Dear Nick,
(cc Arab Newsgroup)
since all GABI-Kat lines are confirmed for the insertion predicted
from the FST before we send them out, there should be a primer pair
that did work in our hands. Since you do not mention which line you
are referring to, I explain using an example:
1) have a look at our web page:
http://www.gabi-kat.de/ and go to:
=> FAQ => Vector & primer info
(use the menue on the left)
You will find a page that lists the primers which we use in-house for
work with the T-DNA.
2) As an example I use the GABI-Kat line 048E04:
NASC-ID for the T3-set: N404564
http://arabidopsis.info/StockInfo?NASC_id=N404564
(On the NASC website there is a link to the page describing this
line: click the line name shown below the NASC ID code.)
insertion locus: At5g43175
Go to the URL
http://www.gabi-kat.de/db/
(or http://www.gabi-kat.de/ and go to:
=> SimpleSearch => SimpleSearch)
- Use the "Line or FST Search" option (on the right) to search for
the line ID, in the example 048E04
- you end up on a page that has the "Line specific information" for
048E04, and also information about the related insertions
- line 048E04 has two FSTs attached, one is confirmed (the one for
the insertion in At5g43175)
- scroll don on the page until you find the "Confirmation Status"
data. If a line has been confirmed, there will be a link named "show
confirmation sequences"
- click on this link, you will end up on a page that contains the
"Confirmation sequences for line 048E04 and hit At5g43175 are shown"
- here, you will find the confirmation sequence. This sequence has
been produced on an amplicon generated with a gene-specific and a T-
DNA primer, and the (usually) two sequences are generated with these
two primers. You will find the information about the sequence of the
primers used.
The database is described in the paper:
Y. Li, M.G. Rosso, P. Viehoever, B. Weisshaar (2007)
NAR 35: D874-878
http://www.ncbi.nlm.nih.gov/sites/entrez?
cmd=Retrieve&db=PubMed&list_uids=17062622&dopt=AbstractPlus
Best regards, Bernd
PS: Please let me know if you have trouble with SimpleSearch, or if
you detect errors or bugs. BW
On 04.10.2007, at 01:35, Siefers, Nicholas A. wrote:
> Dear Arab-Gen List,
>> I have obtained some T-DNA lines from GABI-Kat, which I would like
> to genotype.
> I have tried to design a couple of left border primers to use, but
> they are not
> working properly. Would any of you like to share a sequence of a well
> functioning GABI-Kat left border primer (preferentially with a Tm
> of 65-70C)?
> Thanks in advance!
> Nick Siefers
> _______________________________________________
> Arab-gen mailing list
>Arab-gen from net.bio.net>http://www.bio.net/biomail/listinfo/arab-gen>
______________________________________________
PLEASE NOTE: NEW phone NUMBER, NEW room!
Bielefeld University, Dept. of Biology
Prof. Dr. Bernd Weisshaar
Chair of Genome Research (Lehrstuhl fuer Genomforschung)
D-33594 Bielefeld
Germany
Office: G0-102
Tel.: +49-521-106-8721
Fax: +49-521-106-6423
genomforschung from uni-bielefeld.de (Secretary)
WWW-URL: http://www.genomforschung.uni-bielefeld.de/
Please direct emails regarding GABI-Kat to: info from gabi-kat.de
