAantar f9CROR OK Cencel 4 Enter the path to the RocketPort driver NOTE Use the RocketPort driver located on the bioanalyzer software CD You can find the driver under E Support Drivers RocketPort where E is the letter of the CD ROM drive Contents A33 V Index Insert Disk x Eo ian E Support Drivers RocketPort In the next dialog you are able to choose the driver that should be installed there should only be one choice already pre selected Comtro RocketPort RocketModem 5 Press Ok to start the installation Select OEM Option Choose a software supported by this hardware manufacturer s disk ComtralRocketPort RocketModem S cow tee Contents A35V Index 6 The device wizard will guide you through the rest of the s
6. Autofocus failure Check autofocus using the Hardware Diagnostics 48 If autofocus fails call Agilent Technologies Laser defective Check laser using the Hardware Diagnostics 48 If the laser is defective call Agilent Technologies Back to Symptoms Contents Any Index Noisy Electropherogram 30 25 20 Fluorescence T t E N MLD dor 25 30 35 40 45 50 55 60 65 70 75 80 85 90 Time seconds Show me how to solve Noisy Electropherogram Back to Symptoms Contents Al2V Index Noisy Electropherogram Most Probable Causes Solution Chip not properly primed Air bubble in chip Use a new chip Check chip priming station syringe for good seal see Maintaining the Chip Priming Station 271 Check if clip and base plate of priming station are in the right position see DNA Reagent Kit Guide Chip contaminated Wear powder free gloves only Don t touch the underside of the chip Don t touch the wells of the chip Clean the electrodes Load the chip immediately after taking it out of its sealed bag Vibration of Agilent 2100 Bioanalyzer Don t touch Agilent 2100 Bioanalyzer during a run Remove vibration devices such as vortexers and vacuum pumps from bench Back to Symptoms Contents Anv Index Broad Peaks Fluorescence _ b ho ro emm hm on ao hm on O nn O Si O on on 25 30 35 40 45 50 55 60 65 70 75 80 85 Time
7. Use fresh sample aliquot Heat sample denaturating solution for 5 min at 100 C Sample denaturating solution are dried out Sample denaturating solution were denaturated in 1 5 mL tubes Use 0 5 mL tubes for denaturating Contents A 188 V Index Least Probable Causes Solution Loaded chip kept for too long before run Prepared chips must be used within 10 minutes Back to Symptoms Contents A 189 V Index Too Low Quantitation Results Most Probable Causes Solution Upper marker wrongly assigned Check assignment of upper marker Pipetting error during preparation of mixtures Check dilution procedure Check calibration of pipette Chip pipetting error Use new chip Always insert the pipette tip to the bottom of the well when dispensing the liquid Use appropriate pipette and tips Probable Causes Solution Sample concentration too high Use sample concentration according to the Protein Reagent Kit Guide Don t forget to dilute samples with deionized water after heat denaturation Diluted sample are too old Use diluted samples within one day Lease Probable Causes Solution Loaded chip kept too long before run Prepared chips must be used within 10 min Back to Symptoms Contents A 190 V Index Wrong Sizing Result Most Probable Causes Solution Ladder degraded Refer to the Reagent Kit guide for proper
8. High voltage power supply defective Check high voltage power supply using the Hardware Diagnostics 48 If the power supply is defective call Agilent Technologies Autofocus failure Check autofocus using the Hardware Diagnostics 48 If autofocus fails call Agilent Technologies Laser defective Check laser using the Hardware Diagnostics 48 If the laser is defective call Agilent Technologies Back to Symptoms Contents A9I IV Index Cross Contamination Sample 9 Sample 6 500 400 300 Fluorescence 200 100 25 30 35 40 45 50 55 60 65 70 75 s0 85 90 Time seconds Show me how to solve Cross Contamination Back to Symptoms Contents A998 V Index Cross Contamination Most Probable Causes Solution Sample concentration too high Use sample concentration according to the DNA Reagent Kit Guide Pipetting error during preparation of mixtures Check dilution procedure Check calibration of pipette Chip pipetting error Use new chip and pipette again Use appropriate pipette and tips Probable Causes Solution Leak current due to contaminated electrodes Clean electrodes with analysis grade water and a toothbrush see Maintenance 246 Replace electrode cartridge Back to Symptoms Contents AID V Index Peaks Migrating Late 190 180 170 160 Fluorescence 140 5 130
9. Probable Causes Solution Samples not completly denaturated Use fresh sample aliquot Heat sample denaturating solution for 5 min at 100 C Sample denaturating solution are dried out Sample denaturating solution were denaturated in 1 5 mL tubes Use 0 5 mL tubes for denaturating Pipetting error during preparation of mixtures Check dilution procedure Check calibration of pipette Diluted samples are too old Use diluted samples within one day Contents A216 Y Index The gel dye mix was not replaced after priming Prepare new chip according to the Protein 200 the chip Reagent Kit Guide Least Probable Causes Solution Samples dissolved in acidic buffer Neutralize samples with appropriate buffer or dilute samples in deionized H20 Alternatively dialyze samples against buffer with medium pH Autofocus failure Check autofocus by means of the Hardware Diagnostics 48 If autofocus fails call Agilent Technologies Back to Symptoms Contents A217 V7 Index Apparently Missing Sample Peak well 1 well 2 70 60 50 40 30 Fluorescence 20 15 20 25 30 35 40 45 Time seconds Show me how to solve Apparently Missing Sample Peak Back to Symptoms Contents A218 V Index Apparently Missing Sample Peak Most Probable Causes Solution Wrongly assigned upper marker Refer to the instructions provided with the Reagent Kit guide for storage
10. Time seconds Show me how to solve Poor Baseline Jumps Back to Symptoms Contents A 88 V Index Poor Baseline Jumps Most Probable Causes Solution Vibration of Agilent 2100 Bioanalyzer Remove vibration devices such as vortexers and vacuum pumps from bench Instrument lid was touched during the run Don t touch Agilent 2100 Bioanalyzer during a run Probable Causes Solution Chip not properly primed Air bubble in chip Use a new chip Check chip priming station syringe for good seal see Maintaining the Chip Priming Station 271 Check if clip and base plate of priming station are in the right position see DNA Reagent Kit Guide Least Probable Causes Solution Laser defective Check Laser by using the Hardware Diagnostics 48 If the laser is defective call Agilent Technologies Autofocus failure Check autofocus by means of the Hardware Diagnostics 48 If autofocus fails call Agilent Technologies Contents A899 V Index Poor Baseline Bend 45 40 35 30 25 Fluorescence 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 Time seconds Show me how to solve Poor Baseline Bend Back to Symptoms Contents A 90 V Index Poor Baseline Bend Most Probable Causes Solution Chip preparation was done with cold reagents Prepare a new chip Allow all reagents and reagent mixes to warm up to room temperature before use
11. 10 Fluorescence 10 19 24 29 34 39 44 49 54 59 64 69 Time seconds 2 Show me how to solve Wavy Baseline Back to Symptoms Contents A 180 V Index Cross Contamination well 2 blank well 1 sample 4 0 3 5 3 0 2 5 Fluorescence 19 24 29 34 39 44 49 54 59 64 69 Time seconds 9 Show me how to solve Cross Contamination Back to Symptoms Contents A 181 V7 Index Late Migration of RNA Ladder or Sample 25 20 Fluorescence 19 24 29 34 39 44 49 54 59 Time seconds Show me how to solve Late Migration of RNA Ladder or Sample Back to Symptoms Contents A 182 V Index Troubleshooting the Protein Application Essential Measurement Practices For hints on how to handle chips and chemicals see Essential Measurement Practices Troubleshooting the Protein Application Error messages appearing on the screen describe a problem that has occurred with either the hardware or the software Click the Alor BJ button next to the error message to view a help screen that is specific for that error Additional information regarding the nature of a problem can often be found in the run log for the data file Choose Tools gt View Log File gt Run Log The Run Log lists all the actions and errors that occurred during the run In rare cases results generated by your Agilent 2100 Bioanalyzer might not be what you expected To help you find the reason for the discrepancy see Symptoms
12. 185 Contents A 183 V Index For most observations you will find at least one corresponding example depicting a typical electropherogram or result table Once you have identified the observation that resembles the outcome of your experiment you will get a set of assigned causes listed by priority The causes are grouped into three levels e most probable cause probable cause e least probable cause A list of solutions that help you to fix the problem are assigned to the causes For successful troubleshooting go through all the solution hints listed by priority If you are not able to assign a symptom to your problem compare your electropherogram with the List of Protein Electropherograms 231 Contents A 184 7 Index Symptoms Click the icon to see an example or go straight to the troubleshooting hints Clogged spin filters 187 Too High Quantitation Results 188 Too Low Quantitation Results 190 Wrong Sizing Result 191 Poor Chip Performance 193 Apparently Short Run Time 195 Additional Sample or Ladder Peaks 197 Low or Missing Upper Marker in Ladder 200 Low or Missing Upper Marker in Sample 202 High Lower Marker Variability 205 No Peaks 207 Spikes 209 Poor Reproducibility 212 FAEAABABAE EEE No or Low Sample Peaks 215 Contents A 185 V Index Apparently Missing Sample Peak 218 Low Ladder Peaks 220 Wrong Alignment of Ladder Peaks 222 Broad Peaks 224 Dips 229 ET M
13. Don t touch the wells of the chip Clean the electrodes Load the chip immediately after taking it out of its sealed bag Vibration of Agilent 2100 Bioanalyzer Contents Don t touch Agilent 2100 Bioanalyzer during a run Remove vibration devices such as vortexers and vacuum pumps from bench A149 V Index Probable Causes Solution Loaded chip kept for too long before Prepared chips must be used within 5 min run Dye concentration too low Use dye concentration according to the RNA Reagent Kit Guide Let the dye warm up to room temperature before preparing the gel dye mix Least Probable Causes Solution High voltage power supply defective Check high voltage power supply using the Hardware Diagnostics 48 If the power supply is defective call Agilent Technologies Back to Symptoms Contents A 150 Y Index Broad Peaks 600 550 500 450 400 350 300 250 200 150 100 50 Fluorescence 19 24 29 34 39 44 Time seconds Show me how to solve Broad Peaks Back to Symptoms Contents A 151V 49 54 59 Index Broad Peaks Most Probable Causes Solution Leak current due to contaminated electrodes Clean electrodes with analysis grade water and a toothbrush see Maintenance 246 Replace electrode cartridge Electrodes contaminated with RNAses Clean electrodes with RNAseZAP Follow decontamination procedure see Maintenance 246 Clogg
14. ccccssscsssscssssssessessesseeseesessesseeseeesaees 123 Troubleshooting the Protein Application ccccscssessesssessessesseeseeeessensessesseenaees 183 Maintenant G iadaniss iced pacuiaedi tenes sedcsdatilaneneeen sores reuse ehiati Geeta 246 Parts and PAGO SSG Sse ews en eatin akaaiieane nena Nein icant etna 283 Abo t This UU cece senso asa aaaea evens cada c aaraa paak arara aaa naanin 294 Contents AtV Index Essential Measurement Practices This section lists all user relevant hints on handling tools chips reagents and Agilent 2100 Bioanalyzer For the latest information on assay related hints go to the Lab on a Chip web site at http www agilent com chem labonachip Tools and Handling e Always wear gloves when handling chips to prevent them from getting contaminated e When pipetting sample use pipette tips that are small enough Pipette tips that are too large will lead to poor quantitation accuracy e Change pipette tips between two pipetting steps to avoid cross contamination e Always insert the pipette tip to the bottom of the well when dispensing the liquid Placing the pipette at the edge of the well leads to bubbles and poor results Holding the pipette at a slight angle will ensure proper dispensing of the liquid e Use a new syringe and cleaning chip with each new LabChip Kit Contents AlV Index Chip Priming Station e For the correct position of the syringe clip and base plate please refer to the
15. Apply baseline correction algorithm software revision A 01 20 or higher Chips were stored in the fridge freezer Prepare a new chip Store chips at room temperature Back to Symptoms Contents A9I1V Index No Peaks and High Background Spike to view the baseline level uncheck the Zero Baseline in the software Fluorescence 25 30 35 40 45 50 55 60 65 70 75 s0 85 90 Time seconds Show me how to solve No Peaks and High Background Back to Symptoms Contents AIZ2V Index No Peaks and High Background Most Probable Causes Solution Current leaks due to contaminated electrodes Clean electrodes with analysis grade water and a toothbrush see Maintenance 246 Replace electrode cartridge Probable Causes Solution Chip not properly primed Air bubble in chip Use a new chip Check chip priming station syringe for good seal see Maintaining the Chip Priming Station 271 Check if clip and base plate of priming station are in the right position see DNA Reagent Kit Guide Dye concentration too low marker disappears Use dye concentration according to the DNA Reagent Kit Guide Let the dye warm up to room temperature before preparing the gel dye mix Contents A 93 V Index Least Probable Causes Solution Fingerprint on focusing lens Clean lens like decribed in Lens Maintenance 270 Chip contaminated Wear powder free gloves only Don
16. Back to Symptoms Contents A 154 V Index Missing Peaks Most Probable Causes Solution Laser defective Check laser using the Hardware Diagnostics 48 If the laser is defective call Agilent Technologies No ladder samples in wells Use a new chip Pipette ladder sample in all wells Wrong settings of chip priming station For the correct position of the syringe clip and base plate please refer to the Reagent Kit Guide Leak current due to contaminated electrodes Clean electrodes with analysis grade water and a toothbrush see Maintenance 246 Replace electrode cartridge Contents A 155 V Index Probable Causes Solution Chip pipetting error Use new chip Always insert the pipette tip to the bottom of the well when dispensing the liquid Holding the pipette at a slight angle will ensure proper dispensing of the liquid Use appropriate pipette and tips Dye concentration too low Use dye concentration according to the Reagent Kit Guide Let the dye warm up to room temperature before preparing the gel dye mix Least Probable Causes Solution Autofocus failure Check autofocus by means of the Hardware Diagnostics 48 If autofocus fails call Agilent Technologies High voltage power supply defective Check high voltage power supply using the Hardware Diagnostics 48 If the power supply is defective call Agilent Technologies Back
17. Now you have successfully installed the device driver for the RocketPort PCl Quad DB9 card Contents A 40 V Index Setup of the Device Properties The installation process continues with the setup of the device properties 1 You need to change the range of COM ports Please change the Starting COM Port from COM3 default to COM7 Device Properties RIES Device Setup F m Summary RocketPort 4 PCI Name Rocket H ISA Bus Settings 40 Base Address N A v m COM Port Range Starting COM Port X Cancel Help Contents AMV Index 2 Press Ok to save the settings You can verify your specifications in the next dialog which shows a summary of the RocketPort Setup NOTE Later on you can access this dialog by starting the Setup program of the RocketPort card from the Start menu Comtrol RocketPort RocketModem Setup Main Setup Options MROVATION IW REMOTE ADOEGS m Configuration 5 89 a7 COM1 Add Remove Contents A42V Index 3 Press OK to close the following window Comtrol RocketPort RocketModem Setup x You have to restart Windows before the changes take effect 4 After closing the network setup window you will be requested to restart your computer 5 Close any other open application and press Yes to reboot your computer Network Settings Change A You must shut down and restart your computer before the new settings wil
18. Optics test 39 Options 18 P Particles 46 Peak no 159 Peaks Migrating Late 92 Pipette tips 7 Plastic adapter 275 Poor baseline Index Bend 82 Dips 71 Drift 73 Jumps 79 Noise 76 Poor baseline protein High noise level 232 Poor baseline RNA Dips 148 Noise 153 Poor Chip Performance 51 192 Poor sensitivity 60 136 Precipitated SDS 214 Protein 200 Kit 9 Protein Ladder 10 Q Quantification results DNA Too high 47 Too low 48 Quantification results Protein Too high 185 Too low 187 Quantification results RNA Too high 119 Too low 120 Wrong 121 Contents R Reader tab 18 Reagents 8 Handling 8 Storage 8 Reconstitution of protein ladder 10 Removing the 16 Pin Bajonet Cartridge 264 the 16 Pin Cartridge 258 the Pin Set of the 16 Pin Bajonet Car tridge 266 Replacement Silicon gasket 280 RNAseZAP 13 255 Rocket Port Card Installing the driver 23 Setup 21 RS232 cable 16 RS232 communication 16 S Sample buffer Protein 11 SDS 10 Seal Test 278 Setup Multi Port Card 21 Rocket Port Card 21 SETUP EXE 36 Short circuit test 38 A 292 V Index Short run time 195 Silicon gasket Replacement 280 Silicon gaskets 275 Software troubleshooting 35 Spikes Glitches 57 133 Status indicator 16 Stepper motor test 39 Storage Upper marker 9 Symptoms DNA troubleshooting 44 Protein troubleshooting 182 RNA troubleshooting 117 Syringe adapter Replacement 275 System laptop 18 single instrument 18
19. Troubleshooting the DNA Application 52 Troubleshooting the RNA Application 123 or Troubleshooting the Protein Application 183 5 If the test fails reinstall the Agilent 2100 Bioanalyzer software using the Agilent 2100 Bioanalyzer software CD ROM that is supplied with the system e Insert the Agilent 2100 Bioanalyzer software CD ROM in the CD ROM drive of your PC e Start Windows NT Explorer and go to the CD ROM drive Contents A 46V Index e Double click on the SETUP EXE file and follow the instructions on the screen e Repeat steps 1 through 4 to verify proper installation 6 Ifthe test continues to fail save the result of the test by choosing File gt Save log file as in the Installation Qualification interface and call Agilent Technologies Contents A4 1V Index Hardware Diagnostics Built in Tests Firmware Error Messages Whenever you start a run the firmware of the Agilent 2100 Bioanalyzer checks for errors such as for example defective high voltage supplies or missing conductivity between wells If an error is detected the firmware pops up a message box and aborts the run Further the message box contains hints on how to resolve the problem or tells you to call Agilent Technologies Manual Tests To successfully perform the complete set of hardware diagnostic tests you need a new chip With the chip and a diagnosis software interface you can run system component tests and check all hardware component
20. seconds Show me how to solve Broad Peaks see also Late Migration and Peak Broadening Back to Symptoms Contents Al4V 90 Index Broad Peaks Most Probable Causes Solution Current leaks due to contaminated electrodes Clean electrodes with analysis grade water and a toothbrush see Maintenance 246 Replace electrode cartridge Clogged gasket and plastic adapter of priming station Perform seal test like described in Maintaining the Chip Priming Station 271 Clean replace gasket and plastic adapter If necessary Chip not properly primed Air bubble in chip Use a new chip Check chip priming station syringe for good seal see Maintaining the Chip Priming Station 271 Check if clip and base plate of priming station are in the right position see DNA Reagent Kit Guide Dye concentration too high Use dye concentration according to the Reagent Kit Guide Let the dye warm up to room temperature before preparing the gel dye mix Particles of protective foam pad on electrode cartridge Make sure to remove foam particles of the electrode cartridge before use Contents Al5V Index Least Probable Causes Solution High voltage power supply defective Check high voltage power supply using the Hardware Diagnostics 48 If the power supply is defective call Agilent Technologies Back to Symptoms Contents A l6V Index Missing Peaks or Marker Peaks 0 006 0 00
21. see below Lifting the Housing of the Power Inlet Contents A218 V Index 3 Pull out the fuse drawer as shown in the next figure Fuse Drawer Housing Pulling out the Fuse Drawer Fuse Drawer 4 Check the fuses for conductivity and replace fuses if necessary 5 Slide in the fuse drawer and push till it fits tightly as shown in the next figure Contents A 280 V Index Slide in the Fuse Drawer 6 Slide in the fuse drawer and push till it fits tightly as shown in the figure Close Fuse Drawer Housing 7 Finally close the fuse drawer housing and reconnect the instrument to the power line Parts and Accessories The following parts are available for the Agilent 2100 Bioanalyzer Bundles For up to date details refer to http wadnts02 wad hp com off sc pages unsec bundlist htm Agilent 2100 Bioanalyzer Single Instrument System G2940AA VL400 PC Instrument accessories printer vortexer Agilent 2100 Bioanalyzer Multi Instrument System G2942AA VL800 PC instrument accessories printer vortexer Agilent 2100 Bioanalyzer Laptop System G2943AA Omnibook 6000 instrument accessories printer vortexer Contents A 283 V Index Hardware Software Agilent 2100 Bioanalyzer G2938B comprises 1 chip priming station 1 testchip kit serial cable site amp safet
22. 110 Time seconds Show me how to solve Poor Baseline Jumps Back to Top of List Contents A115 V7 Index Poor Baseline Bend Fluorescence 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 Time seconds Show me how to solve Poor Baseline Bend Back to Top of List Contents A 116 V Index No Peaks and High Background 500 450 Spike to view the baseline level 400 uncheck the Zero Baseline in the software 350 2 300 Q Oo w 250 oO iL 200 150 100 50 25 30 35 40 45 50 55 60 65 70 75 80 85 90 Time seconds Show me how to solve No Peaks and High Background Back to Top of List Contents A117 V Index No Peaks and Low Background 250 Spike to view the baseline level uncheck 200 Zero Baseline in the p software 150 Q Oo wo D S 100 iL 50 o 50 25 30 35 40 45 50 55 60 65 70 75 80 85 90 Time seconds Show me how to solve No Peaks and Low Background Back to Top of List Contents A118 Y Index Cross Contamination Sample 9 Sample 6 500 400 300 200 Fluorescence 100 25 30 35 40 45 50 55 60 65 70 75 80 85 90 Time seconds Show me how to solve Cross Contamination Back to Top of List Contents A119 V Index Peaks Migrating Late 190 180 170 160 Fluorescence 140 130 120 ol T Fat Tl IaT ie Fel ala en eTEN oe Pe i T
23. 65 8 60 S 55 9 50 g _ 45 v t 40 35 ES 30 lt 4 Time seconds Show me how to solve Bend Ladder Baseline Back to Symptoms Index A 1047Y Contents Bend Ladder Baseline Most Probable Causes Solution Chip preparation was done with cold reagents Prepare a new chip Allow all reagents and reagent mixes to warm up to room temperature for 30 min before use Apply baseline correction algorithm software revision A 01 20 or higher Chips were stored in the fridge freezer Prepare a new chip Store chips at room temperature Back to Symptoms Contents A 105 Y Index List of DNA Electropherograms Additional Sample or Ladder Peaks 25 Fluorescence Additional Peaks 5 S D xs ao 6 Es s a Ss 70 75 a ss sa 55 10 105 110 Time seconds 11 Show me how to solve Additional Sample or Ladder Peaks Back to Symptoms Contents A 106 Y Index Spikes Glitches Characteristic shape of spike Fluorescence Time seconds 1i Show me how to solve Spikes Glitches Back to Top of List Contents A 107 V Index Poor Sensitivity 3 0 2 5 2 0 Fluorescence 0 5 0 0 0 5 25 30 35 40 45 50 55 60 65 70 75 80 85 90 Time seconds Show me how to solve Poor Sensitivity Back to Top of List Contents A 108 V Index Noisy Electropherogram 30 25 20 Fluorescence T k H ON HLD UO h CO 25 30 35 40 45 5
24. Chip Priming Station 271 Check if clip and base plate of priming station are in the right position see DNA Reagent Kit Guide Probable Causes Solution Chip preparation was done with cold reagents Prepare a new chip Allow all reagents and reagent mixes to warm up to room temperature before use Chips were stored in the fridge freezer Prepare a new chip Store chips at room temperature Amount of liquid pipetted is too low or chip is empty Check assay procedure on amount of liquid to be pipetted Least Probable Causes Solution High voltage power supply defective Check high voltage power supply using the Hardware Diagnostics 48 If the power supply is defective call Agilent Technologies Back to Symptoms Contents A61 V Index Chip Not Detected Most Probable Causes Solution Amount of liquid pipetted is too low or chip is empty Check assay procedure on amount of liquid to be pipetted Pipette sample or buffer in all wells Chip not properly primed Air bubble in chip Use a new chip Check chip priming station syringe for good seal see Maintaining the Chip Priming Station 271 Check if clip and base plate of priming station are in the right position see DNA Reagent Kit Guide Probable Causes Solution No communication between Agilent 2100 Bioanalyzer and PC Check instrument communication like described under Troubleshooti
25. T Temperature test 39 Tools 7 Troubleshooting 15 DNA application 42 Protein application 180 RNA application 115 Contents U Upper Marker Missing or low in ladder 201 Missing or low in sample 204 Storage 9 Upper marker Usage 9 Usage Protein ladder 10 WwW Wrong Alignment of Ladder Peaks Protein 223 Sizing result DNA 49 Sizing result Protein 189 A293 V Index About This Guide Copyright 2001 Agilent Technologies Use Reproduction and Distribution is subject to approval of Agilent Technologies Edition 03 02 Reorder number G2941 90003 Adobe and Acrobat are U S registered trademarks of Adobe Systems Incorporated Microsoft Windows Windows 2000 and Windows NT are U S registered trademarks of Microsoft Corporation LabChip and the LabChip logo are registered trademarks of Caliper Technologies Corp in the US and other countries RNAseZAP is a registered trademark of Ambion Inc Contents A294 V Index Did You Know e The Agilent Technologies logo on the cover page launches your PC s default browser and goes to the lab on a chip pages Try it here Agg Agilent Technologies e To link to the User s Guide click on the green bar on the cover page Contents A 295 V Index
26. appropriate Reagent Kit Guide e Replace the syringe with each new LabChip Kit e Check the performance of the chip priming station by applying the seal test on a monthly basis For details see Maintaining the Chip Priming Station 271 If necessary replace the gasket and or adapter reorder no for gasket kit G2938 68716 Contents A8V Index Reagents and Reagent Mixes General e Handle and store all reagents according to the instructions given in the specific Reagent Kit Guide e Keep all reagents and reagent mixes for example the gel dye mixture refrigerated at 4 C when not in use for more than 1 hour Reagents might decompose leading to poor measurement results e Allow all reagents and samples to equilibrate to room temperature for 30 min before use e Protect dye and dye mixtures from light Remove light covers only when pipetting Dye decomposes when exposed to light Gel and Gel Dye e Use gel dye mixture within four weeks of preparation The gel dye mixture might decompose and lead to poor measurement results Samples e Refer to the assay specific Reagent Kit Guides for maximum allowed sample and salt concentration e For RNA assays Heat denature all RNA samples and RNA ladder for 2 min at 70 C before use Contents AIV Index e For protein assays Use 0 5 ml tubes for denauration Using larger tubes lead to poor results Chips e Prepared chips must be used within 5 minutes Reagents might evapora
27. change from open to closed Lid open Lid closed Instrument switched off of not connected to PC If the icon doesn t change L Check whether the status indicator is on If it is off replace the fuses as described under Maintenance L Check whether the status indicator is red If it is red turn off line power to the Agilent 2100 Bioanalyzer and turn on again If the problem persists call Agilent Technologies L Check that the RS232 communication cable is connected correctly L Check if another harware devive is connected to your computer via RS232 cable L Check the Com port settings in the Agilent 2100 Bioanalyzer software see Changing the COM Port Settings 16 L Replace the RS232 Multiport cable _ Reinstall the Agilent 2100 Bioanalyzer software If the Agilent 2100 Bioanalyzer will still not communicate call Agilent Technologies Contents A15V Index Changing the COM Port Settings NOTE The number of COM Ports available depents on your bundle PC Laptop system only one COM Port is available Single instrument system two COM Ports A and B are available Multi instrument system up to 4 COM Ports 1 to 4 are available In case of a Multi instrument system a Multi Port Card e g RocketPort PCl Quad DB9 is installed in your PC Only connect the Agilent 2100 bioanalyzer via the Multi Port Card Multi Port cable with your computer Do not use the default COM Ports of your PC Port A or B Setting up
28. electrodes Clean electrodes with analysis grade water and a toothbrush see Maintenance 246 Replace electrode cartridge Loaded chip kept for too long before run Prepared chips must be used within 5 min Dye concentration too low Use dye concentration according to the Reagent Kit Guide Let the dye warm up to room temperature before preparing the gel dye mix Chip not properly primed Air bubble in chip Use a new chip Check chip priming station syringe for good seal see Maintaining the Chip Priming Station 271 Check if clip and base plate of priming station are in the right position see DNA Reagent Kit Guide Clogged gasket and plastic adapter of priming station Perform seal test like described in Maintaining the Chip Priming Station 271 Clean replace gasket and plastic adapter If necessary Contents A83V Index Probable Causes Solution Chip contaminated Wear powder free gloves only Don t touch the underside of the chip Don t touch the wells of the chip Clean the electrodes Load the chip immediately after taking it out of its sealed bag Least Probable Causes Solution Changes of ambient temperature of more than 5 C during the run Place Agilent 2100 Bioanalyzer in thermally stable environment High voltage power supply defective Check high voltage power supply using the Hardware Diagnostics 48 If the power supply is defective
29. ladder storage Optional prepare ladder aliquot Use a fresh ladder aliquot Upper and or lower marker wrongly assigned Store Sample Buffer Denaturating Solution according to the instructions given in the Reagent Kit Guide See Low or Missing Upper Marker in Ladder 200 Ladder peaks wrongly assigned Check assignment of ladder peaks See Wrong Alignment of Ladder Peaks 222 for details Protein ladder not properly denaturated Use fresh ladder aliquot Heat ladder for 5 min at 100 C Probable Causes Solution Protein ladder not properly denaturated Use fresh ladder aliquot Heat ladder for 5 min at 100 C Contents A 191V Index Least Probable Causes Solution Vibration of Agilent 2100 Bioanalyzer Don t touch Agilent 2100 Bioanalyzer during a run Remove vibration devices such as vortexers and vacuum pumps from bench Changes of ambient temperature of more than 5 C during the run Place Agilent 2100 Bioanalyzer in thermally stable environment High voltage power supply defective Check high voltage power supply using the Hardware Diagnostics 48 If the power supply is defective call Agilent Technologies Back to Symptoms Contents A 192 V Index Poor Chip Performance Most Probable Causes Solution Chip not properly primed Air bubble in chip Use a new chip Check chip priming station syringe for good seal see Maint
30. marker in were not assigned correctly by the software ladder set upper marker manually If necessary adjust peak find settings If peaks are detected that are not part of the ladder exclude them For better upper marker identification Turn off the analysis For correct alignment overlay electropherograms of multiple wells to clearly identify the upper marker See Low or Missing Upper Marker in Ladder 201 for probable causes Back to Symptoms Contents A 196 V Index Additional Sample or Ladder Peaks Fluorescence 15 20 25 30 35 40 45 Time seconds L Show me how to solve Additional Sample or Ladder Peaks Back to Symptoms Contents A197 V7 Index Additional Sample or Ladder Peaks Most Probable Causes Solution Sample or ladder not denaturated properly Use fresh sample aliquot Heat sample denaturating solution and ladder for 5 min at 100 C Sample denaturating solution and or ladder are dried out during denaturation Sample denaturating solution and or ladder were denaturated in 1 5 mL tubes Use 0 5 mL tubes for denaturating Chip contaminated Dust particles in separation channels Contents A 198 V Wear powder free gloves only Don t touch the wells of the chip Clean the electrodes See Maintenance 246 for additional information Load the chip immediately after taking it out of its sealed bag Index Probable Causes Solution Ladder deg
31. of the Hardware Diagnostics 48 If autofocus fails call Agilent Technologies High voltage power supply defective Check high voltage power supply using the Hardware Diagnostics 48 If the power supply is defective call Agilent Technologies Back to Symptoms Contents A193 V Index Poor Baseline Dips 125 100 75 50 Fluorescence 25 25 25 30 35 40 45 50 55 60 65 70 75 80 85 90 Time seconds Show me how to solve Poor Baseline Dips Back to Symptoms Contents A 80 V Index Poor Baseline Dips Probable Causes Solution Too high sample concentration Use sample concentration according to the DNA Reagent Kit Guide Sample impurities e g genomic DNA ss DNA etc Check DNA isolation protocol If possible clean up samples Least Probable Causes Solution Autofocus failure Check autofocus by means of the Hardware Diagnostics 48 If autofocus fails call Agilent Technologies Back to Symptoms Contents A81V Index Poor Baseline Drift 50 50 Fluorescence 100 150 k pa iae ena a R H a A atara an pip a TG Lise hA gana dT Lo hm CN COP LO CO CO ee INNNNNANN ANNAN MOM COMO CIGD at sesso z F 2 25 20 35 40 45 50 55 60 65 70 75 80 85 90 Time seconds Show me how to solve Poor Baseline Drift Back to Symptoms Contents A82V Index Poor Baseline Drift Most Probable Causes Solution Leak current due to dirty
32. specific for that error Additional information regarding the nature of a problem can often be found in the run log for the data file Choose Tools gt View Log File gt Run Log The Run Log lists all the actions and errors that occurred during the run In rare cases results generated by your Agilent 2100 Bioanalyzer might not be what you expected To help you find the reason for the discrepancy see Symptoms 125 Contents A 123 V Index For most observations you will find at least one corresponding example depicting a typical electropherogram or result table Once you have identified the observation that resembles the outcome of your experiment you will get a set of assigned causes listed by priority The causes are grouped into three levels e most probable cause probable cause e least probable cause A list of solutions that help you to fix the problem are assigned to the causes For successful troubleshooting go through all the solution hints listed by priority If you are not able to assign a symptom to your problem compare your electropherogram with the List of RNA Electropherograms 169 Contents A124V Index Symptoms Click the icon to see an example or go straight to the troubleshooting hints Too High Quantification Results 127 Too Low Quantification Results 128 Wrong Quantification Result 130 Chip Not Detected 133 Poor Chip Performance 134 Additional Sample or Ladder Peaks 135 Genomic DNA C
33. supply is defective call Agilent Technologies Autofocus failure Check autofocus using the Hardware Diagnostics 48 If autofocus fails call Agilent Technologies Back to Symptoms Contents A 164 V7 Index Cross Contamination J well 2 blank well 1 sample 4 0 3 5 3 0 2 5 Fluorescence 19 24 29 34 39 44 49 54 59 64 69 Time seconds 9 Show me how to solve Cross Contamination Back to Symptoms Contents A 165 V Index Cross Contamination Most Probable Causes Solution Sample concentration too high Use sample concentration according to the RNA Reagent Kit Guide Pipetting error during preparation of mixtures Check dilution procedure Check calibration of pipette Chip pipetting error Use new chip and pipette again Use appropriate pipette and tips Probable Causes Solution Leak current due to contaminated electrodes Clean electrodes with analysis grade water and a toothbrush see Maintenance 246 Replace electrode cartridge Back to Symptoms Contents A 166 V Index Late Migration of RNA Ladder or Samples Fluorescence 19 24 29 34 39 44 49 54 59 Time seconds Show me how to solve Late Migration of RNA Ladder or Sample Back to Symptoms Contents A 167 V Index Late Migration of RNA Ladder or Sample Most Probable Causes Solution Clogged gasket and plastic adapter of priming Perform seal
34. the Multi Port Card might be necessary after PC repair or reinstallation of the operating system Contents A 16 V Index NOTE If you have selected a demo assay It is not possible to change the COM settings 0 ptions Serial Port None 7 Contents A1 V Index Laptop and single instrument system 1 Choose Options from the Tools menu The dialog box that appears contains four tabbed sections labeled Data Files Reader Chip Alert and Advanced Click the Reader tab The dialog box should look like this your COM setting may be different A Options x Data Files Reader Chip Alert Advanced Serial Port COM1 OK Cancel 2 Try choosing a COM Port setting that is different from the one that is currently selected If you know which port is in use on the PC choose that port Contents A18V Index NOTE If you have a laptop connected to your instrument you must choose COM1 3 Check the icon of the Agilent 2100 Bioanalyzer on the screen If it is no longer dimmed communication between the Agilent 2100 Bioanalyzer and PC is working properly In addition hardware information is displayed NOTE If you have a PC connected to your instrument and the icon is still dimmed repeat step 2 choosing a different Com Port each time until it is not dimmed anymore If you cannot resolve the communication problem in this way check the troubleshooting help for more information 4 When you are finished with the Opt
35. tip to the bottom of the well when dispensing the liquid Use appropriate pipette and tips Insufficient vortexing of chip Vortex chip for 1 minute Only use the IKA vortexer Adjust the speed to the set point Inaccurate reference measurement e g UV absorption due to remaining UV aborbing solvent in the sample Purify sample for UV measurement Probable Causes Solution Loaded chip kept for too long before run Prepared chips must be used within 5 min Sample concentration too high Contents A 128 V Use sample concentration according to the RNA Reagent Kit Guide Index Least Probable Causes Solution Dye concentration too high Use dye concentration according to the RNA Reagent Kit Guide Let the dye warm up to room temperature before preparing the gel dye mix Back to Symptoms Contents A129 V Index Wrong Quantification Result Most Probable Causes Solution RNA ladder degraded Use new ladder aliquot chip Always wear gloves when handling chips RNA samples to prevent them from getting contaminated Follow decontamination procedure see Maintenance 246 Electrodes contaminated with RNAses Clean electrodes with RNAseZAP Follow decontamination procedure see Maintenance 246 Wrong time window in ribosomal peak assignment selected Select correct time window Loaded chip kept for too long before run Prepared chips must be used
36. to Symptoms Contents A 156 V Index Poor Baseline Dips Fluorescence 19 24 29 34 39 44 49 54 59 Time seconds Show me how to solve Poor Baseline Dips Back to Symptoms Contents A 157 V Index Poor Baseline Dips Probable Causes Solution Too high sample concentration Use sample concentration according to the RNA Reagent Kit Guide Sample impurities e g genomic DNA ss DNA etc Check RNA isolation protocol If possible clean up samples Probable Causes Solution Clogged gasket and plastic adapter of priming station Perform seal test like described in Maintaining the Chip Priming Station 271 Clean replace gasket and plastic adapter if necessary Least Probable Causes Solution Autofocus failure Check autofocus by means of the Hardware Diagnostics 48 If autofocus fails call Agilent Technologies Back to Symptoms Contents A 158 V Index Poor Baseline Drift 0 25 wo oO C Ho 50 uy a O L 75 100 19 24 29 34 39 44 49 54 59 64 69 Time seconds RNA Area 97 05 RNA Conc 21 00 ng ul 288 188 0 31 Show me how to solve Poor Baseline Drift Back to Symptoms Contents A 159 V Index Poor Baseline Drift Most Probable Causes Solution Leak current due to dirty electrodes Clean electrodes with analysis grade water and a toothbrush see Maintenance 246 Replace electrode cartridge Load
37. 0 55 60 65 70 75 80 85 g0 Time seconds Show me how to solve Noisy Electropherogram Back to Top of List Contents A 109 V Index Broad Peaks Fluorescence 25 30 35 40 45 50 55 60 65 70 75 80 85 90 Time seconds 1i Show me how to solve Broad Peaks SBack to Top of List Contents A110 V Index Missing Peaks or Marker Peaks 0 006 0 005 0 004 0 003 0 002 0 001 0 000 Fluorescence 0 001 0 002 0 003 0E SE OF SP 0S SS 09 9 of G 08 S8 06 G6 DOL SOL OLL Time seconds Show me how to solve Missing Peaks or Marker Peaks Back to Top of List Contents A111 V7 Index Poor Baseline Dips 125 100 75 50 Fluorescence 25 25 25 30 35 40 45 50 55 60 65 70 T9 80 85 90 Time seconds Show me how to solve Poor Baseline Dips Back to Top of List Contents A112 V Index Poor Baseline Drift 50 50 Fluorescence 100 150 SHAM TOR DHOK AY ODM OMOK NI TOD OMS Tor ING 25 30 35 40 45 50 55 60 65 70 75 80 85 90 Time seconds Show me how to solve Poor Baseline Drift Back to Top of List Contents A113 V Index Poor Baseline Noise Fluorescence 25 30 35 40 45 50 55 60 65 70 75 80 85 90 Time seconds Show me how to solve Poor Baseline Noise Back to Top of List Contents A114 V Index Poor Baseline Jumps 20 0 17 5 15 0 12 5 10 0 7 5 Fluorescence 5 0 2 5 0 0 2 5 dD xs ao 5 s s a Ss 70 7s a Bs sa ss 1m 105
38. 25 30 35 40 45 Time seconds Show me how to solve No or Low Sample Peaks Back to the Top of List Contents A 239 V Index Apparently Missing Sample Peak well 1 well 2 70 60 50 40 30 Fluorescence 20 15 20 25 30 35 40 45 Time seconds Show me how to solve Apparently Missing Sample Peak Back to the Top of List Contents A 240 V Index Low Ladder Peaks Fluorescence 15 20 25 30 35 40 45 Time seconds L Show me how to solve Low Ladder Peaks Back to the Top of List Contents A 241V Index Wrong Alignment of Ladder Peaks Fluorescence 15 20 25 30 35 40 45 Time seconds L Show me how to solve Wrong Alignment of Ladder Peaks Back to the Top of List Contents A242 W Index Broad Peaks Fluorescence 15 20 25 30 35 40 45 Time seconds 9 Show me how to solve Broad Peaks Back to the Top of List Contents A243 V7 Index Cross Contamination 80 4mgmi Carbonic Anit rane in well 5 60 50 Fluores cence Carbonic Andras carmyowr Inwell 10 22 23 24 235 235 7 B a Ei Time seconds Show me how to solve Cross Contamination Back to the Top of List Contents A 24V Index Dips Fluorescence 15 20 25 30 35 40 45 Time seconds Show me how to solve Dips Back to the Top of List Contents A245 V Index Maintenance Care and Cleaning of the Agilent 2100 Bioanalyzer The Agilent 2100 bioanalyzer should be kept clean Cleaning should be d
39. 398 for use with luer lock syringe Multiport Cable G2938 81610 for rocketport card Contents A 288 V Index Index A Additional sample or ladder peaks DNA 54 Protein 197 RNA 126 Advanced tab 18 Agilent 2100 bioanalyzer 12 Agilent 2100 bioanalyzer software 16 Apparently Missing Sample Peak 219 Autofocus failure 69 Autofocus test 39 B Background low 159 Bend Ladder Baseline 96 Broad peaks 66 141 225 Bubbles 7 C Changing 16 Pin Bajonet Cartridge 263 16 Pin Cartridge 257 Com port settings 17 Chip Alert tab 18 Contents Chip not detected 124 Chips 11 Cleaning Electrodes 12 the 16 pin Cartridge 259 the Pin Set of the 16 pin Cartridge 271 Clogged spin filters 46 184 Com port settings 16 Communication 15 Communication test 38 COM Port setting 18 Contaminated electrode tips 254 Cross contamination 7 90 161 235 254 D Data Files tab 18 Decontamination Procedure for RNA Assay 13 Degraded DNA Ladder 56 Protein ladder 191 199 209 222 RNA Ladder and or Samples 131 Denaturation Protein ladder 10 A 289 V Index Diagnostics 15 Autofocus test 39 Communication test 38 Electrode diode test 39 Electronic test 38 Fan test 39 High voltage test 39 Laser LED Optics 39 Leak current test 39 Lid test 38 Short circuit test 38 Stepper motor test 39 Temperature test 39 Dimmed icon 15 Diode test 39 Dye concentrate Protein 11 E Electrode Cartridge Maintenance 254 Electrode cleaner 12 255
40. 5 0 004 0 003 0 002 0 004 Fluorescence 0 000 0 001 0 002 0 003 0E SE OF SP 0S SS 09 S93 of Gi 08 S8 06 G6 00L SOL OLL Time seconds 1 Show me how to solve Missing Peaks or Marker Peaks Back to Symptoms Contents A77 Index Missing Peaks or Marker Peaks Most Probable Causes Solution Laser broken Perform Laser LED Optics test and Autofocus test like described in Hardware Diagnostics 48 If tests fail call Agilent Technologies No ladder samples in wells Use a new chip Pipette ladder sample in all wells Clogged priming station Check the performance of the chip priming station by applying the seal test For details see Maintaining the Chip Priming Station 271 Wrong settings of chip priming station For the correct position of the syringe clip and base plate please refer to the Reagent Kit Guide Current leaks due to contaminated electrodes Clean electrodes with analysis grade water and a toothbrush see Maintenance 246 Replace electrode cartridge Probable Causes Solution Chip pipetting error Contents Al18V Use new chip Always insert the pipette tip to the bottom of the well when dispensing the liquid Holding the pipette at a slight angle will ensure proper dispensing of the liquid Use appropriate pipette and tips Index Least Probable Causes Solution Autofocus failure Check autofocus by means
41. 5 40 45 50 55 60 65 70 75 80 85 90 Time seconds Show me how to solve Poor Sensitivity Back to Symptoms Contents A 69 V Index Poor Sensitivity Most Probable Causes Solution Dye concentration too low marker disappears Use dye concentration according to the Reagent Kit Guide Let the dye warm up to room temperature before preparing the gel dye mix Pipetting error during preparation of mixtures Check dilution procedure Check calibration of pipette Chip pipetting error Pipette new chip Always insert the pipette tip to the bottom of the well when dispensing the liquid Holding the pipette at a slight angle will ensure proper dispensing of the liquid Use appropriate pipette and tips Probable Causes Solution Fingerprint on focusing lens Clean lens like decribed in Lens Maintenance 270 Insufficient vortexing of chip Vortex chip for 1 minute Only use IKA shaker for chip vortexing Adjust speed to set point Contents Al0V Index Least Probable Causes Solution Chip contaminated Wear powder free gloves only Don t touch the underside of the chip Don t touch the wells of the chip Clean the electrodes Load the chip immediately after taking it out of its sealed bag Vibration of Agilent 2100 Bioanalyzer Don t touch Agilent 2100 Bioanalyzer during a run Remove vibration devices such as vortexers and vacuum pumps from bench
42. A i a oe So oe a e p a a on a 6 6 7 5 80 8 9 95 Time seconds Show me how to solve Peaks Migrating Late Back to Top of List Contents A 120 V Index Late Migration and Peak Broadening 45 40 AS 30 25 20 Fluorescence 25 30 35 0 45 so 55 60 65 70 75 80 35 30 Time seconds Show me how to solve Late Migration and Peak Broadening Back to Top of List Contents A121 V7 Index Bend Ladder Baseline 175 L L 170 E 165 F o 160 T S F oY i E a a o C Wo dL ore of tbe om a S L fod yr Yi i C Io HI JA eee ponds 7 of I bt Tenant he 150 ll J eer C IAN IA A L A N 45 Jy 4 ee oR 140 Hit oe Q D A ol ol DD op N s co o lt o lt o Oo on oOo Sz oO o Oo o oO o Oo o Oo o oO oO Oo o oO Time seconds Show me how to solve Bend Ladder Baseline Back to Top of List Contents A122 V Index Troubleshooting the RNA Application Essential Measurement Practices For hints on how to handle chips and chemicals see Essential Measurement Practices Troubleshooting the Application Error messages appearing on the screen describe a problem that has occurred with either the hardware or the software Click the Alor BJ button next to the error message to view a help screen that is
43. E FE EN EN IE Cross Contamination 227 List of Protein Electropherograms 231 Contents A 186 V Index Clogged spin filters Most Probable Causes Solution Gel was centrifuged at too low g value Refer to the Protein Reagent Kit Guide for proper centrifuge settings Cooled centrifuge was used for preparation of gel dye mix and or destaining solution Repeat centrifugation step without cooling Least Probable Causes Solution Particles in the gel dye mix and or destaining solution Repeat the preparation of the gel dye mix and or destaining solution Wear powder free gloves only Back to Symptoms Contents A 187 V Index Too High Quantitation Results Most Probable Causes Solution Upper marker wrongly assigned Check assignment of upper marker Diluted samples are too old Use diluted samples within one day Sample buffer and or Denaturating Solution not handled according to the instructions For proper preparation and storage of the sample buffer and denaturating solution refer to the Protein Ragent Kit Guide Pipetting error during preparation of mixtures Check dilution procedure Check calibration of pipette Chip pipetting error Pipette new chip Always insert the pipette tip to the bottom of the well when dispensing the liquid Use appropriate pipette and tips Probable Causes Solution Samples not completly denaturated
44. Electrode diode test 39 Electrodes 255 Cleaning 12 Electronic test 38 Errors 38 Essential Measurement Practices 7 Evaporation of liquid 256 Contents F Fan test 39 Firmware 38 Firmware error messages 38 Focusing lens 12 14 G Gel 8 Gel Dye 8 Gel dye mixture 8 Genomic DNA Contamination 129 Growth medium 214 H Handling Chips 11 Reagents 8 Handling tools chips and reagents 7 Hardware diagnostic tests 38 Hardware Diagnostics 38 Hardware diagnostics 262 273 High voltage test 39 Inserting the 16 Pin Bajonet Cartridge 270 the 16 Pin Cartridge 261 Pin Set of 16 Pin Bajonet Cartridge 268 A 290 V Index lsopropanol 274 L Lab on a Chip web site 7 Ladder degraded 49 Laser test 39 Late Migration and Peak Broadening 94 Late Migration of RNA Ladder or Samples 163 Leak current 256 Leak current test 39 LED Test 39 Lens maintenance 274 Lens paper 274 Lid 255 Lid Sensor broken 52 Lid test 38 Liquid spill 274 List of DNA Electropherograms 98 Protein Electropherograms 238 RNA Electropherograms 165 Low Protein ladder peaks 221 Protein sample peaks 216 M Maintenance 254 Contents A 291 V Chip Priming Station 275 Electrode Cartridge 254 Missing Peaks RNA 144 Peaks or marker peaks DNA 68 Sample peaks Protein 228 Multi Port Card Setup 21 N No peaks High background DNA 84 High Background RNA 156 Low background DNA 87 protein 213 Noisy electropherogram 63 139 0
45. J button next to the error message to view a help screen that is specific for that error Additional information regarding the nature of a problem can often be found in the Run Log for the data file Choose Tools gt View Log File gt Run Log The Run Log lists all the actions and errors that occurred during the run In rare cases results generated by your Agilent 2100 Bioanalyzer might not be what you expected To help you find the reason for the discrepancy see Symptoms 4 Contents A52V Index For most observations you will find at least one corresponding example depicting a typical electropherogram or result table Once you have identified the observation that resembles the outcome of your experiment you will get a set of assigned causes listed by priority The causes are grouped into three levels e most probable cause probable cause e least probable cause A list of solutions that help you to fix the problem are assigned to the causes For successful troubleshooting go through all the solution hints listed by priority If you are not able to assign a symptom to your problem compare your electropherogram with the List of DNA Electropherograms 106 Contents A53 V Index Symptoms Click the icon to see an example or go straight to the troubleshooting hints FAEAABABAEE EE Clogged Spin Filters 56 Too High Quantification Results 57 Too Low Quantification Results 58 Wrong Sizing Result 59 Poor Chip Perfo
46. Port Card The setup process is described on the following pages For support on configuring the RocketPort PCl Quad DB9 Multi Port Serial card please contact Agilent service personnel Contents A21V Index Step1 Disabling the Standard PC Serial Ports COM1 and COM2 The embedded serial ports of your PC must be disabled before you can use your RocketPort card To do so 1 Select Start gt Settings gt Control Panel gt System gt Hardware gt Device Manager Action View e am Ele A MULTISYSTEM2000 Computer ZS Disk drives E Display adapters da DYD CD ROM drives 3 Floppy disk controllers amp Floppy disk drives 3 IDE ATA ATAPI controllers 3 Keyboards T Mice and other pointing devices 3 Monitors J Multi port serial adapters EF Network adapters BAP orts COM amp LPT g Sound video and game controllers m System devices Universal Serial Bus controllers E cs E E cs Es Es Es es E E H E E z n Contents A22V Index 2 Double click the symbol called Ports COM amp LPT Contents Action view gt m ef ay H Computer H E Disk drives H Display adapters H A DVD CD ROM drives aS Floppy disk controllers Floppy disk drives H 6 IDE ATA ATAPI controllers ee Keyboards He Mice and other pointing devices 8 Monitors H E Network adapters E Ea a Se Multi port serial adapters BE Ports COM amp LPT seen 3 Commu
47. Probable Causes Solution Dye concentration too low marker disappears Use dye concentration according to the DNA Reagent Kit Guide Let the dye warm up to room temperature before preparing the gel dye mix Least Probable Causes Solution Loaded chip kept for too long before run Prepared chips must be used within 5 min Back to Symptoms Contents A5 V Index Too Low Quantification Results Most Probable Causes Solution Pipetting error during preparation of mixtures Check dilution procedure Check calibration of pipette Chip pipetting error Use new chip Always insert the pipette tip to the bottom of the well when dispensing the liquid Use appropriate pipette and tips Insufficient vortexing of chip Vortex chip for 1 minute Only use the IKA vortexer Adjust the speed to the set point Probable Causes Solution Loaded chip kept for too long before run Prepared chips must be used within 5 min Sample concentration too high Use sample concentration according to the DNA Reagent Kit Guide Least Probable Causes Solution Dye concentration too high Use dye concentration according to the DNA Reagent Kit Guide Let the dye warm up to room temperature before preparing the gel dye mix Back to Symptoms Contents A 58 V Index Wrong Sizing Result Most Probable Causes Solution DNA ladder degraded Check expira
48. aining the Chip Priming Station 271 Check if clip and base plate of priming station are in the right position see Protein Reagent Kit Guide Amount of liquid pipetted is too low or chip is empty Check Reagent Kit Guide on amount of liquid to be pipetted Fill unused wells with ladder or sample replicate Check calibration of pipette Chip pipetting error Use new chip Always insert the pipette tip to the bottom of the well when dispensing the liquid Use appropriate pipette and tips Contents A 193 V Index Probable Causes Solution Chip preparation was done with cold reagents Prepare a new chip Allow all reagents and reagent mixes to warm up to room temperature before use Chips were stored in the fridge freezer Prepare a new chip Store chips at room temperature Least Probable Causes Solution High voltage power supply defective Check high voltage power supply using the Hardware Diagnostics 48 If the power supply is defective call Agilent Technologies Back to Symptoms Contents A 194 V Index Apparently Short Run Time 45 40 35 30 25 20 Fluorescence 15 20 25 30 35 40 45 Tire seconds Show me how to solve Apparently Short Run Time Back to Symptoms Contents A 195 V Index Apparently Short Run Time Most Probable Causes Solution Low intensity of upper marker in the ladder They To correct for wrong selected upper
49. and preparation of Sample buffer denaturating solution not handled ihe sample butte denaturating solution according to the instructions To correct for wrong selected upper marker set upper marker manually If necessary adjust peak find settings Because of low intensity the software identified sample peak as upper marker For better upper marker identification Turn off the analysis For correct alignment overlay electropherograms of multiple wells to clearly identify the upper marker Back to Symptoms Contents A219 V Index Low Ladder Peaks Fluorescence 15 20 25 30 35 40 45 Time seconds L Show me how to solve Low Ladder Peaks Back to Symptoms Contents A220 V Index Low Ladder Peaks Most Probable Causes Solution Ladder degraded Refer to the Protein Reagent Kit Guide for proper ladder storage Optional Prepare ladder aliquots Use a new aliquot Ladder not diluted after denaturation Refer to the Ragent Kit Guide for proper chip preparation Probable Causes Solution Ladder not completly denaturated Use fresh ladder aliquot Heat ladder for 5 min at 100 C Ladder dried out Ladder was denaturated in 1 5 mL tubes Use 0 5 mL tubes for denaturating Diluted ladder is too old Use diluted ladder within one day Pipetting error during preparation of mixtures Check dilution procedure Check calibration of pipette Back to Symptom
50. as added in one sample and not in the other Contents A 213 V Refer to the Reagent Kit Guide for proper sample reduction Index Probable Causes Solution Diluted samples are too old Use diluted samples within one day Buffer component interfers with LDS SDS in See Protein Reagent Kit Guide for a list of sample buffer compatible buffers and buffer compounds For an updated list please refer to the web site www agilent com chem labonachip If necessary dilute dialyze or desalt the sample Back to Symptoms Contents A214 V Index No or Low Sample Peaks 40 35 30 25 20 15 Fluorescence 10 15 20 25 30 35 40 45 Time seconds Show me how to solve No or Low Sample Peaks Back to Symptoms Contents A 215 V Index No or Low Sample Peaks Most Probable Causes Solution Protein concentration in samples too low Use protein concentration accorting to specifications given in the Reagent Kit Guide Too high salt concentration in samples Sensitivity is strongly affected by salt concentration Dilute samples in deionized H30 dialyze samples against low salt buffer or desalt samples using spin filters SDS not completely dissolved in dye concentrate Let dye concentrate equilibrate to room temperature for 20 min before use Check for undissolved SDS cristals in the tube Vortex dye concentrate well before use If necessary heat the sample buffer to 37 C for 2 min
51. ation cleaning procedure on a daily basis before running any RNA assays See Maintenance 246 for more information regarding the use of the electrode cleaner and or the procedures for cleaning and or decontamination Decontamination 1 Slowly fill an electrode cleaner with 350 uL RNAseZAP Label this electrode cleaner for RNAse ZAP 2 Open the lid place the electrode cleaner in the instrument and close the lid for approximately 1 minute 3 Open the lid remove the RNAse ZAP electrode cleaner and store it for future use You can reuse this electrode cleaner for all the chips in the kit Empty the electrode cleaner for overnight storage 4 Then follow the instructions below for cleaning the electrodes Cleaning 1 Slowly fill another electrode cleaner with 350 uL RNAse free water Label this electrode cleaner RNAse free water 2 Open the lid load this electrode cleaner into the instrument and close the lid immersing the electrodes in the water Contents A12V Index 3 After approximately 10 seconds remove the electrode cleaner Put this electrode cleaner aside for future use as well 4 Wait another 10 seconds for the water on the electrodes to evaporate Contents A13V Index Troubleshooting the Instrument Communication Communication To check whether your PC communicates with the Agilent 2100 Bioanalyzer 1 Start the Agilent 2100 Bioanalyzer software 2 Open and close the lid the icon in the main screen should
52. call Agilent Technologies Back to Symptoms Contents ASLV Index Poor Baseline Noise Fluorescence 25 30 35 40 45 50 55 60 65 70 75 80 85 90 Time seconds Show me how to solve Poor Baseline Noise Back to Symptoms Contents A8V Index Poor Baseline Noise Most Probable Causes Solution Chip not properly primed Air bubble in chip Use a new chip Check chip priming station syringe for good seal see Maintaining the Chip Priming Station 271 Check if clip and base plate of priming station are in the right position see DNA Reagent Kit Guide Probable Causes Solution Loaded chip kept for too long before run Prepared chips must be used within 5 min Contents A 86 V Index Least Probable Causes Solution Chip contaminated Wear powder free gloves only Don t touch the underside of the chip Don t touch the wells of the chip Clean the electrodes Load the chip immediately after taking it out of its sealed bag Autofocus failure Check autofocus by means of the Hardware Diagnostics 48 If autofocus fails call Agilent Technologies High voltage power supply defective Check high voltage power supply using the Hardware Diagnostics 48 If the power supply is defective call Agilent Technologies Back to Symptoms Contents A8 V Index Poor Baseline Jumps 20 0 17 5 15 0 10 0 7 5 Fluorescence 5 0 2 5 0 0 2 5
53. e lid closure WARNING Make sure that the electrode cartridge is completely dry before replacing it back into the electrode base Even small amounts of liquid on the pin set can damage the high voltage power supply Contents A 256 V Index Changing the 16 Pin Bajonet Cartridge The 16 pin bayonet cartridge see Figure 4 reorder number 5065 4413 contains 16 electrodes These are configured to fit in to the wells of a LabChip The electrodes make contact with the liquid in the wells when the lid of the Agilent 2100 bioanalyzer is closed The cartridge which includes the pin set can be removed if the electrodes become contaminated or damaged Figure 4 16 Pin Cartridge and Pin Set of Cartridge Pin Set Contents A 257 V Index Removing the 16 Pin Bajonet Cartridge WARNING Do not touch the electrodes while the cartridge is in the 2100 bioanalyzer this could cause damage to the electrodes and high voltage power supplies 1 Turn off line power to the 2100 bioanalyzer The line switch is located at the rear of the 2100 bioanalyzer 2 Open the lid 3 Pull the metal lever on the inside left of the lid to the vertical position as shown in Figure 2 When the lever is in the vertical position the cartridge is released from the lid by about 10 mm 4 Gently pull the cartridge out of the lid as shown in the Figure 5 Contents A 258 V Index Figure 5 Removing the 16 Pin Cartridge
54. e sample or buffer in all wells Chip not properly primed Air bubble in chip Use a new chip Check chip priming station syringe for good seal see Maintaining the Chip Priming Station 271 Check if clip and base plate of priming station are in the right position see RNA Reagent Kit Guide Probable Causes Solution No communication between Agilent 2100 Bioanalyzer and PC Check whether serial cable is connected Check status control image of Agilent 2100 Bioanalyzer open and close the lid Least Probable Causes Solution High voltage power supply defective Check high voltage power supply using the Hardware Diagnostics 48 If the power supply is defective call Agilent Technologies Back to Symptoms Contents A 133 V Index Poor Chip Performance Most Probable Causes Solution Chip not properly primed Air bubble in chip Use a new chip Check chip priming station syringe for good seal see Maintaining the Chip Priming Station 271 Check if clip and base plate of priming station are in the right position see RNA Reagent Kit Guide Probable Causes Solution Chip preparation was done with cold reagents Prepare a new chip Allow all reagents and reagent mixes to warm up to room temperature before use Chips were stored in the fridge freezer Prepare a new chip Store chips at room temperature Amount of liquid pipetted is too low or chip
55. eck if clip and base plate of priming station are in the right position see Protein Reagent Kit Guide Leak Current due to contaminated electrodes Chip was left in instrument after run Contents A225 V Clean electrodes with analysis grade water and a toothbrush see Maintenance 246 Don t leave chip in instrument after run Clean electrodes after each run Replace electrode cartridge Index Probable Causes Solution Sample was not denaturated properly Use fresh sample aliquot Heat sample denaturating solution for 5 min at 100 C Reducing agent BME or DIT was added in one Refer to the Reagent Kit Guide for proper sample sample and not in the other reduction High voltage power supply defective Check high voltage power supply using the Hardware Diagnostics 48 If the power supply is defective call Agilent Technologies Back to Symptoms Contents A 226 V Index Cross Contamination 80 70 4mgmi Carbonic Anit crass In well 5 60 50 Fluorescence Carbonic Anydrais carmowr Inwell 10 22 23 24 235 2 7 B 23 wv Time seconds Show me how to solve Cross Contamination Back to Symptoms Contents A221 V Index Cross Contamination Most Probable Causes Solution Sample concentration too high Use sample concentration according to the Protein Reagent Kit Guide Contaminated electrodes Chip left in instrument after run Clean electrodes with analysis g
56. ed chip kept for too long before run Prepared chips must be used within 5 min Dye concentration too low Use dye concentration according to the Reagent Kit Guide Let the dye warm up to room temperature before preparing the gel dye mix Chip not properly primed Air bubble in chip Use a new chip Check chip priming station syringe for good seal see Maintaining the Chip Priming Station 271 Check if clip and base plate of priming station are in the right position see DNA Reagent Kit Guide Clogged gasket and plastic adapter of priming station Perform seal test like described in Maintaining the Chip Priming Station 271 Clean replace gasket and plastic adapter If necessary Contents A 160 V Index Probable Causes Solution Chip contaminated Wear powder free gloves only Don t touch the underside of the chip Don t touch the wells of the chip Clean the electrodes Load the chip immediately after taking it out of its sealed bag Least Probable Causes Solution Changes of ambient temperature of more than 5 C during the run Place Agilent 2100 Bioanalyzer in thermally stable environment High voltage power supply defective Check high voltage power supply using the Hardware Diagnostics 48 If the power supply is defective call Agilent Technologies Back to Symptoms Contents A 161 V7 Index Wavy Baseline 40 35 30 25 20 15 10 Fl
57. ed gasket and plastic adapter of priming station Perform seal test like described in Maintaining the Chip Priming Station 271 Clean replace gasket and plastic adapter if necessary Chip not properly primed Air bubble in chip Use a new chip Check chip priming station syringe for good seal see Maintaining the Chip Priming Station 271 Check if clip and base plate of priming station are in the right position see RNA Reagent Kit Guide Dye concentration too high Use dye concentration according to the Reagent Kit Guide Let the dye warm up to room temperature before preparing the gel dye mix Contents A 152 V Index Probable Causes Solution Clogged channel due to too high sample Use sample concentration according to the RNA concentration in previous lane Reagent Kit Guide Particles of protective foam pad on electrode Make sure to remove foam particles of the cartridge electrode cartridge before use Least Probable Causes Solution High voltage power supply defective Check high voltage power supply using the Hardware Diagnostics 48 If the power supply is defective call Agilent Technologies Back to Symptoms Contents A 153 V Index Missing Peaks 0 006 0 005 0 004 0 003 0 002 0 001 Fluorescence 0 000 0 001 0 002 0 003 0E SE OF SP 0S SS 09 S93 of Gi 08 S8 06 G6 00L SOL OLL Time seconds 1 Show me how to solve Missing Peaks
58. etup You can navigate between the different dialogs by clicking on the Back and Next buttons Add Device Wizard x hm This wizard will help you quickly install and Po configure your new Comtrol hardware OOM rcweccer i Cancel Help 7 On the second window of the Add Device Wizard you must specify the bus type of the installed RocketPort card Choose the option PCI bus Contents A 36 V Index Add Device Wizard x Select the bus type for your board 7 N ARETE Aronen aAA eoecccor C ISA bus 4 EEEN PCI bus TrRecnseenvennnned lt Back Cancel Help 8 Then you must specify the board model You must keep the proposed setting RocketPort 9 Press Next to continue to the following dialogue Contents A3 V Index Add Device Wizard x Select your board model Min ELE raver 000 Og eewccncer RocketPort lt Back Cancel Help 10 The next step is to specify the number of ports supported by the installed card Change the number of supported ports from 8 default value to 4 as this is the number of physical ports of the installed card 11 Press Next to continue to the following dialogue Contents A38 V Index Add Device Wizard x How many ports are on the hardware A lt m cme eo 12 Click the Finish button to finish the installation Contents A39 V Index Add Device Wizard x Select Finish to complete adding the hardware A lt p lt Back
59. he hardware tests you want to apply from the list given in the interface The recommendation is to apply all tests Diagnosis Instrument Communication Test Electronics Test Lid Sensor Test Short Circuit Test Laser LED 7 Optics Test Select All Tests High Voltage Test Stepper Motor Test Unselect All Tests Fan Test Temperature Test Autofocus Test Electrode Diode Test Leak Current Test KKK K K K K K K K K You may execute only a subset of the available tests by deselecting some of 3 Click the Start diagnosis button to execute the tests Contents A50V Index NOTE If there is no communication between the Agilent 2100 Bioanalyzer and the PC the software will prompt you See Troubleshooting the Instrument Communication 14 for troubleshooting hints 4 Follow the instructions as given by the Agilent 2100 Bioanalyzer software 5 At the end of the procedure all tests must be passed 6 If the tests are not passed redo the tests 7 If failures still persist call Agilent Technologies Contents A51V Index Troubleshooting the DNA Application Essential Measurement Practices For hints on how to handle chips and chemicals see Essential Measurement Practices Troubleshooting the Application Error messages appearing on the screen describe a problem that has occurred with either the hardware or the software Click the Alor B
60. ions dialog box click the OK button to close it Contents A19V Index Multi instrument system Setting up the Serial Interface of your Agilent 2100 bioanalyzer Multi Instrument System G2942AA General In case you have to re install your operating system using the recovery CD provided you also need to setup the RocketPort PCl Quad DB9 Multi Port Serial card in your PC This will enable multi instrument support for the Agilent Technologies bioanalyzer 2100 again NOTE Reloading the software might be necessary after severe PC system crashes or in case part of the software installation has been corrupted Please make sure to have the RocketPort PCI Quad DB9 Multi Port Serial card properly installed before trying to configure the serial ports as described in this document The necessary steps to enable multi instrument support for the Agilent Technologies bioanalyzer 2100 depends on the installed operating system Coose MultiPort Card Setup Process Windows 2000 MultiPort Card Setup Process Windows NT Contents A20 V Index MultiPort Card Setup Process Windows 2000 NOTE After re installation of the operating system make sure that the MultiPort Cable reorder number G2938 81610 is plug in Windows 2000 will automatically detect the MultiPort Card and install the necessary driver The setup process of the MultiPort Card requires 2 steps Step1 Disabling the standard serial ports Step 2 Assigning COM1 to COM4 to the Rocket
61. is empty Check assay procedure on amount of liquid to be pipetted Least Probable Causes Solution High voltage power supply defective Check high voltage power supply using the Hardware Diagnostics 48 If the power supply is defective call Agilent Technologies Back to Symptoms Contents A 134V Index Additional Sample or Ladder Peaks 80 maui d w 50 Peak oO 5 o 40 wm 2 5 30 iL 20 10 o A 8 21 26 31 36 41 46 51 56 61 66 Time seconds Show me how to solve Additional Sample or Ladder Peaks Back to Symptoms Contents A 135 V Index Additional Sample or Ladder Peaks Most Probable Causes Solution Chip contaminated Wear powder free gloves only Dust particles in separation channels Don t touch the wells of the chip Clean the electrodes Load the chip immediately after taking it out of its sealed bag Particles of protective foam padon Make sure to remove foam particles of the electrode electrode cartridge cartridge before use Contamination with Genomic DNA Refer to Genomic DNA Contamination 139 Contents A 136 V Index Probable Causes Solution RNA ladder sample not denaturated properly Heat ladder samples at 70 C for 2 min Chip not properly primed Air bubble in chip Use a new chip Check chip priming station syringe for good seal see Maintaining the Chip Priming Station 271 Check if clip and base plate of priming sta
62. is device enable Do not use this device disable Contents A2V Index 5 Repeat the previous steps to disable Communication Port COM2 Return to the Device Manager a Device Manager Action View MULTISYSTEM2000 Computer Disk drives Display adapters J DYD CD ROM drives E3 Floppy disk controllers 9 Floppy disk drives E3 IDE ATASATAPI controllers Keyboards E Mice and other pointing devices 3 Monitors Si multi port serial adapters BD Network adapters Y Ports COM amp LPT E 2 Communications Port COM1 eee Communications Port COM2 Y Comtral Port 0 COM3 Y Comtral Port 1 COM4 Y Comtrol Port 2 COMS Y Comtrol Port 3 COM6 ow ECP Printer Port LPT1 GENIS Sound video and game controllers H System devices 2 Universal Serial Bus controllers g g H g H g E g g E g E Contents A26V Index Step2 Assigning COM1 to COM4 to the RocketPort Card 1 Select Start gt Settings gt Control Panel gt System gt Hardware gt Device Manager Double click the symbol called Multi port serial adapters MULTISYSTEM2000 Computer Disk drives Display adapters 23 DYD CD ROM drives 3 Floppy disk controllers Floppy disk drives Sy IDE ATA ATAPI controllers Keyboards g Mice and other pointing devices 3 Monitors O 8 2 SY Multi port serial adapters Be WERocketPort PCI 4 Port PCI BUS BY Network adapte
63. is verified if the plunger moves back up to the 0 3 ml mark within less than 1 second Contents A215 V Index NOTE If the plunger doesn t move up to the 0 3ml mark within a second the syringe chip connection is probably not tight enough Re tighten the syringe and or replace the syringe adapter and or syringe to fix the problem If Seal Test fails A failed seal test indicates the gasket must be replaced Replacement procedure 1 Use a needle to pull out the silicon gasket NOTE Avoid scratching the plastic adapter when removing the silicon gasket 2 Insert new gasket and gently push into place 3 Apply the seal test Contents A 276 V Index Figure 17 Syringe Adapter with Gasket Figure 18 i Disassembled Syringe Adapter AN S d i N N A S J KA S SOS sea Contents A 271W Index Changing the Fuses of the Agilent 2100 Bioanalyzer You need to change the fuses if the status indicator is off and the cooling fan is not running Material Needed Refer to for the type of fuses needed Specifications of Fuses Description Part Number Number of Items Fuse T 1A 250V 2110 0007 2 Changing the Fuse WARNING Disconnect the Agilent 2100 Bioanalyzer from line power before changing a fuse 1 Disconnect the power cable from the power input socket at the rear of the Agilent 2100 Bioanalyzer 2 To access the fuse drawer gently lift the outer plastic housing of the power inlet socket using a screwdriver
64. l take effect Do you want to restart your computer now After the reboot the RocketPort card is set up properly to work with the Agilent bioanalyzer 2100 Software The instruments connected to the card can be referred as COM1 to COM4 Contents A43V Index NOTE The warning message Warning PCI num ports mismatch may appear in the event logbook of your PC This is NOT an error and can be ignored It happens only if you have no instrument connected to the RocketPort card After connecting an instrument no event is logged after startup Contents A44V Index Troubleshooting the Agilent 2100 Bioanalyzer Software If your Agilent 2100 Bioanalyzer software is no longer working properly you can check for corrupted or missing files 1 If the Bio sizing is running close it 2 Start the software test tool by clicking Installation Qualification in the Agilent 2100 Bioanalyzer program group Programs gt ES Agilent 2100 Bioanalyzer gt FS Utilities 3 The Installation Qualification interface appears Click Start Validation to start the software test tool The result of the installation qualification test depends on whether the software installation is complete and no files are corrupted Result Result 4 Ifthe test passes and the Agilent 2100 Bioanalyzer system still does not function correctly see Communication 14 and Hardware Diagnostics 48 for further troubleshooting procedures Finally check your application see
65. lectrode base by pushing the plastic lever of the bayonet cover to the right as shown in Figure 9 Figure 9 Closing the Socket of the Pin Set Plastic lever Contents A264 V Index Inserting the 16 Pin Cartridge WARNING Make sure the pin set is be completely dry before putting in the 16 pin cartridge Even small amounts of liquid on the pin set can damage the high voltage power supply of your instrument 1 Slide the 16 pin cartridge into the bioanalyzer lid as shown in Figure on next page 2 Move the metal lever in the flat closed position 3 Push the metal front of the 16 pin cartridge to ensure a tight connection to the 2100 bioanalyzer Contents A 265 V Index Figure 10 Metal lever Contents Inserting the 16 Pin Cartridge seid A 266 V Push here to ensure that a tight connection is made Index Cleaning the Pin Set of the 16 pin Cartridge After removing the pin set from the 16 pin cartridge you can clean it by either using e de ionized water e isopropanol or e RNAse Zap Figure 11 Pin Set Contents A 267 V Index On a regular quarterly basis or after contamination gently clean the pin set with a lint free surgical cotton swab damped in de ionized water WARNING The pins of the pin se
66. lyzer during a run Remove vibration devices such as vortexers and vacuum pumps from bench RNA ladder sample not denaturated properly Heat ladder samples at 70 C for 2 min Least Probable Causes Solution Power outlett Install power filter Back to Symptoms Contents A144V Index Poor Sensitivity 1 1 1 0 0 9 0 8 0 7 0 6 0 5 0 4 Fluorescence 0 3 0 2 0 1 0 0 4 0 1 17 22 27 32 37 42 47 52 Time seconds Show me how to solve Poor Sensitivity Back to Symptoms Contents A 145 V 57 62 67 72 Index Poor Sensitivity Most Probable Causes Solution Dye concentration too low Use dye concentration according to the Reagent Kit Guide Let the dye warm up to room temperature before preparing the gel dye mix Pipetting error during preparation of mixtures Check dilution procedure Check calibration of pipette Chip pipetting error Pipette new chip Always insert the pipette tip to the bottom of the well when dispensing the liquid Use appropriate pipette and tips Probable Causes Solution Fingerprint on focusing lens Clean lens like described in Lens Maintenance 270 Insufficient vortexing of chip Vortex chip for 1 minute Only use IKA shaker for chip vortexing Adjust speed to set point Contents A 146 V Index Least Probable Causes Solution Chip contaminated Wear powder free gloves only Don
67. ng the Instrument Communication 14 Least Probable Causes Solution High voltage power supply defective Check high voltage power supply using the Hardware Diagnostics 48 If the power supply is defective call Agilent Technologies Back to Symptoms Contents A62V Index Additional Sample or Ladder Peaks 25 Fluorescence rp Additional Peaks 10 i DdD xs ao 5 Es s a Ss 70 75 a 5 so 55 10 105 110 Time seconds 1i Show me how to solve Additional Sample or Ladder Peaks Back to Symptoms Contents A 63 V Index Additional Sample or Ladder Peaks Most Probable Causes Solution Chip contaminated Dust particles in separation channels Wear powder free gloves only Don t touch the wells of the chip Clean the electrodes Load the chip immediately after taking it out of its sealed bag Particles of protective foam pad on electrode cartridge Make sure to remove foam particles of the electrode cartridge before use Probable Causes Solution Chip not properly primed Air bubble in chip Use a new chip Check chip priming station syringe for good seal see Maintaining the Chip Priming Station 271 Check if clip and base plate of priming station are in the right position see DNA Reagent Kit Guide Vibration of Agilent 2100 Bioanalyzer Don t touch Agilent 2100 Bioanalyzer during a run Remove vibration devices such as vortexers and vacuum p
68. nications Port COM1 see K d Communications Port COM2 A Comtrol Port 0 COM3 A Comtrol Port 1 COM4 A Comtrol Port 2 COMS a Comtrol Port 3 COME on ECP Printer Port LPT1 iH fi Sound video and game controllers e System devices E Universal Serial Bus controllers A23V Index 3 Double click the symbol called Communication Port COM1 to open the Communication Port COM1 Properties box Communications Port COM1 Properties 21x General Port Settings Driver Resources F Communications Port COM1 Device type Ports COM amp LPT Manufacturer Standard port types Location on Generic Bus Device status This device is working properly IF you are having problems with this device click Troubleshooter to start the troubleshooter Device usage Use this device enable Contents A2V Index 4 To disable the COM1 port select Do not use this device disable from the drop down menue Communications Port COM1 Properties l 2 x General Port Settings Driver Resources F Communications Port COM1 fa Device type Ports COM amp LPT Manufacturer Standard port types Location on Generic Bus r Device status This device is working properly If you are having problems with this device click Troubleshooter to start the troubleshooter Troubleshooter Device usage Use this device enable Use th
69. nt 2100 Bioanalyzer 7 Close the lid and leave it closed for about 10 seconds 8 Open the lid and remove the electrode cleaner Wait another 10 seconds for the water on the electrodes to evaporate Contents A249 V Index Every 3 Months Evaporation of liquid from the chip could cause salt to coat the electrodes and the area between the electrodes Leak currents which distort the measurement results could result Remove electrode cartridge from the Agilent 2100 Bioanalyzer For changing the cartridge please select your cartridge type Changing the 16 Pin Cartridge 251 Changing the 16 Pin Bajonet Cartridge 25 Contents A 250 V Index Changing the 16 Pin Cartridge The 16 pin cartridge reorder number 5064 8244 contains 16 electrodes configured to fit in the wells of a LabChip The electrodes make contact with the liquid in the wells when the lid of the Agilent Technologies 2100 bioanalyzer is closed see Figure 1 The cartridge can be removed if the electrodes become contaminated or damaged Figure 1 16 Pin Cartridge Contents A251 V7 Index Removing the 16 Pin Cartridge WARNING Do not touch the electrodes while the cartridge is in the 2100 bioanalyzer the electrodes and high voltage power supplies can be easily damaged 1 Turn off line power to the 2100 bioanalyzer The line switch is located at the rear of the 2100 bioanalyzer 2 Open the lid Move the metal lever on the left of the inside of the lid to the ve
70. of the gel dye mix and destaining solution Let the dye warm up to room temperature for 20 min before preparing the gel dye mix Chip not properly prepared Prepare a new chip Allow all reagents and samples to warm up to room temperature before use Contents A210 V Index Probable Causes Solution Vibration of Agilent 2100 Bioanalyzer Don t touch Agilent 2100 Bioanalyzer during a run Remove vibration devices such as vortexers and vacuum pumps from bench Least Probable Causes Solution Power outlett Install power filter Back to Symptoms Contents A211 V7 Index Poor Reproducibility 20 Fluorescence 20 25 30 35 40 45 Time seconds Show me how to solve Poor Reproducibility Back to Symptoms Contents A212 V Index Poor Reproducibility Most Probable Causes Solution Wrong peak alignment Check if alignment is correct wrong alignment might cause broad peaks compared to the rest of the chip For better identification of the lower and upper marker Turn off the analysis For correct alignment overlay electropherograms of multiple wells to clearly identify the lower and upper marker One Sample not denaturated properly Use fresh sample aliquot Heat samples with denaturating solution for 5 min at 100 C One Sample dried out during denaturation Samples were denatured in 1 5 mL tubes Use 0 5 mL tubes for denaturating Reducing agent BME or DTT w
71. one with a damp lint freecloth Do not use an excessively damp cloth allowing liquid to drip into the Agilent 2100 bioanalyzer WARNING Do not let liquid drip into the Agilent 2100 bioanalyzer It could cause a shock or it could damage the Agilent 2100 bioanalyzer 1 Open the lid 2 Take out the electrode or the pressure cartridge 3 If any solutions have dried on the electrodes or pressure adapter use a damp lint free cloth to clean the electrodes or adapter WARNING When working with solvents please observe appropriate safety procedures for example goggles safety gloves and protective clothing as described in the material handling and safety data sheet supplied by the solvent vendor especially when toxic or hazardous solvents are used Contents A 246 V Index WARNING _ If pathogenic toxic or radioactive samples are intended to be used inthis instrument it is the responsibility of the user to ensure that all necessary safety regulations guidelines precautions and practices are adhered to accordingly Ask your laboratory safety officer to advise you about the level of containment required for your application and about proper decontamination or sterilization procedures to follow if fluids escape from containers Contents A 241 W Index Electrode Cartridge Maintenance Daily Basis Electrode Cleaner To avoid cross contamination due to contaminated electrode tips clean electrodes after each run 1 Slowly fill one of the well
72. ontamination 138 Degraded RNA Ladder and or Samples 140 Spikes Glitches 142 Poor Sensitivity 145 Noisy Electropherogram 148 Broad Peaks 151 Missing Peaks 154 FAEABABAE EEE Poor Baseline Dips 15 7 Contents A 125 V Index Poor Baseline Drift 159 Noisy Electropherogram 148 Wavy Baseline 162 Cross Contamination 165 FEE EE Late Migration of RNA Ladder or Samples 167 List of RNA Electropherograms 169 Contents A 126 V Index Too High Quantification Results Most Probable Causes Solution Pipetting error during preparation of mixtures Check dilution procedure Check calibration of pipette Chip pipetting error Pipette new chip Always insert the pipette tip to the bottom of the well when dispensing the liquid Use appropriate pipette and tips Probable Causes Solution Dye concentration too low Use dye concentration according to the RNA Reagent Kit Guide Let the dye warm up to room temperature before preparing the gel dye mix Least Probable Causes Solution Loaded chip kept for too long before run Prepared chips must be used within 5 min Back to Symptoms Contents A127 V Index Too Low Quantification Results Most Probable Causes Solution Pipetting error during preparation of mixtures Check dilution procedure Check calibration of pipette Chip pipetting error Use new chip Always insert the pipette
73. ot Heat samples with denaturating solution for 5 min at 100 C Samples dried out during denaturation Samples were denatured in 1 5 mL tubes Use 0 5 mL tubes for denaturating Least Probable Causes Solution Upper marker was digested by proteases cell Add protease inhibitor cocktails to cell lysate lysates samples Back to Symptoms Contents A204 Y Index High Lower Marker Variability Sample 1 Sample 2 Fluorescence 15 20 25 30 35 40 45 Time seconds Show me how to solve High Lower Marker Variability Back to Symptoms NOTE As long as the lower marker is detected the assay performance is not affected by lower marker variability Contents A 205 V Index High Lower Marker Variability Most Probable Causes Solution Buffer components of the sample e g salts See Protein Reagent Kit Guide for a list of detergents other additives etc interfere with the compatible buffers and buffer compounds lower marker If necessary dilute dialyze or desalt the sample Variability of ionic strength of the sample influence the lower marker intensity Back to Symptoms Contents A 206 V Index No Peaks 0 006 0 005 0 004 0 003 0 002 0 001 0 000 1 MUI COLOCILe 0 001 0 002 0 003 amp amp D mn ou on on D D N J n oO n oO n oO n DE 08 S8 06 S6 ool SOL OLL Time seconds 1 Show me how to solve No Peaks Back to Symptoms Contents A 207 V Index No Peaks
74. ower supply Contents A 269 V Index Lens Maintenance Liquid spill may lower the light throughput of the focusing lens underneath the chip To avoid reduced signal to noise ratios or absorbing coatings on the lens apply the following procedure on a quaterly basis or after liquid has been spilled on the lens 1 Switch off the instrument The line switch is located at the rear of the 2100 bioanalyzer 2 Remove chip from the Agilent 2100 Bioanalyzer 3 Dampen a lens tissue with reagent grade isopropanol and gently swab the surface of the lens Repeat several times with clean tissues and alcohol each time WARNING Do not drip liquid inside the instrument Use special care to ensure safety 4 Wait for alcohol to evaporate before use Contents A210 V Index Maintaining the Chip Priming Station Perform the following two steps on a regular 3 months basis after heavy use or after scratching the tip of syringe or bending the syringe or the plunger or breaking the silicone gasket of the syringe Replace syringe and syringe adapter in order to ensure for proper sealing Apply the seal test in order to check if a replacement gasket and syringe is needed Replacing the Syringe Adapter Part No G2938 68716 The Kit includes e 1 plastic adapter e 1 mounting ring e 10 silicon gaskets Replacement procedure 1 Remove the syringe by gently pulling it out of the adapter 2 Open the Chip Priming Station 3 Move the ring holding the ada
75. pter in place to the left as shown in Figure 12 The ring will come off Contents A217 Index Figure 12 Releasing the Mounting Ring of the Syringe Adapter 4 Press the syringe adapter out of its mount and replace it as shown in Figure 13 Figure 13 Replacing the Syringe Adapter Part No G2938 68716 Contents A212 V Index 5 Put the mounting ring and the syringe adapter back in Move the ring to the right in order to fix the syringe adapter as shown in Figure 14 Figure 14 Fixing the Syringe Adapter Contents A213 V Index Checking the Chip Priming Station for Good Seal Seal Test 1 Make sure the syringe Is tightly connected to the Chip Priming Station 2 Pull the plunger of the syringe to the 1 0 ml position plunger pulled back 3 Place an empty chip in the Chip Priming Station 4 Close the Chip Priming Station and make sure to lock it by pressing the cover The lock of the latch will audibly click when it closes 5 Press the plunger down until it is locked by the clip This is shown in Figure 15 Figure 15 Locking the Plunger of the Syringe with the Clip press plunger _ clip holds plunger in es place Contents A 274W Index 6 Wait for 5 seconds and press the side of the clip to release the plunger as shown in Figure 16 Figure 16 Releasing the Plunger of the Syringe 7 Appropriate sealing
76. quires 2 steps Step 1 Disabling the standard serial ports Step 2 Installing the RocketPort driver The setup process is described on the following pages For support on configuring the RocketPort PCl Quad DB9 Multi Port Serial card please contact Agilent service personnel Step 1 Disabling the Standard PC Serial Ports COM1 and COM2 The embedded serial ports of your PC must be disabled before you can use your RocketPort card To do so 1 open the Control Panel from the Settings menu 2 Double click the symbol called Devices and look for the Device named Serial This is the Standard device driver for the embedded serial ports Contents A31V Index 3 To disable these serial ports press the Stop button to halt the active process answer the following dialog with Yes and then change the startup mode from Automatic to Disabled follow the instructions of the dialog presented after you have pressed the button Startup 4 Close this dialog Device Staus Startup System a Started Autonatic Step 2 Installing the RocketPort PCI Driver Installing the PCI Card as Network Adapter Disabled Sfloapy System Shuttle Saarer Autonatic Stop Simbad Disabled sledz Disabled po ame dy anieri Disahled l tw Fiufiles Spock Disabled n Srv Manual v Een The RocketPort card will be installed as an additional network adapter 1 From the Control Panel open the Network dialog and click on the Adapters tab
77. r Ladder Peaks Back to the Top of List Contents A 232 V Index Low or Missing Upper Marker in Ladder 50 39 5 40 40 5 Time seconds Fluorescence TE 15 20 25 30 35 45 Time seconds Show me how to solve Low or Missing Upper Marker in Ladder Back to the Top of List Contents A 233 V Index Low or Missing Upper Marker in Sample 80 70 60 50 40 30 Fluorescence 20 15 20 25 30 35 40 45 Time seconds Show me how to solve Low or Missing Upper Marker in Sample Back to the Top of List Contents A234 V Index High Lower Marker Variability Sample 1 Sample 2 Fluorescence Time seconds 15 20 25 30 35 40 45 r 6 Show me how to solve High Lower Marker Variability Back to the Top of List Contents A 235 V Index No Peaks 0 006 0 005 0 004 0 003 0 002 0 001 1 MUI COLoCIMLe 0 000 0 001 0 002 0 003 0 G 0 G 0 G 0 G 0 G ool Sol OL Time seconds Show me how to solve No Peaks Back to the Top of List Contents A 236 V Index Spikes Characteristic shape of spike CIUUIESLerite Time seconds 10 Show me how to solve Spikes Back to the Top of List Contents A 237 V Index Poor Reproducibility 20 Fluorescence Time seconds Show me how to solve Poor Reproducibility Back to the Top of List Contents A 238 V Index No or Low Sample Peaks 40 35 30 25 20 16 Fluorescence 10 15 20
78. r Sensitivity Back to Symptoms Contents A173 V Index Noisy Electropherogram Fluorescence 17 22 27 32 37 42 47 52 57 62 67 72 Time seconds L Show me how to solve Noisy Electropherogram Back to Symptoms Contents A 174W Index Broad Peaks 600 550 500 450 400 350 300 250 200 150 100 Fluorescence 50 19 24 29 34 39 44 Time seconds Show me how to solve Broad Peaks Back to Symptoms Contents A 1 5 V 49 54 59 Index Missing Peaks 0 006 0 005 WN 0 004 0 003 0 002 0 001 AT AN 0 000 Fluorescence 0 001 0 002 0 003 w en amp h on n ap a3 oO on o n nn a oO on 08 S8 06 S6 ool SOL OL Time seconds Show me how to solve Missing Peaks Back to Symptoms Contents A176 V Index Poor Baseline Dips Fluorescence 19 24 29 34 39 44 49 54 59 Time seconds Show me how to solve Poor Baseline Dips Back to Symptoms Contents A177 Y Index Poor Baseline Drift Fluorescence 19 24 29 34 39 44 49 54 59 64 69 Time seconds RNA Area 97 05 RNA Conc 21 00 ng ul 285 185 0 31 Show me how to solve Poor Baseline Drift Back to Symptoms Contents A 178 V Index Noisy Electropherogram 0 7 0 6 Fluorescence 17 22 27 32 37 42 47 52 57 62 67 72 Time seconds Show me how to solve Noisy Electropherogram Back to Symptoms Contents A 179V Index Wavy Baseline 40 35 30 25 20 15
79. rade water and a toothbrush see Maintenance 246 Dont t leave chip in instrument after run Clean electrodes after each run Probable Causes Solution Pipetting error during preparation of mixtures Check dilution procedure Check calibration of pipette Chip pipetting error Use new chip and pipette again Use appropriate pipette and tips Back to Symptoms Contents A 228 V Index Fluorescence 15 20 25 30 35 40 45 Time seconds NOTE As long as the lower marker is detected the assay performance Is not affected by dips Show me how to solve Dips Back to Symptoms Contents A 229V Index Dips Most Probable Causes Solution Sample contains additional detergents and or dyes See Protein Reagent Kit Guide for a list of compatible buffers and buffer compounds For an updated list please refer to the web site www agilent com chem labonachip If necessary dilute dialyze or desalt the sample Back to Symptoms Contents A 230 V Index List of Protein Electropherograms Apparently Short Run Time 45 40 35 30 25 20 Fluorescence 15 20 25 30 35 40 45 Time seconds Show me how to solve Apparently Short Run Time Back to the Top of List Contents A231 V7 Index Additional Sample or Ladder Peaks 200 150 Fluorescence o wn Oo I 15 20 25 30 35 40 45 Tire seconds L r Show me how to solve Additional Sample o
80. raded Refer to the Protein Reagent Kit Guide for proper ladder storage Optional Prepare ladder aliquots Use a new aliquot Vibration of Agilent 2100 Bioanalyzer Don t touch Agilent 2100 Bioanalyzer during a run Remove vibration devices such as vortexers and vacuum pumps from bench Back to Symptoms Contents A 199 V Index Low or Missing Upper Marker in Ladder 40 40 5 Time seconds Fluorescence 15 20 25 30 35 45 Time seconds Show me how to solve Low or Missing Upper Marker in Ladder Back to Symptoms Contents A 200 V Index Low or Missing Upper Marker in Ladder Most Probable Causes Solution Ladder degraded For correct ladder storage and denaturation refer to the Protein Reagent Kit Guide To correct for wrong selected upper marker set upper marker manually If necessary adjust peak find settings If peaks are detected that are not part of the ladder exclude them For better upper marker identification Turn off the analysis For correct alignment overlay electropherograms of multiple wells to clearly identify the upper marker Diluted ladder is too old Use diluted ladder within one day Probable Causes Solution Ladder not denaturated properly Use fresh ladder aliquot Heat ladder for 5 min at 100 C Ladder dried out during denaturation Ladder was denatured in 1 5 mL tubes Use 0 5 mL tubes for denaturating Back to Symptoms Con
81. rmance 61 Chip Not Detected 62 Additional Sample or Ladder Peaks 63 Spikes Glitches 66 Poor Sensitivity 69 Noisy Electropherogram 2 Broad Peaks 4 Missing Peaks or Marker Peaks 7 Poor Baseline Dips 80 Poor Baseline Drift 82 Poor Baseline Noise 85 Contents Ab4lV Index Poor Baseline Jumps 88 Poor Baseline Bend 90 No Peaks and High Background 92 No Peaks and Low Background 95 Cross Contamination 98 Peaks Migrating Late 100 Late Migration and Peak Broadening 102 Bend Ladder Baseline 104 AEBAA EEE List of DNA Electropherograms 106 Contents A55V Index Clogged Spin Filters Most Probable Causes Solution Gel dye mix was centrifuged at too low g value Refer to the DNA Reagent Kit Guide for proper centrifuge settings Cooled centrifuge was used for preparation of Repeat centrifugation step without cooling gel dye mix Probable Causes Solution Particles in the gel dye mix Repeat the preparation of the gel dye mix Wear powder free gloves only Back to Symptoms Contents A 56 V Index Too High Quantification Results Most Probable Causes Solution Pipetting error during preparation of mixtures Check dilution procedure Check calibration of pipette Chip pipetting error Pipette new chip Always insert the pipette tip to the bottom of the well when dispensing the liquid Use appropriate pipette and tips
82. rs oy Ports COM amp LPT Sound video and game controllers m System devices Universal Serial Bus controllers co co i cs oo Contents A21V Index 2 Double click the symbol called RocketPort PCl 4 Port PCI BUS to open the RocketPort PCl 4 Port PCI BUS Properties box RocketPort PCI 4 Port PCI BUS Properties 2j x General Main Setup Options Driver Resources alll RocketPort PCI 4 Port PCI BUS Device type Multi port serial adapters Manufacturer Comtrol Corporation Location PCI Slot 3 PCI bus 2 device 9 function 0 Device status This device is working properly IF you are having problems with this device click Troubleshooter to start the troubleshooter iz Device usage Use this device enable Contents A28V Index 3 Select Main Setup General Main Setup Options Driver Resources IMB OVATION Ih REMOTE ACOOEGS Configuration Properties Contents A 29V Index 4 Alter the names from COMX to COM1 COM4 RocketPort PCI 4 Port PCI BUS Properties 2x General Main Setup Options Driver Resources IMB OVATION Ih REMOTE ACOEGS Configuration E B RocketPort PCI 4 Port PCI BUS a coMm1 COM2 COM3 J yy Properties 5 Select OK to confirm the changes Contents A30V Index MultiPort Card Setup Process Windows NT The setup process of the MultiPort Card re
83. rtical position as shown in Figure 2 When the lever is in the vertical position the cartridge protrudes by about 10 mm 3 Gently pull the cartridge out of the lid as shown the Figure below Figure 2 Removing the 16 Pin Cartridge Cartridge protrudes here by about 10 mm Metal lever Contents A 252 V Index Cleaning procedure NOTE After cleaning the electrode cartridge do not use it for 2 days to allow any water residuals to evaporate Residual water will lead to bad performance of the instrument and eventually failed runs Cleaning procedure 1 While holding the assembly with the pins facing downward gently but thoroughly brush the electrodes with a soft bristled toothbrush dipped in RNase Zap RNase away for a few minutes being careful not to get liquid into the openings on the electrode plate The detergent ingredient in the RNase Zap will cause foam to form 2 Let the cassette sit atop a beaker with the pins faced downwards Allow the electrode pins to be free from any contact 3 After the foam has dissipated brush the electrodes with RNase free water 4 Follow by brushing the electrodes with ethanol 5 Complete with RNase free water rinse 6 Dry the electrodes with compressed air WARNING Do not heat the electrode cartridge in an oven The magnets inside may loose their magnetization Thus the sensors can not detec
84. s Contents A 221V Index Wrong Alignment of Ladder Peaks Fluorescence 15 20 25 30 35 40 45 Tirne seconds L Show me how to solve Wrong Alignment of Ladder Peaks Back to Symptoms Contents A 222 V Index Wrong Alignment of Ladder Peaks Most Probable Causes Solution Low intensity of upper marker The software If necessary adjust peak find settings and identifies ladder peak as upper marker exclude low intensity peaks See Low Ladder Peaks 221 for probable causes For better upper marker identification Turn off the analysis For correct alignment overlay electropherograms of multiple wells to clearly identify the upper marker Back to Symptoms Contents A 223V Index Broad Peaks 300 250 200 100 Fluorescence 50 15 20 25 30 35 40 45 Time seconds 9 Show me how to solve Broad Peaks Back to Symptoms Contents A 224 V Index Broad Peaks Most Probable Causes Solution Wrong peak alignment Check if alignment is correct wrong alignment might cause broad peaks compared to the rest of the chip For better identification of the lower and upper marker Turn off the analysis For correct alignment overlay electropherograms of multiple wells to clearly identify the lower and upper marker Chip not properly primed Air bubble in chip Use a new chip Check chip priming station syringe for good seal see Maintaining the Chip Priming Station 271 Ch
85. s of the Agilent 2100 Bioanalyzer Here is a complete list of hardware diagnostic tests Test Description Instrument Checks for proper communication between PC and Agilent 2100 Bioanalyzer communication test Electronic test Verifies proper functioning of all electronic boards in the Agilent 2100 Bioanalyzer Lid sensor test Checks for the devices sensing for open or closed lid and for laser and LED off when lid is being closed Short circuit test Checks for instrument leak currents Contents A48V Index Test Description Laser LED Optics Checks for proper alignment of internal optics and proper function of the laser and LED High voltage test Checks the calibration of all 16 high voltage power supplies in the Agilent 2100 Bioanalyzer Stepper motor test Checks for proper movement of stepper motor Fan test Checks that the fan is running at the appropriate speed Temperature test Checks that the temperature ramp up speed of the heater plate is within specifications Autofocus test Checks focusing capability of optical system Electrode diode test Checks photodiode and current versus voltage performance of Agilent 2100 Bioanalyzer system Leak current test Measures electrode cartridge leak current s between pins Contents A49V Index Test Procedure 1 Access the hardware diagnostic tests by selecting Tools and then Diagnose Instrument in the Agilent 2100 Bioanalyzer software 2 Select any of t
86. s of the the electrode cleaner with 350 ul deionized analysis grade water NOTE Never fill too much water in the electrode cleaner This could cause liquid spill or contamination of the electrodes 2 Open the lid and place electrode cleaner in the Agilent 2100 Bioanalyzer 3 Close the lid and leave it closed for about 5 seconds 4 Open the lid and remove the electrode cleaner 5 Wait another 10 seconds for the water on the electrodes to evaporate Depending on the sensitivity of your measurements and the adhesive forces of your sample you have to change the water in the electrode cleaner after each use WARNING Never use a cloth to clean the electrodes Electrostatic discharge might damage the high voltage power supplies Daily Basis For RNA Assay Only To avoid decomposition of your RNA sample follow this electrode decontamination procedure on a daily basis Contents A 248 V Index 1 Slowly fill one of the wells of an electrode cleaner with 350 ul RNAseZAP 2 Open the lid and place electrode cleaner in the Agilent 2100 Bioanalyzer 3 Close the lid and leave it closed for about 1 minute 4 Open the lid and remove the electrode cleaner label the electrode cleaner and keep for future use You can reuse the electrode cleaner for all the chips in the kit If the electrode cleaner dries out simply refill 5 Slowly fill one of the wells of another electrode cleaner with 350 ul RNAse free water 6 Place electrode cleaner in the Agile
87. t should not be bent or misaligned Both will lead to poor quality results or pre terminated assay runs In case of highly contaminated or dirty pins you may autoclave the pin set NOTE For autoclaving the pin set follow your standard procedures for plastic material 1 sonicate the pin set for 10 minutes 2 gently clean the pin set with a soft tooth brush WARNING Make sure thatthe pin set is completely dry before replacing it back into the electrode base Even small amounts of liquid on the pin set can damage the high voltage power supply Contents A 268 V Index Run the hardware diagnostics Run the hardware diagnostics to ensure that the reader is functioning properly Perform the short circuit diagnostic test See Hardware Diagnostics 48 for details This test takes approximately three minutes and the software will walk you through the steps When prompted place an unused RNA or DNA chip into the reader the chip can be used later for a regular run If the short circuit test fails the assembly may still be wet Take the assembly out of the instrument dry it with compressed air and repeat the test WARNING Do not heat the electrode cartridge in an oven The magnets inside may loose their magnetization Thus the sensors can not detect the lid closure WARNING Make sure thatthe pin set is completely dry before replacing it back into the electrode base Even small amounts of liquid on the pin set can damage the high voltage p
88. t the lid closure Contents A 253 V Index 7 As instep 2 place electrode assembly atop of beaker allow it to dry for at least two hours WARNING Do not use the 2100 bioanalyzer for at least two days following the cleaning procedure Contents A 254 V Index Inserting the 16 Pin Cartridge 1 Slide the 16 pin cartridge in the lid as shown in the Figure 3 2 Move the metal lever in the flat closed position 3 Push the metal front of the 16 pin cartridge to ensure a tight connection to the 2100 bioanalyzer NOTE Make sure the 16 pin cartridge is connected tightly to the 2100 bioanalyzer Figure 3 Inserting the 16 Pin Cartridge Push here to ensure tight connection Metal lever Contents A 255 V Index Run the hardware diagnostics Run the hardware diagnostics to ensure that the reader is functioning properly Perform the short circuit diagnostic test See Hardware Diagnostics 48 for details This test takes approximately three minutes and the software will walk you through the steps When prompted place an unused RNA or DNA chip into the reader the chip can be used later for a regular run If the short circuit test fails the assembly may still be wet Take the assembly out of the instrument dry it with compressed air and repeat the test WARNING Do not heat the electrode cartridge in an oven The magnets inside may loose their magnetization Thus the sensors can not detect th
89. t touch the underside of the chip Don t touch the wells of the chip Clean the electrodes Load the chip immediately after taking it out of its sealed bag High voltage power supply defective Check high voltage power supply using the Hardware Diagnostics 48 If the power supply is defective call Agilent Technologies Autofocus failure Check autofocus using the Hardware Diagnostics 48 If autofocus fails call Agilent Technologies Back to Symptoms Contents AAV Index No Peaks and Low Background 250 Spike to view the baseline level uncheck 200 Zero Baseline in the M software 150 Q Oo w D S 100 iL 50 o 50 25 20 35 40 45 50 55 60 65 70 75 80 85 90 Time seconds Show me how to solve No Peaks and Low Background Back to Symptoms Contents A595 V Index No Peaks and Low Background Most Probable Causes Solution Dye concentration too low marker disappears Use dye concentration according to the DNA Reagent Kit Guide Let the dye warm up to room temperature before preparing the gel dye mix Probable Causes Solution Chip not properly primed Air bubble in chip Use a new chip Check chip priming station syringe for good seal see Maintaining the Chip Priming Station 271 Check if clip and base plate of priming station are in the right position see DNA Reagent Kit Guide Contents A 96 VY Index Least Probable Causes Solution
90. t touch the underside of the chip Don t touch the wells of the chip Clean the electrodes Load the chip immediately after taking it out of its sealed bag Vibration of Agilent 2100 Bioanalyzer Don t touch Agilent 2100 Bioanalyzer during a run Remove vibration devices such as vortexers and vacuum pumps from bench Autofocus failure Check autofocus using the Hardware Diagnostics 48 If autofocus fails call Agilent Technologies Laser defective Check laser using the Hardware Diagnostics 48 If the laser is defective call Agilent Technologies Back to Symptoms Contents A 147 W Index Noisy Electropherogram 0 7 0 6 Fluorescence 17 22 27 32 37 42 47 52 57 62 67 72 Time seconds L Show me how to solve Noisy Electropherogram Back to Symptoms Contents A 148 V Index Noisy Electropherogram Most Probable Causes Solution Chip not properly primed Air bubble in chip Use anew chip Check chip priming station syringe for good seal see Maintaining the Chip Priming Station 271 Check if clip and base plate of priming station are in the right position see RNA Reagent Kit Guide Clogged gasket and plastic adapter of priming station Perform seal test like described in Maintaining the Chip Priming Station 27 1 Clean replace gasket and plastic adapter if necessary Chip contaminated Wear powder free gloves only Don t touch the underside of the chip
91. te leading to poor results e Vortex chips at the appropriate time of 1 minute Inappropriate vortexing leads to poor results Use only the IKA vortexer for chip vortexing Replace the chip adapter p n 5022 2190 if it is wore out e Do not touch wells of the chip The chip could get contaminated and this leads to poor measurement results Do not leave any wells of the chip empty or the assay will not run properly Add 1 pl of sample buffer to each unused sample well so that the total liquid volume in each well is at least 6 ul For protein assays pipette a sample or ladder replicate in any empty sample well Do not touch the underside of the chip Agilent 2100 Bioanalyzer e Don t touch the Agilent 2100 Bioanalyzer during a run and never place it on vibrating ground Contents A10V Index e Do not use force to press the chip in the receptacle of the Agilent 2100 Bioanalyzer The electrode assembly might get damaged when you close the lid Check if the chip selector is in the correct position e Clean electrodes on a daily basis using the cleaning chip For more details see Maintenance 246 e Clean electrodes on a quaterly basis using a toothbrush and distilled water For more details see Maintenance 246 e Clean the focusing lens once a month or after any liquid spill using isopropanol see Lens Maintenance 270 Contents Al11V Index Decontamination Procedure for RNA Assays Perform the following decontamin
92. tents A201 V7 Index Low or Missing Upper Marker in Sample Fluorescence 15 20 25 30 35 40 45 Time seconds Show me how to solve Low or Missing Upper Marker in Sample Back to Symptoms Contents A 202 V Index Low or Missing Upper Marker in Sample Most Probable Causes Solution Sample buffer denaturating solution not handled according to the instructions Refer to the instructions provided with the Reagent Kit guide for storage and preparation of the sample buffer denaturating solution To correct for wrong selected upper marker set upper marker manually If necessary adjust peak find settings For better upper marker identification Turn off the analysis For correct alignment overlay electropherograms of multiple wells to clearly identify the upper marker Incompatible sample component Some components of the buffer e g CHAPS TFA etc interfere with the upper marker and decrease sensitivity See Protein Reagent Kit Guide for a list of compatible buffers and buffer compounds For an updated list please refer to the web site www agilent com chem labonachip If necessary dilute dialyze or desalt the sample It is recommended to dilute the samples 1 2 1 4 with water to find the optimal dilution Diluted samples are too old Use diluted samples within one day Contents A 203 V Index Probable Causes Solution Samples not denaturated properly Use fresh sample aliqu
93. test like described in Maintaining station the Chip Priming Station 271 Clean replace gasket and plastic adapter if necessary Probable Causes Solution Vortex adapter not connected tightly Press vortex adapter tightly on mount vortex adapter must not rock Only use the IKA vortexer Replace adapter If necessary Back to Symptoms Contents A 168 V Index List of RNA Electropherograms Additional Sample or Ladder Peaks 80 a o 50 Peak a Cc 40 w 2 5 30 Ww 20 10 a 8 8 21 26 31 36 4 46 51 56 61 66 Time seconds Show me how to solve Additional Sample or Ladder Peaks Back to Symptoms Contents A 169 V Index Genomic DNA Contamination 60 50 40 30 7 genomic DNA 20 Fluorescence 19 24 29 34 39 44 49 54 59 Time seconds Show me how to solve Genomic DNA Contamination Back to Symptoms Contents A170 V Index Degraded RNA Ladder and or Samples Fluorescence 19 24 29 34 39 44 49 54 59 Time seconds Show me how to solve Degraded RNA Ladder and or Samples Back to Symptoms Contents A1 1V Index Spikes Glitches 30 25 20 MUVIES CENCE nn i 19 24 29 34 39 44 49 54 59 Time seconds Show me how to solve Spikes Glitches Back to Symptoms Contents A1 2V 64 Characteristic shape of spikes 69 Index Poor Sensitivity Fluorescence 17 22 27 32 37 42 47 52 57 62 67 72 Time seconds Show me how to solve Poo
94. tion are in the right position see RNA Reagent Kit Guide Vibration of Agilent 2100 Bioanalyzer Don t touch Agilent 2100 Bioanalyzer during a run Remove vibration devices such as vortexers and vacuum pumps from bench Loaded chip kept for too long before run Prepared chips must be used within 5 min Too high salt concentration in sample Use salt concentration according to the RNA Reagent Kit Guide Least Probable Causes Solution RNA ladder degraded Use new ladder aliquot chip Always wear gloves when handling chips RNA samples to prevent them from getting contaminated Follow decontamination procedure see Maintenance 246 Contents A 137 V Index Genomic DNA Contamination 60 50 40 30 m genomic DNA 20 Fluorescence 19 24 29 34 39 44 49 54 59 Time seconds Show me how to solve Genomic DNA Contamination Back to Symptoms Contents A 138 V Index Genomic DNA Contamination Most Probable Causes Solution RNA Isolation Protocol Check RNA isolation protocol To remove genomic DNA perform DNAse treatment Back to Symptoms Contents A 139 V Index Degraded RNA Ladder and or Samples 70 60 Fluorescence S w oO a o fo Oo o m 19 24 29 34 39 44 49 54 59 Time seconds Show me how to solve Degraded RNA Ladder and or Samples Back to Symptoms Contents A 140 V Index Degraded RNA Ladder and or Samples Most Probable Ca
95. tion date of chemicals Loaded chip kept for too long before run Prepared chips must be used within 5 min Chip not properly primed Air bubble in chip Use a new chip Check chip priming station syringe for good seal see Maintaining the Chip Priming Station 271 Check if clip and base plate of priming station are in the right position see DNA Reagent Kit Guide Chip contaminated Wear powder free gloves only Don t touch the underside of the chip Don t touch the wells of the chip Clean the electrodes Load the chip immediately after taking it out of its sealed bag No ladder in ladder well Use a new chip Contents A593 V Index Least Probable Causes Solution Vibration of Agilent 2100 Bioanalyzer Don t touch Agilent 2100 Bioanalyzer during a run Remove vibration devices such as vortexers and vacuum pumps from bench Changes of ambient temperature of more than 5 C during the run Place Agilent 2100 Bioanalyzer in thermally stable environment High voltage power supply defective Check high voltage power supply using the Hardware Diagnostics 48 If the power supply is defective call Agilent Technologies Back to Symptoms Contents A 60 V Index Poor Chip Performance Most Probable Causes Solution Chip not properly primed Air bubble in chip Use a new chip Check chip priming station syringe for good seal see Maintaining the
96. umps from bench Contents Ab4V Index Least Probable Causes Solution DNA ladder degraded Check expiration date of chemicals Back to Symptoms Contents A 65V Index Spikes Glitches 30 3 Characteristic shape of spike Fluorescence T Time seconds 1i Show me how to solve Spikes Glitches Back to Symptoms Contents A 66 V Index Spikes Glitches Most Probable Causes Solution Chip gel dye mix contaminated Prepare new chip with new gel dye mix Wear powder free gloves only Don t touch the underside of the chip Don t touch the wells of the chip Clean the electrodes Load the chip immediately after taking it out of its sealed bag Gel dye mix not properly prepared Refer to the Reagent Kit Guide for proper preparation of the gel dye mix Let the dye warm up to room temperature before preparing the gel dye mix Chip not properly prepared Contents Prepare a new chip Allow all reagents and samples to warm up to room temperature before use A6 V Index Probable Causes Solution Vibration of Agilent 2100 Bioanalyzer Don t touch Agilent 2100 Bioanalyzer during a run Remove vibration devices such as vortexers and vacuum pumps from bench Least Probable Causes Solution Power outlett Install power filter Back to Symptoms Contents A 68 V Index Poor Sensitivity 3 0 2 5 2 0 0 5 Fluorescence 0 0 0 5 25 230 3
97. uorescence 10 19 24 29 34 39 44 49 54 59 64 69 Time seconds 2 Show me how to solve Wavy Baseline Back to Symptoms Contents A 162 V Index Wavy Baseline Most Probable Causes Solution Current leaks due to contaminated electrodes Clean electrodes with analysis grade water and a toothbrush see Maintenance 246 Replace electrode cartridge Clogged gasket and plastic adapter of priming station Perform seal test like described in Maintaining the Chip Priming Station 271 Clean replace gasket and plastic adapter If necessary Probable Causes Solution Chip not properly primed Air bubble in chip Use a new chip Check chip priming station syringe for good seal see Maintaining the Chip Priming Station 271 Check if clip and base plate of priming station are in the right position see RNA Reagent Kit Guide Dye concentration too low Use dye concentration according to the Reagent Kit Guide Let the dye warm up to room temperature before preparing the gel dye mix Contents A 163 V Index Least Probable Causes Solution Chip contaminated Wear powder free gloves only Don t touch the underside of the chip Don t touch the wells of the chip Clean the electrodes Load the chip immediately after taking it out of its sealed bag High voltage power supply defective Check high voltage power supply using the Hardware Diagnostics 48 If the power
98. ures Click here to go to the Click here to go to the index table of contents Here s the current page number A displays previous page VY displays next page Contents AAV Index Navigating within Acrobat Reader When you ve chosen a topic with the bookmarks use the buttons in Acrobat Reader s tool bar to move around within a topic Returns to the previous view Click several times to redo more view changes ee Returns to the next view Click several times to redo more view changes Displays the next page Displays the previous page HE Displays the first page Displays the last page For more information see the Reader Online Guide in the Help menu Contents A5V Index Contents RNG MN esac acetate eet enctcal ec au te araa a eenamsateannacatidecesvacaeiceatnatemansaienssasansadsesenetinneantes 3 Essential Measurement Practices csssscsscssssssecsssseesessecsssesseceeseesaesessesneeessaneeaneaees 7 Troubleshooting the Instrument Communication ccssssescesssecseeseseseeeseeeeeeees 14 Troubleshooting the Agilent 2100 Bioanalyzer Software c ccccsssssssesseeees 45 Hardware Diagnostics sesssesessssesensnsunnsannsnnnnnnnnnunnnnnnnnnnnnnnnnnnnnnnnunnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnna 48 Troubleshooting the DNA Application ccccsscssssseesessessesesessesseesessessessessaesaeeaes 52 Troubleshooting the RNA Application
99. uses Solution RNAse contamination of the cartridge Clean the electrode cartridge Refer to Maintenance 246 for details RNAse contamination of chips and or reagents Use a new chip and or fresh reagents Wear powder free gloves when preparing the chip Back to Symptoms Contents A 141V Index Spikes Glitches Characteristic shape of spikes PIUDIESLETILe ar 19 24 29 34 39 44 49 54 59 64 69 Time seconds Show me how to solve Spikes Glitches Back to Symptoms Contents A 142 V Index Spikes Glitches Most Probable Causes Solution Chip gel dye mix contaminated Prepare new chip with new gel dye mix Wear powder free gloves only Don t touch the underside of the chip Don t touch the wells of the chip Clean the electrodes Load the chip immediately after taking it out of its sealed bag Gel dye mix not properly prepared Refer to the Reagent Kit Guide for proper preparation of the gel dye mix Let the dye warm up to room temperature before preparing the gel dye mix Probable Causes Solution Chip not properly primed Air bubble in chip Use a new chip Check chip priming station syringe for good seal see Maintaining the Chip Priming Station 271 Check if clip and base plate of priming station are in the right position see RNA Reagent Kit Guide Contents A143 V Index Vibration of Agilent 2100 Bioanalyzer Don t touch Agilent 2100 Bioana
100. within 5 min Chip not properly primed Air bubble in chip Use a new chip Check chip priming station syringe for good seal see Maintaining the Chip Priming Station 271 Check if clip and base plate of priming station are in the right position see RNA Reagent Kit Guide Contents A 130 V Index Chip contaminated Wear powder free gloves only Don t touch the underside of the chip Don t touch the wells of the chip Clean the electrodes Load the chip immediately after taking it out of its sealed bag No ladder in ladder well Use a new chip Probable Causes Solution Insufficient vortexing of chip Vortex chip for 1 minute Only use the IKA vortexer Adjust the speed to the set point Contents A 131 V Index Least Probable Causes Solution Changes of ambient temperature of more than Place Agilent 2100 Bioanalyzer in thermally 5 C during the run stable environment High voltage power supply defective Check high voltage power supply using the Hardware Diagnostics 48 If the power supply is defective call Agilent Technologies Laser defective Check laser using the Hardware Diagnostics 48 If the laser is defective call Agilent Technologies Back to Symptoms Contents A 132 V Index Chip Not Detected Most Probable Causes Solution Amount of liquid pipetted is too low or chip is empty Check assay procedure on amount of liquid to be pipetted Pipett
101. y manual setup poster Agilent 2100 Bioanalyzer System Software G2941AA Agilent 2100 Bioanalyzer Data Organizer G2945AA Contents A 284 V Index Reagent Kits and Reagents RNA 6000 Nano Kit 5065 4476 Chips reagents Kit Guide Syringe Box DNA 500 Kit 5064 8284 Chips reagents Kit Guide Syringe Box DNA 1000 Kit 5065 4449 Chips reagents Kit Guide Syringe Box DNA 7500 Kit 5064 8230 Chips reagents Kit Guide Syringe Box DNA 12000 Kit 5064 8231 Chips reagents Kit Guide Syringe Box Contents A 285 V Index Protein 200 Plus Kit 5065 4480 Chips reagents Kit Guide Syringe Box RNA 6000 Nano Reagents 5065 4475 Cooled Reagents DNA 500 Reagents 5065 4440 Cooled Reagents DNA 1200 Reagents 5065 4438 Cooled Reagents DNA 7500 Reagents 5065 4437 Cooled Reagents Protein 200 Plus Reagents 5065 4482 Cooled Reagents Contents A 286 V Index Accessories Vortex Mixer Adapter 5022 2190 for IKA vortexer 16 pin cartridge bayonet 5065 4413 no extra electrode pin set pin set not re orderable Chip Priming Station 5065 4401 comprises 1 gasket kit 1 adjustable clip TestChip Kit G2938 68100 comprises 1 autofocus 1 Electrode Diode 5 Leak Current Clips Contents A 287 V Index Spare Parts RS 232 Cable G2938 81605 communication cable PC instrument Fuse 2110 0007 two fuses needed for G2938A Gasket Kit G2938 68716 comprises 1 plastic adapter 10 gaskets Adjustable Clip 5042 1

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