** Our apologies if you receive multiple copies of this announcement **
Dear colleagues,
In 2006-2007 JGI generated ESTs from 200000 cDNA clones from a French mixed
stage (cleavage to neurula) Gateway library and 100000 clones from a
Japanese mature adult Gateway. The resulting 530000 ESTs are now available
on the ANISEED browser. You can also scan the ESTs directly from Mike
Gilchrist database (see links at bottom of this message).
In addition, you will find on these browsers the selected full ORF Gateway
compatible Unigene set that was picked in Stanford. This set includes 19000
clones grouped in fifty 384-well plates. The set covers approximately 9000
coding Aniseed v3.0 gene models. We have just received a first "hard" copy
of the clone set in Marseille, which we are now analysing (sequencing clones
at random to make sure they are what they should be...).
This work was of course only possible because of JGI's involvement via a
community sequencing project. In addition, the project has involved several
groups and in particular those of Ken Hastings (Montreal), Mike Gilchrist
(Cambridge), Yutaka Satou (Kyoto) and myself (Marseille).
We would like to stress that these data are being released to the community
prior to their publication (or even the writing of the paper). Use of these
data for small scale experiments is absolutely free (eg MO design,
improvement of individual gene models). We however kindly ask that you do
not carry out large scale data analyses without seeking our prior consent,
as this may interfere with our own work.
The next important step for the community is to make this collection freely
available to all. For this we need your help!!!
We had reached some time ago an agreement on the distribution of this
collection and of the much larger global JGI EST collection with a German
Biotech company which unfortunately decided to drop this activity in 2008. I
am therefore contacting you to encourage you to send suggestions of
alternative companies we could contact to:
1) make a few tens of replica of the Unigene collection for distribution to
the various labs of the community.
2) distribute these as well as individual clones from the large EST collection.
Thanks for your help, please do not hesitate to distribute this message to
colleagues that I may have omitted from the list.
Best,
Mike Gilchrist, Ute Rothbächer, Erika Lindquist, Jun Matsumoto, Pierre
Khoueiry, Ken Hastings, Yutaka Satou and Patrick Lemaire
Database links:
Aniseed genome browser:
http://crfb.univ-mrs.fr/ciona-bin/gbrowse/intestinalis/
The following tracks can be activated at the bottom of the page of the
ANISEED browser in the "ESTs and cDNAs" section
Full ORF Gateway clones (Mike Gilchrist)
Gateway-compatible Mature adult library (Satou lib, JGI sequenced)
Gateway-compatible Mixed Cleavage to neurula stages library (Marseille
lib, JGI sequenced)
Gateway-compatible adult digestive gland library (Satou lib, NIG sequenced)
Gateway-compatible Mature adult library (Satou lib, NIG sequenced)
Gateway-compatible mixed embryonic to larval stages library (Satou lib,
NIG sequenced)
By Clicking on the full ORF gateway ESTs, and of the clusters you will be
directed to Mike Gilchrist EST clustering database. By cliking on individual
ESTs, you will access their sequence.
To access the locus of a gene of interest on the Aniseed browser, the
easiest is to first connect to the Aniseed database
(http://aniseed-ibdm.univ-mrs.fr/ ) and use the Anisearch or the "Find a
gene" interface in the "Genes/clones/Cis-reg". Once you reach the desired
"gene card" page, click on the image extracted from the browser. You will
automatically be directed to the relevant locus on the Aniseed genome browser.
Mikes Ciona EST database:
http://informatics.gurdon.cam.ac.uk/cgi-bin/public.exe/dbe=http&dbs=INFO-PUBLIC&uid=guest&font=7&species=Ci¤t=ESTs&full=Guest+User&src=public&tgt=public&menu=main_organism&menu=organism_clusters&option=clusters&proteins=y&variants=y&message=y&project_key=1000000180&version=1
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