GABI-Kat: generation of flanking sequence tags (FSTs) from
T-DNA mutagenised A. thaliana plants
T-DNA mutagenised A. thaliana plants
Over time, an increasing number of lines will become available from NASC. Please read about details here. The "show sequence" page of SimpleSearch will display if a GABI-Kat line for a given FST has already been donated to NASC. Lines that have so far not been regrown and confirmed are only available from GABI-Kat directly.
We request that you cite our most recent paper that has been published recently in the 2012 database issue of NAR. Please note that we ask you to cite this NEW publication if you use our lines in your experiments. See here for more detail.
The current GABI-Kat grant that initially terminated at the end of June 2014 has been extended (without additional money) to the end of 2014. This means that GABI-Kat will have to close down by the end of December 2014. Have a look at older "News & History" articles (e.g. the one from 2014-03-26) for some more information.
The general procedure for ordering seeds from GABI-Kat is as follows:
(please also check the notes on ordering and supplier information)
You search for insertions in a AtYFG (Your Favorite A. thaliana Gene) using GABI-Kat SimpleSearch. The search interface allows searching for relevant insertions by AGI gene code, keyword, GABI-Kat line ID, GenBank accession number of the FST or by BLAST with a sequence.
Please note that the AGI gene code must be present in TAIRv10. See FAQ 12
If you detect a hit, use the sequence which is presented to you by SimpleSearch (grab it with copy and paste) to confirm our automatic annotation of the FST in question.
From this sequence, you can also deduce the approximate location of the insertion in the AtYFG. Please note that the insertion position deduced from FSTs is not absolutely reliable, especially when no T-DNA sequence is detected at the beginning the FST. In addition, reliability also depends on the quality of the respective sequence read. The FST sequence information does tell about the (potential) detection of T-DNA sequences at the beginning the FST read in the field designated "T-DNA Border".
Decide if the insertion looks interesting to you. Please note that it is your own responsibility to decide if you want the line or not. If you do want the line and the line is available from GABI-Kat, note the Line ID and AGI gene code which is presented to you (e.g. Line ID 051G10 and gene code At4g23270). If you use the BLAST option and end up with an FST that is not overlapping an annotated gene, please note the BAC ID.
Decide if the GABI-Kat MTA (version of 20050624v4) is acceptable to you. If yes, use our web order form to provide us with your complete contact information and the details about the lines you want. Be careful to provide identical name, address and line information on the MTA and via the web order form. We need both, MTA and submitted web order to start the confirmation process. Note that orders with incomplete or inconsistent information (e.g. different addresses and/or different line IDs on the MTA when compared to the data provided via the web order form) will not be processed.
Send a valid purchase order (usually your institution will have a form for that, please do not pre-pay) and three copies of signed MTA to the address given below. Some additional relevant information can be found in our info file line order notes.
Please send a "snail mail" letter of these documents with original signatures. Do not forget to mention the GABI-Kat Line ID, the respective AGI gene code (or the BAC ID if there is no gene code). This information should be on the purchase order and on the MTA.
After we received all the necessary documents of your order, a notification e-mail will be send to you to confirm the order. Please note that nothing will happen before we received all the documents and you have done the web order form submission. We will check our stocks for the line, and if the line has set seed, we will grow up some seedlings and do a QC (quality control) for that line. The QC will include a PCR reaction and a sequencing reaction of the expected PCR fragment on DNA extracted from the T2 seedlings. One of the primers for the PCR will be designed according to the expected insertion allele of the AtYFG; the other will be from either RB or LB of the T-DNA.
You will only need to pay if QC was successful, and the cost is 100.- EURO per line. This cost is for the QC, for reproduction of seed to fill up our stocks, and for postage and package.
If the QC was successful, we will send T2 seeds to you, together with an "reimbursement note" and one executed MTA. You will also receive information on the sequencing result of the QC PCR fragment. This data can also be obtained electronically from the "get confirmation sequence" page.
Once you have received the seeds, you need to pay according to the information on the "reimbursement note". You are also responsible for forwarding the executed MTA or a copy to your contract administrator.
CeBiTec / GABI-Kat II
c/o Bernd Weisshaar
The PI's for GABI-Kat are: Bernd Weisshaar, Koen Dekker, Bernd Reiss and Heinz Saedler
Postdoc in GABI-Kat is at present: Gunnar Huep; the DB is maintained by Nils Kleinboelting
Postdocs who left the group: Nicolai Strizhov, Sabine Steiner-Lange, Yong Li, Mario Rosso and Andreas Klassen
Please contact us by e-mail to infogabi-kat.de if there are questions regarding GABI-Kat material or the project inself. Also, any error report is welcome!