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Old 11-04-2012, 04:10 PM   #1
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Location: CA, USA

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Default Disagreement between bioanalyzer and agarose gel for PCR amplicon library


We are setting up for an illumina MiSeq run using a PCR amplicon-based library (adding the Illumina adaptors using nested PCR). Our results look quite clean via agarose gel (expected size ~310nt), but when our facility ran bioanalyzer we had quite variable results (ranging between 400 and 500nt, depending on the sample). There are seven samples, each with a different barcode, labeled 1-7.

I'm attaching both the gel and the bioanalyzer report - has anyone seen anything like this before?

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File Type: jpg gel result.jpg (63.9 KB, 129 views)
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File Type: pdf Bioanalyzer result.pdf (431.4 KB, 173 views)
mbirnb is offline   Reply With Quote
Old 11-05-2012, 03:47 AM   #2
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I can only speculate. Maybe the agarose gel was run either without EtBr, then post run stained, or no EtBr was put in the gel or loading solution, but was put in the buffer? In either of these cases, the products would migrate mostly or entirely in the absence of EtBr.

Why is that important? Well, I have not tested this myself, but Dave Cook at Sage Science told me that in the absence of EtBr (or other DNA binding dyes) the difference in mobility between fully double-stranded amplicons, and "bubble products" (double stranded only at the adapter ends) does not happen. I.e. everything basically runs at the "correct" size.

So, if this is the issue you see, your amplicons are fine, but consist of variable amounts of normal and bubble-products. The Bioanalyzer chip faithfully displays the difference with the bubble products migrating slower than their true molecular weight.

Again, just a guess.

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Old 11-13-2014, 01:47 PM   #3
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Make sure you aren't overloading the chip. The first 3-5 samples look really hot relative to the standard. You could also try a DNA1000 chip since your products are so small.
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Old 07-30-2015, 03:45 PM   #4
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Hi Michael--
I was curious how this worked out for you. I recently prepared an amplicon library for TnSeq and had a similar discrepancy between my gel (the expected 190-bp band) and my bioanalyzer results (around 220 bp). I couldn't figure out why this happened.
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Old 08-03-2015, 09:28 AM   #5
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I think this has to do with the mobility of the y-forked adapters. Agarose is more difficult for migration because it's a solid phase, whereas the Bioanalyzer chip's gel matrix is much more fluid. I think the DNA 7500 chip gives the best representation of the "real" size.
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