Anomalous runs on the ABI 377

M. M.
Thu Aug 28 08:20:17 EST 1997


I need a little help with the ABI 377 and GeneScan analysis.  These days
I am trying to run more then one GeneScan gel per day, the gel that I
run in the morning runs fine but then when I try to run another gel on
the same set of plates, after washing them, I start getting problems. 
It seems that the migration of the fragments on the second gel is
invariably slower and so the size of the fragments that I get is greater
on the second gel.  This is without changing anything else including the
buffer and the acrylamide.  I am stymied and do not understand what I am
doing wrong or what to do?  It seems like the sequencer gets tired by
the end of the day so the migration anomaly ;-)  If anyone has
experienced a similar problem and found out how to solve it please let
me know as I am pressed for time and have to get a lot of data out as
soon as possible.

BTW I have encountered this problem a number of times and now I have
made a standards file based on this "Bad gel" and analyse my samples on
these slower migrating gels on the basis of this set of standards file,
is this valid to do?  I have tried to re-run and compare the size of the
alleles on the slower and the normally running gels and find that: for
the smaller fragments the sizes are the same.  However, for the larger
fragments the sizes usually do not compare between the gels.

My instrument is relatively new so it could not be that the electrodes
have corroded. 

Hoping to hear from you all.

Raheel Qamar

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