Peggy,
This is one (of the many) problems we had. There were a few things wrong
with our machine (at different times). The most appropriate (I think):
1. The load bar was not draining well enough (an engineer noticed and
corrected this)
2. The wash volume was too low (increasing this (to 600ul) eliminated the
problem on one occasion)
Also, if a capillary has very strong sequence in it, and the capillary next
door has no sequence in it, then the 'no sequence' capillary will pick up a
VERY small signal (signal strength of 8-10). Unfortunately, the software
has picked this up on occasions to give 500 bases of beautiful sequence!
The only way to tell is to look at the raw data. ABI (UK) know about this,
but there is nothing that can be done.
Good luck!
Andrew
_______________________________________________________________
AstraZeneca R&D Charnwood
Molecular Biology, Bakewell Road, Loughborough, Leics, LE11 5RH, England
Tel: +44 (0)1509 644753 Fax: +44 (0)1509 645557 Mobile: +44 (0)787
9615913
andrew.walding@astrazeneca.com
-----Original Message-----
From: Peggy Grow [mailto:grow@genetics.med.harvard.edu]
Sent: 16 April 2001 23:21
To: Recipients of ABRF List
Subject: 3700 problems
Hello all:
I am having curious problems with my 3700 and was wondering if anyone else
has experienced the same things.
I am in a core facility, so we run samples for many different people on the
same 96 well plate. I noticed on a recent plate that the contig maps were
showing mismatches. It seems that samples the software is calling one thing
are actually something else. In other words, the sequence from what it
calls well A2 is actually from another well, but I have no idea which well.
I have no way of knowing or figuring out what should be where.
We confirmed that there is a problem by taking the same plate to another
3700 in another facility, where it's results were fine and everything made
sense and matched up.
I then ran two staggered Pgem control plates. One plate had pgem in rows A,
C, E and G with the other rows blank. The second plate had pgem in 1, 3, 5,
7, 9, and 11, with the others blank. This plate also confirms that there is
a problem somewhere because there was sequence in places where there
shouldn't have been and vice-versa. It doesn't seem to be a problem with
the actual loading, based on the results from these staggered plates. It
just makes no sense at all!
I currently have the 1-800 ABI Tech support looking at the problem, but
have not heard back from them. Has anyone else experienced this strange,
aggravating problem??
Many thanks,
Peggy
Peggy Grow
Biopolymers Facility
Howard Hughes Medical Institute
Harvard Medical School
Warren Alpert Building, rm. 341
200 Longwood Avenue
Boston, Massachusetts 02115
phone: 617/432-7481
This archive was generated by hypermail 2b29 : Tue May 01 2001 - 14:07:05 EDT