[Automated-sequencing] Weird chromat

Phillip San Miguel pmiguel at purdue.edu
Thu Jun 23 15:09:00 EST 2005


Hi Brynn,

(I'm going to assume from the "Hello All" in your email that you 
actually intended to reply to the whole list--hence my reply to you will 
also go to the whole list. If that was not your intention, I apologize. 
As the settings stand, to reply to the whole list *through email*, one 
must manually type in the email address "autoseq at net.bio.net". That 
makes it pretty hard to get a discussion going. So I'm thinking about 
changing the group settings.)

Anyway, we're running an ABI 3730XL using BD v3.1 with POP6. These 
samples were cleaned-up using BioRad squeeky-cleen 96-well plate 
clean-up columns. (That would be a size exclusion column method). The 
samples are in water and our caps are 50 cm. We're using the standard 2 
hour run protocol--except our injection time is only 7 s, instead of 15 
seconds.

Phillip

Brynn Kaplen wrote:

>Hello All!
>
>We have seen similarly sloped peaks on occasion, and I also do not know
>what the cause is.  We are using BD v3.1, running on either a 3730 48 cap
>with POP7, or on a 3100 with a 36cm cap., and either POP6 or POP4.  We are
>using Agencourt's CleanSeq for reaction clean-up, and are running our
>samples out of water.  What kind of chemistry and instrumentation are you
>running?
>_________________
>Brynn Anne Kaplen
>DNA Core Facility
>Canadian Science Centre for Human and Animal Health
>1015 Arlington St., Suite H3390
>Winnipeg, MB   R3E 3R2
>Phone: (204) 789-6035
>Fax: (204) 789-2018
>Email: brynn_kaplen at phac-aspc.gc.ca
>
>
>                                                                                                                                              
>                      Phillip San Miguel                                                                                                      
>                      <pmiguel at purdue.edu>            To:       bionet-genome-autosequencing at moderators.isc.org                               
>                      Sent by:                        cc:                                                                                     
>                      autoseq-bounces at oat.bio.        Subject:  [Automated-sequencing] Weird chromat                                          
>                      indiana.edu                                                                                                             
>                                                                                                                                              
>                                                                                                                                              
>                      23/06/2005 11:58 AM                                                                                                     
>                                                                                                                                              
>                                                                                                                                              
>
>
>
>
>
>Take a look at this screen capture:
>
>
>http://data.genomics.purdue.edu/~pmiguel/technical/06-22-2005read.htm
>
>
>(It is only a 74 kbyte .png file.)
>
>Anyone have an idea of what is going on? Note that the peaks look pretty
>good around 200 bases, but by 500 bases something is clearly wrong. The
>right-side edge of the peaks come up pretty high above baseline. But the
>left-side edge looks much better. I guess the peaks are "skewed".
>
>Has anyone seen this before?
>
>--
>Phillip
>
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