[Arabidopsis] Re: Arab-gen Digest, Vol 51, Issue 7

[Cesar Barragan]

Hello Abo-Ogiala

Another source you might want to check is our website (http:// 
signal.salk.edu), here you can find more information about these  
lines or any other you may be interested. As an example, you will  
find that line SALK_146631 is a contaminated line so you could try  
instead SALK_139052 or SALK_127904 (http://signal.salk.edu/cgi-bin/ 
tdnaexpress). Information about this problem  can be found in the FAQ  
section (http://signal.salk.edu/tdna_FAQs.html) as follow:

16. Q:  On the T-DNA Express website, some insertion lines are very  
close in number or have the same number. For example SALK_005299,  
005300, 005301, and 005305) have the same sequence. How can this be?

    A: We have found that the ABI 384-well sequence precipitation  
method can lead to cross-contamination of samples. A new protocol was  
devised to reduce the number of contaminating sequences. When  
verifying insertions of interest you should order and test all lines  
listed for that gene. The most definitive test to determining if the  
line contains the expected gene insertion is to use Southern  
blotting. Often times PCR can give a false negative result. We  
strongly suggest that you carry out Southern blotting and  
hybridization with the labeled gene as a probe to determine if the  
line you received contains an insertion in the expected gene.

We hope these information and links can be useful for you and the  
community.
Best Wishes.

Cesar Barragan
The Salk Institute for Biological Studies
Genomic Analysis Laboratory
10010 North Torrey Pines Road
La Jolla, CA 92037
Tel 858-453-4100 ext 1796
barragan from salk.edu




>> Mr, Abo-Ogiala
>>
>> You were targeting seeds for segregated lines.  Do you have any  
>> PCR pictures we could see?  How did you genotype these lines?
>> A homozygous line has being already isolated for gene At5g02020,  
>> you can request SALK_064028C to ABRC.
>> Thanks
>>
>> Cesar Barragan
>> The Salk Institute for Biological Studies
>> Genomic Analysis Laboratory
>> 10010 North Torrey Pines Road
>> La Jolla, CA 92037
>> Tel 858-453-4100 ext 1796
>> barragan from salk.edu
>>
>> On Jul 15, 2009, at 11:11 AM, Ronan OMalley wrote:
>>
>>> ---------- Forwarded message ----------
>>> From:  <arab-gen-request from oat.bio.indiana.edu>
>>> Date: Wed, Jul 15, 2009 at 9:03 AM
>>> Subject: Arab-gen Digest, Vol 51, Issue 7
>>> To: arab-gen from magpie.bio.indiana.edu
>>>
>>>
>>> Send Arab-gen mailing list submissions to
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>>> Today's Topics:
>>>
>>>   1. At5g02020 (Abo-Ogiala, Atef)
>>>
>>>
>>> -------------------------------------------------------------------- 
>>> --
>>>
>>> Message: 1
>>> Date: Tue, 14 Jul 2009 11:14:26 +0200
>>> From: "Abo-Ogiala, Atef" <Atef.Abo-Ogiala from forst.uni-goettingen.de>
>>> Subject: [Arabidopsis] At5g02020
>>> To: <arab-gen from magpie.bio.indiana.edu>
>>> Message-ID:
>>>        <99392551BB49ED458ACFE796416D3189E1DBD3 from VS3.exc.top.gwdg.de>
>>> Content-Type: text/plain;       charset="iso-8859-1"
>>>
>>> Hello,
>>>
>>> We ordered SALK_040413 of the geneSALK_040413. We have problem  
>>> with this line.
>>> The whole plants that we get from the seeds are wild type. Please  
>>> if you have
>>> homozygous line for At5g02020 gene except Salk_146631 tell me  
>>> from which
>>> source I can get it.
>>>
>>> Best regards
>>>
>>> Atef Abo-Ogiala
>>>
>>> PhD student
>>>
>>> Büsgen-Institut
>>>
>>> Forstbotanik und Baumphysiologie
>>>
>>> Georg-August Universität
>>>
>>> Büsgenweg 2
>>>
>>> 37077 Goettingen
>>>
>>> Germany
>>>
>>>
>>>
>>> Tel:  +49 (0)551 - 39 9362
>>>
>>> Fax: +49 (0)551 - 39 22705
>>>
>>>
>>>
>>>
>>>
>>> ------------------------------
>>>
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>>> End of Arab-gen Digest, Vol 51, Issue 7
>>> ***************************************
>>>
>>
>
> Joseph R. Ecker
> Professor,  The Salk Institute for Biological Studies
> Plant Biology/Genomic Analysis  Laboratories
> 10010 North Torrey Pines Road
> La  Jolla, CA 92037
> Phone (858) 453-4100 x1752
> FAX (858) 558-6379
>
> Web addresses:
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> http://signal.salk.edu
> http://pbio.salk.edu/pbioe/finaleckerhomepage.html
> http://www.salk.edu/faculty/ecker.html
>
> Administrative Assistant:
>
> Nancy Benson
> Phone (858) 453-4100 x1106
> Fax (858) 558-6379
> email: nbenson from salk.edu
>
>
>
>