Thermo Fisher Scientific ABI PRISM® 3700 User guide

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

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.

Turquoise 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.

Run the cuvette flush module, this may require several flushes until bubbles are

removed.

Leak in sheath flow syringe

Replace the sheath flow syringe using the change syringe wizard.

Impaired movement of the

syringe pump.

Check the syringe pump, refer to the Verifying Syringe Pumps module.

Leak at the inline filter

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.

Presence of bubbles in the

sheath flow syringe.

Verify that the tubing in the polymer bottle is immersed in polymer.

Yellow Color

Go to larger picture

Sheath flow syringe or pump

may not be functioning

Verify the syringe pump movement with and without the sheath flow syringe, refer to

the Verifying the Syringe Pumps module.

Array View Colors Module pn 4375401 .doc

Rev A Page 1 of 19

Observations

Possible Causes

Recommended Actions

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.

Polymer

mixing of polymer from two

bottles.

polymer was not at room temp.

precipitate in bottle.

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.

Striations

Go to larger picture

Presence of foreign fluids in the

1X running buffer or DI water

reservoirs. 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.

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.

Presence of bubbles

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.

Green color

Go to larger picture

Contamination in reagents:

water, buffer or polymer

Rinse the buffer and water reservoirs with DI-water and replenish with a fresh stock.

Array View Colors Module pn 4375401 .doc

Rev A Page 2 of 19

Observations

Possible Causes

Recommended Actions

Use another source of DI water. Check the filtration system for the DI water.

Leak in sheath flow syringe

Replace the sheath flow syringe using the change syringe wizard.

Sample Contamination

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.

Loss in communication

Restart the system

Optics

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.

Sample loading issue

Bubbles in the sample

transfer lines.

Replace the sample transfer syringe(s) using the change syringe wizard.

Bubbles in the sample wells

Spin down samples before placing on the instrument.

Clogged loading tips

Replace the loading tips. Refer to the change tips wizard for instructions

Black color

entire array is

affected

Go to larger picture

Electrophoresis Issues

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.

Some lanes are not

affected

Sample loading issue

bubbles in the sample

transfer lines

Verify that the autoloader tips are screwed in, they should be finger tight.

Array View Colors Module pn 4375401 .doc

Rev A Page 3 of 19

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

Replace the autoloader tips. Refer to the change tips wizard for instructions

Check the array 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.

Capillary specific

The capillary may be clogged. Block the capillary in the Data Collection software to

prevent loading at the capillary or replace the array.

Sample issue

Run sequencing standard controls, if these work but samples do not, contact

technical support for troubleshooting the sample.

Spatial calibration may have

shifted

Run a spatial calibration.

Sections of the array

view are black

Refer to the Missing Lanes

Module

Refer to the Missing Lanes Module

Array View Colors Module pn 4375401 .doc

Rev A Page 4 of 19

Turquoise Array

Large bubble in cuvette, affects entire run small bubble in cuvette

Array View Colors Module pn 4375401 .doc

Rev A Page 5 of 19

Yellow Array

Array View Colors Module pn 4375401 .doc

Rev A Page 6 of 19

Striations

Array View Colors Module pn 4375401 .doc

Rev A Page 7 of 19

Green

Array View Colors Module pn 4375401 .doc

Rev A Page 8 of 19

Black

Array View Colors Module pn 4375401 .doc

Rev A Page 9 of 19

Checking fittings on the syringe pumps

Array Fill Syringe Sample Transfer Syringes Sheath Flow syringe and pump

From syringe to

robot tip

From water

reservoir to

syringe

Port 8: From polymer

bottle to syringe

Port 8: From

polymer bottle to

syringe

Port 9: From

syringe to array. Port 9: From syringe to

cuvette.

From syringe to

robot tip

From water

reservoir to

syringe

Array View Colors Module pn 4375401 .doc

Rev A Page 10 of 19

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.

Array View Colors Module pn 4375401 .doc

Rev A Page 11 of 19

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

Array View Colors Module pn 4375401 .doc

Rev A Page 12 of 19

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.

Array View Colors Module pn 4375401 .doc

Rev A Page 13 of 19

A

fter selecting run method, the steps of the service module will be listed.

The module selected should be listed.

Array View Colors Module pn 4375401 .doc

Rev A Page 14 of 19

Select Run Method.

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.

Array View Colors Module pn 4375401 .doc

Rev A Page 15 of 19

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.

Array View Colors Module pn 4375401 .doc

Rev A Page 16 of 19

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.

Array View Colors Module pn 4375401 .doc

Rev A Page 17 of 19

Fluid Line Sinkers

Fluid line sinkers

Autoloader tips

Tips should be screwed to finger tight and the bottom of the tips should be even.

Array View Colors Module pn 4375401 .doc

Rev A Page 18 of 19

Contacting Technical Support

By phone: 1-800-831-6844, option 5

By email: ABTechnicalSupport@appliedbiosystems.com

pn 4375401

Stock # 106GU05-01

Array View Colors Module pn 4375401 .doc

Rev A Page 19 of 19

Thermo Fisher Scientific ABI PRISM® 3700 User guide

Thermo Fisher Scientific ABI PRISM® 3700 User guide

Related papers

Other documents