Why Am I Seeing a Blue Background on My ABI 3730?

Sometimes running into problems can make us better people and build our character. Other times running into problems can make us want to pull our hair out. If you happen to run into a blue background on your array view, don’t stress just yet. Hopefully, this post will keep you from reaching for some Rogaine. 


If you see a blue background in the array viewer of your ABI 3730 after a run, you are not alone. This is a common issue seen amongst our ABI 3730 users. On machines including the 3730xl, a blue background screen may show up after an attempt to validate your data on your array view of your runs. This may prevent your runs from reaching their full potential, and can cause major frustration if you are unsure why this is happening.

If your array viewer resembles the picture above, you are noticing high background noise and really ugly runs. In some cases, end users will change the polymer in their machine thinking this will resolve any issues. However, this is an expensive fix and could be completely unnecessary. Luckily for you, SeqGen has the answer. 

In about 80% of the cases, the blue haze is caused by contamination within the pump, buffer, or water. So there’s the problem; but now the solution. Your best bet would be to change out the reagents in your machine. We suggest three cycles of warm water wash to see if this helps. After the washes are complete, change out your buffer and water. 

Follow up the buffer and water change with a blank water plate run to assess the background and to ensure that the background signals are within the acceptable range. You should be able to see just the black background with no hint of blue. Run your sample once again. If you do not notice a marked improvement, don’t give up yet. If this blue screen of doom continues, it might mean that the contamination has spread to your capillary. To fix this, an acid wash for your capillary is the best course of action to take. 

If you've tried everything we've said and you're still having problems, you may need to check your machine for a leak, or contact us for more helpful hints. You also may want to check out our free capillary array wash guide. This is your guide to extending the life of your capillary array and improving sample results in the process.

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Written by Susan Henry

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