Disgruntled POP5 user

Paul Shinn pshinn at mail2.sas.upenn.edu
Tue Feb 1 22:47:10 EST 2000


   I posted this earlier but I lost my connection.

POP5 problem solved.

   Well, I tallied the capillaries that resulted in missing bases from 2 
POP5 runs on 2 different days.  Out of 96 samples, 38 from each plate 
exhibited the missing bases problem.  Of those 38, 63% had the same 
capillaries in common.  A run done with POP6 on the same array only 
gave me 7 bad ones.
   I then thought there may be something wrong with the spatial.  I never 
really considered this before because PE says you only need a new spatial 
when you move the capillary end.  It has not been moved since the 
install.  However, the spatial was done with POP6.  Interestingly enough, 
though, there is a different spatial for POP5 and POP6.  Maybe they 
should stick that in the book.  After running the spatial using POP5, I 
ran a plate and no more missing bases!  I suppose the polymer flows out 
of the capillary end differently with POP5 than POP6.  I'm only guessing 
but maybe it moves faster past the detector.  Anyway, that did the 
trick.  And since I've got a POP6 spatial for the same array, I guess I 
can just go between the two if needed.


Next challenges:

--run more than 2 BDPs in a 4 session run with POP6
--improve injection parameters with POP6 and POP5 modules under 1.1
--run one 384 with POP5 then 2 384s for whole-day unattended run (with 
foil piercing) AND write perl script to automate sample sheets.

					Paul

Paul Shinn    
Sequencing Coordinator                                    ,___o
pshinn at neomorph.bio.upenn.edu                            _-\_<,
Arabidopsis thaliana Genome Center                      (*)/'(*)
http://genome.bio.upenn.edu/ATGCUP.html
(215) 573-7256






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