Eric Buxton wrote:
> Recently we have noticed that we are getting a large T blob at around
> base 220 and shortly after that a G blob. Sometimes this blob is enough
> to distort base calling, other times it doesn't affect the calls, and
> other times it does not appear. Has anyone else seen this? I am
> guessing it may have to do with our cleanup method. We spin purify our
> plates.
> [...]
Yes, I have seen this. Except I don't remember the G-blob. PE claims it
was probably ethanol contamination. Could have been. I also use filter plate
clean up. Back then we used Qiagen turbo preps and it was difficult to get
rid of all the ethanol from the wash solutions. PE's big dye kit seemed to
work (to some extent) even with DNA somewhat contaminated with ethanol. (We
switched to Qiagen REAL preps.)
If you completely dry your samples after they come off the filter plate,
then there should be no ethanol remaining--but if you just load the samples
on the 3700 without drying, then you could still have a little ethanol
around.
Phillip San Miguel
Purdue Genomics Core Facility
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