2015-11-14 More than 13.600 lines donated to NASC
Batch number 151 containing 100 newly confirmed GABI-Kat lines has just been donated to NASC. This is the first batch donated after public funding of GABI-Kat ended at 2014-12-31. We are on the way to reach 14.000 GK lines at NASC; we expect to donate about 275 additional lines by the end of 2015. See here for exact numbers of donated lines.
2015-11-02 Paper about analyses of insertion sites published
By using the confirmation sequence data that accumulated at GABI-Kat, and also by systematically addressing the 2nd border of about 1,200 insertions that had been confirmed at one border, we generated a large dataset describing the structure of T-DNA insertion sites. These data are now available in print and appeared in MOLECULAR PLANT 8:1651-1664 (2015). The title is "The structural features of thousands of T-DNA insertion sites are consistent with a double-strand break repair based insertion mechanism." by Nils Kleinboelting et al.
2015-08-20 Final report for GKat (GABI-Kat) submitted to PtJ
Since funding of GABI-Kat did terminate on 2014-12-31, we had to prepare and submit the "Final Report" for the GKat project to PtJ (Projekttraeger Juelich). We were a bit late and got "reminded" by PtJ. In the context of preparing the report, the "output statistics" have been updated with new numbers. As of the end of 2014, about 255,000 stocks have been distributed to the Arabidopsis community via NASC and ABRC (see here). About 56 percent of the CDSi alleles predicted within the GABI-Kat collection have been donated to NASC (see here). This means that there are about 6,000 CDSi alleles (alleles that have a very good chance to be NULL, so a real knock-out) in the population that are not yet confirmed and secured. Since the germination rate of the seed that we have in stock is decreasing, the prospects for this material are not very good.
2015-05-29 CMS tool for GABI-Kat website updated
The "engine" of the GABI-Kat website has been updated. Joomla! is the content management system (CMS) we use to maintain this site. Note that only the "static" part of the website is provided via Joomla. The dynamic parts like the SimpleSearch tool are generated by using PHP.
2015-05-17 Keeping the GABI-Kat service alive
Funding of GABI-Kat did terminate on 2014-12-31. We thank PtJ/BMBF (German Ministry of Education and Research and the Projekttraeger Juelich) for many years of very helpful funding. We, that is some people from the "Plant Genome Research" group at Bielefeld University (Weisshaar lab), try to keep the community service alive. However, due to lack of hands and time, we might be slower than before. The "GABI-Kat Team" is now a very small team that usually needs to do quite some other jobs. It took until today (Sunday, 2015-05-17) to update the homepage, to update the GABI-Kat history page, and to write this note.
2015-05-06 Delivery of seed in 2015
During the last weeks, we were able to get some of the new seed requests in queue confirmed. We are now referring to our project as "GABI-Kat III". Quite some seeds left our lab today.
2014-11-03 SimpleSearch now includes not-yet-submitted FSTs
From time to time it happens that we detect insertions that have not been predicted on the basis of a FST. Most of these cases happen when we do get a "confirmation amplicon", but the sequence of this amplicon does not fit the predicted insertion site. We use these "wrong sequence results" to deduce a new insertion site prediction, and these "ConfSeq predictions" enter the confirmation process resulting often in a positive result for the new predictions. We generate FST equivalents from the sequences we got, and these are also submitted to ENA/GenBank. However, to avoid the need for submission of very small batches of sequences, we allow SimpleSearch (since September 2014) to display FSTs that are "queueing for submission to ENA/GenBank". An example is line 038B07.
2014-10-18 Paper describing the primer design tool published
The tool for design of primers which we implemented in the context of SimpleSearch - see GK primer tool - has been published in Plant Methods (Kleinboelting et al. (2014)). As of today, the paper is also available via PubMed. In case you run into trouble with the tool, please contact us at infogabi-kat.de. Obviously, we would also be happy about positive feedback.