Observations Possible Causes Recommended Actions. Turquoise color

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1 ABI PRISM 3700 Instrument-Hardware-Array View Troubleshooting Module Please contact technical support if you have any questions regarding the document. Text in blue indicates a link to another section or another document. Observations Possible Causes Recommended Actions Turquoise color Go to larger picture Yellow Color Go to larger picture Presence of bubbles in the cuvette. The source of the bubbles will need to be identified, refer to the Checking for Bubbles module. Leak in sheath flow syringe Impaired movement of the syringe pump. Leak at the inline filter Presence of bubbles in the sheath flow syringe. Sheath flow syringe or pump may not be functioning Refer to the Checking the CCD calibration window Module to determine if bubbles have been removed from the cuvette. Verify that within the polymer bottle, the tubing is immersed in polymer. Check for leaking (dried polymer) at the in-line filter or syringes and if necessary replace components. Verify that the fittings on the port above the sheath flow syringe are finger tight. Run the cuvette flush module, this may require several flushes until bubbles are removed. Replace the sheath flow syringe using the change syringe wizard. Check the syringe pump, refer to the Verifying Syringe Pumps module. Clean dried polymer from the area and replace the inline filter. Verify that the fittings on the port above the sheath flow syringe are finger tight. Verify that the tubing in the polymer bottle is immersed in polymer. Verify the syringe pump movement with and without the sheath flow syringe, refer to the Verifying the Syringe Pumps module. Page 1 of 19

2 Observations Possible Causes Recommended Actions Striations Go to larger picture Green color Polymer mixing of polymer from two bottles. polymer was not at room temp. precipitate in bottle. Presence of foreign fluids in the 1X running buffer or DI water reservoirs. Presence of bubbles Use a new bottle of polymer, we do not recommend the mixing of polymer from different bottles. Bring polymer to room temperature before placing on instrument and gently mix. Verify that the precipitates have gone into solution. When changing polymer, use the change polymer wizard to flush the old polymer out of the system. Thoroughly rinse the running buffer and DI water reservoirs with DI water and replenish with a fresh stock. Run sequencing standards to verify the system. Refer to the Checking the CCD calibration window Module to determine if bubbles have been removed from the cuvette. Verify that within the polymer bottle, the tubing is immersed in polymer. Go to larger picture Contamination in reagents: water, buffer or polymer Check for leaking (dried polymer) at the in-line filter or syringes and if necessary replace components. Verify that the fittings on the port above the sheath flow syringe are finger tight. Run the cuvette flush module, this may require several flushes until bubbles are removed. Verify the reagents on the instrument. Check expiry dates and length of time on the instrument. Replace reagents if necessary. Rinse the buffer and water reservoirs with DI-water and replenish with a fresh stock. Page 2 of 19

3 Observations Possible Causes Recommended Actions Use another source of DI water. Check the filtration system for the DI water. Leak in sheath flow syringe Sample Contamination Replace the sheath flow syringe using the change syringe wizard. Run a HiDi Formamide only plate to eliminate sample issues. If color is not seen in the HiDi Formamide run please contact Technical Support to troubleshoot sample. Black color entire array is affected Go to larger picture Some lanes are not affected Loss in communication Optics Sample loading issue Bubbles in the sample transfer lines. Bubbles in the sample wells Clogged loading tips Electrophoresis Issues Sample loading issue bubbles in the sample transfer lines Restart the system Check the CCD window, for raman lines. Refer to the Checking CCD Window module. If raman lines are not present, contact service. Check the water reservoir. Replenish the water and verify that the fluid line sinkers for the tubing are at the bottom of the reservoir. Verify that the autoloader tips are screwed in until finger tight. Verify the fittings on the port above the syringes are finger tight. Determine the source of the bubbles. Refer to the Checking for Bubbles module. Replace the sample transfer syringe(s) using the change syringe wizard. Spin down samples before placing on the instrument. Replace the loading tips. Refer to the change tips wizard for instructions Refer to the Electrophoresis Troubleshooting Module Check the water reservoir. Replenish the water and verify that the fluid line sinkers for the tubing are at the bottom of the reservoir. Verify that the autoloader tips are screwed in, they should be finger tight. Page 3 of 19

4 Observations Possible Causes Recommended Actions Verify the fittings above the syringes are finger tight. Locate the source of the bubbles, refer to the Checking for bubbles module. Replace the sample transfer syringe(s) using the change syringe wizard. Clogged loading tips Capillary specific Replace the autoloader tips. Refer to the change tips wizard for instructions Check the arrayt for any broken capillaries at the loading end or along the length of the array. Block the capillary in the Data Collection software to prevent loading at the capillary or replace the array. The capillary may be clogged. Block the capillary in the Data Collection software to prevent loading at the capillary or replace the array. Sections of the array view are black Sample issue Spatial calibration may have shifted Refer to the Missing Lanes Module Run sequencing standard controls, if these work but samples do not, contact technical support for troubleshooting the sample. Run a spatial calibration. Refer to the Missing Lanes Module Page 4 of 19

5 Turquoise Array Large bubble in cuvette, affects entire run small bubble in cuvette Page 5 of 19

6 Yellow Array Page 6 of 19

7 Striations Page 7 of 19

8 Green Page 8 of 19

9 Black Page 9 of 19

10 Checking fittings on the syringe pumps Array Fill Syringe Sample Transfer Syringes Sheath Flow syringe and pump From water reservoir to syringe Port 8: From polymer bottle to syringe From syringe to robot tip Port 8: From polymer bottle to syringe Port 9: From syringe to array. From water reservoir to syringe Port 9: From syringe to cuvette. From syringe to robot tip Page 10 of 19

11 Polymer bottle diagram Verifying that the polymer volume is sufficient for the run will prevent the introduction of bubbles into the system. Ensuring that the polymer is at room temperature before placing on the instrument will prevent degassing of the polymer while on the instrument. Verifying that precipitates have been dissolved and gently mixed back into solution will ensure that the polymer is homogenous. Do not combine polymer bottles. Page 11 of 19

12 Running service modules within Data Collection Step 1: Go to the Instrument menu > Select Utilities > Select Run Service Module > Step 2:Click the Select Module button Page 12 of 19

13 The service module utility should automatically search the Service Modules Folder, if not the folder can be found in the D://AppliedBio/Support Files/Data Collection Support Files/ Service Modules Double click on the module, in this example CuvetteFlush.mod. Page 13 of 19

14 After selecting run method, the steps of the service module will be listed. The module selected should be listed. Select Run Method. Page 14 of 19

15 When this window appears the module has completed, if there is an error during the module, please contact technical support. Array Diagram Check these 2 areas for any capillary breakage. Broken capillaries along the length of the array can be problematic if the array is not changed. Polymer will still flow through the capillary causing buildup of polymer in the area and potentially affecting the performance of neighboring capillaries. Page 15 of 19

16 Using the wizards Step 1: Go to the Instrument menu > Select Wizards > Select appropriate wizard Replacing the inline filter Step 1: The filter needs to be primed. Step 2: After installing the filter, run the CuvetteFlush module, which will flush lines, filter and cuvette with polymer and purge bubbles from the cuvette. Page 16 of 19

17 Restarting the 3700 DNA Analyzer IMPORTANT To prevent firmware and software memory problems, we recommend that you restart the instrument and the software once a week. To shut down and restart the instrument: Step 1: The instrument should not be running or extracting data. Step 2: Close the 3700 Data Collection software by selecting Shutdown from the File menu. Note You cannot use the Close button to exit the software. Step 3: Close the OrbixWeb Daemon software by right-clicking on its button in the taskbar and selecting Close from the pop-up menu. If you get a run-time message, click OK to close the message. IMPORTANT Do not shut down the OrbixWeb Daemon until after you have shut down the Data Collection program. Step 4: Restart the computer. After logging in, OrbixWeb Daemon should have automatically launched. Do not start Data Collection at this time. Step 5: a. Turn off the instrument using the On/Off button. b. Wait 30 seconds. c. Turn on the instrument. Step 6: When the green status light is steady, wait 1 minute. Step 7: Restart the 3700 Data Collection software. Page 17 of 19

18 Fluid Line Sinkers Fluid line sinkers Autoloader tips Tips should be screwed to finger tight and the bottom of the tips should be even. Page 18 of 19

19 Contacting Technical Support By phone: , option 5 By ABTechnicalSupport@appliedbiosystems.com Page 19 of 19