bob,
the problem we have seems similiar. We had some real bad problems
with a new array we installed in october. After beating our heads against
the wall for a few months, we were able to get a confession that some of
the arrays from abi had some problems. After we replaced the array in
january, things started going better. But over time we have been seeing a
slow degradation. A lot more noisy sequences and more outright
failures. We have run the abi bid dye standard and the machine appears to
be working correctly. (although if you have used these before the signal
strengths are about 20 times the signal you get from a normal sequencing
reaction). It has recently gotten much worse. We have either a bad lot of
polymer, bad big dyes or a different chemical problem. It still might be
an array issue though. We just did a regeneration and that did not seem to
correct the problem. We are at about run 100 on this array. I have
ordered in a different lot of big dyes to try that. Hopefully this helps
and I can stop beating the wall.
At 09:06 AM 3/14/01, you wrote:
>Thomas J Stelick wrote:
> >
> > hello,
> > We have been getting some inconsistant results on some of our sequencing
> > and one problem may be the lot of big dye. The problem showed up around
> > the time we started using a new lot. The lot # is 0101047. Is anyone else
> > having problems. We are using a 3700. Or is anyone having a problem with
> > pop-6 polymer lot # 0101130.
>
>
>We have been questioning POP6 lot 0101130 ourselves. An instrument that was
>working very well with read lengths of 700-800 suddenly changed to reads of
>350-450 after only a POP6 lot switch. ABI had no other reports of a problem
>with that lot.
>
>There were reasons to suspect other problems: perhaps a bad array (regenerate
>array improved the situation and switching arrays got us up to 650 nt reads)
>and perhaps an instrument problem (we started seeing strange drop-outs in the
>array image data in caps 90-96).
>
>The symptoms after the POP lot change were (i) decreased resolution - broad
>run-together peaks, (ii) *leading*-edges of peaks had reverse "tails" (did
>that make any sense? I can't figure out how else to describe it) and (iii)
>numerous capillaries suddenly gave no resolution at all. With such a routine
>procedure as POP lot change, I can't image what we could have done that would
>have toasted the array. I am still highly suspicious of the POP6 lot.
>
>To re-iterate, yes we were suspicious of POP6 Lot 0101130, but no, we could
>not prove it was a bad lot, and it is currently giving us modest resolution
>but NOT great. I would be very interested in hearing of others using that
>lot of POP6 and what results they are achieving.
>
>Bob Lyons
>University of Michigan
Tom Stelick
DNA Sequencing Facility manager
Bioresource Center
Cornell University
Ithaca, NY 14853
(607)254-4857
http://brcweb.bio.cornell.edu
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