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Old 11-07-2014, 11:05 AM   #1
Junior Member
Location: Chicago

Join Date: Oct 2014
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Default DNA 1000 Ladder Slow Migration - Agilent Bioanalyzer

Hi all,

I'm having a consistent problem with the bioanalyzer not reading the last peak or peaks for the DNA 1000 ladder. All of the other assays seem to read OK.

I've tried:
1) Replacing the primer parts
2) increasing the drying time after cleaning the pins
3) Replacing all of the reagents

The problem seems to get worse throughout the day. Any suggestions are appreciated!
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Old 11-07-2014, 01:29 PM   #2
Location: Irvine, CA

Join Date: Mar 2014
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Some Agilent reps told me to clean the pins with a brush after heavy use (like a toothbrush).
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Old 11-09-2014, 01:38 PM   #3
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Location: Monash University, Melbourne, Australia.

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Some things that we've experienced with slow migration: Does the priming syringe return to the recommended level after you release the clamp? Are all your reagents within their expiry date? Is the gel-dye mix fresh? Have you centrifuged the gel-dye mix hard before use?

Also, I'm not sure whether this would solve your problem, but on the topic of washing Bioanalyzer pins:

On the odd occasion that we have some really bad pin contamination or if someone has forgotten about a chip and left it to dry in the machine, we clean our Bioanalyzer pins by soaking them in detergent and scrubbing very thoroughly with a toothbrush (holding the pin array at an angle and scrubbing across the side of each row of pins). We then rinse very thoroughly in distilled water and dry them for a couple of hours in our 50oC incubator. Maybe it's a bit harsh compared to the recommendations, but it works and it doesn't do any harm.
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Old 12-06-2014, 06:26 AM   #4
Location: San Diego, CA

Join Date: Oct 2014
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Sorry for the late post but I experienced this problem before also. For my lab, it turns out the ambient temperature was too cold. We ended up creating an enclosure for the BA which kept the air surrounding it much warmer and we encountered this issue much less.
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Old 12-09-2014, 01:36 AM   #5
Location: Cardiff

Join Date: Jul 2012
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Hi jlei_face
That's quite interesting what you were saying about the ambient temperature. We a have similar problem quite often with the High sensitivity ladder. What temperature did you find was optimum?
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Old 12-09-2014, 04:27 AM   #6
Location: San Diego, CA

Join Date: Oct 2014
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I've been out of that lab for some time but I believe our optimum temperature was right at RT (25degrees C) or slightly above. The lab that contained the BA also contained other instruments that needed to be kept cool so the AC was usually on full blast.
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Old 12-09-2014, 04:45 AM   #7
Location: Paris

Join Date: Apr 2012
Posts: 17

We had this problem a few years ago - make sure that your priming station is fine (the little white seal is unbroken, the syringe is new and set at the right position).

For us the problem was that the little hole underneath the syringe was clogged - cleaning it solved everything. Look through in while pointing at a bright light to make sure the path is clear.
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