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Xenbase | Current Xine

Xine Volume 9 - number 3, October 2009


Dear ,

Welcome to Xine, the source for Xenopus news and information. Here's
what's happening...
_____________________________________________________________
An important request for letters of support

Dear all,

On behalf of the Xenopus laevis genome DNA sequencing task force of
the Xenopus Community in Japan (XCIJ) chaired by Dr. Masanori Taira, I
am writing to ask if you would write a letter of support for the
complete genome DNA sequencing of Xenopus laevis to be proposed to
National Institute of Genetics (NIG) in Japan. Selected members of
XCIJ are currently discussing with the genome sequencing group at NIG
whether it is feasible with the aid of their sequencing capacity.
To convince them and make the project initiated, we need your letter
of support with the emphasis on the necessity and importance of the
Xenopus laevis genome sequencing.

We understand this is not an easy task, but we believe the
accomplishment of the project will bring us a number of benefits to
pursue biochemistry, cell and developmental biology with Xenopus laevis.
We also expect that the mechanism and biological significance of
tetraploidization will be uncovered by the complete genome sequencing
of Xenopus laevis.

Japanese Xenopus community is now building teams for gene annotation,
FISH, and for BAC library from the inbred J-stain maintained in Japan,
to cooperatively work with the genome sequencing group at NIG.
We would greatly appreciate it if you could write a letter addressed
to "Xenopus community in Japan" hopefully with the letterhead of your
affiliation, by October 31.

The letter can be sent electronically to my e-mail address.

Sincerely yours,
Masanori Taira, Chair of X. laevis genome sequencing task force
Makoto Asashima, Chair of XCIJ
Naoto Ueno

*several e-mail addresses are obtained from the past proposal for
Xenopus laevis genome sequencing at the initiative of Professor Don
Brown.
Naoto Ueno
National Institute for Basic Biology
38 Nishigonaka, Myodaiji-cho
Okazaki 444-8585, Japan
TEL: +81-564-55-7570
FAX:+81-564-55-7571

___________________________________________________
From Gert Veenstra

Recently we published Xenopus gastrula chromatin state and transcriptome maps. These include ChIP-seq profiles of H3K4me3, H3K27me3 and RNA Polymerase II, in addition to deep sequencing of cDNA (RNA-seq). We also have made a collection of experimentally validated, improved gene models.

Robert C. Akkers*, Simon J. van Heeringen*, Ulrike G. Jacobi*, Eva M. Janssen-Megens, Kees-Jan Fran´┐Żoijs, Hendrik G. Stunnenberg and Gert Jan C. Veenstra. 2009. A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos. Developmental Cell, 17: 425-434.

<http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=19758566&itool=pubmed_DocSum>

The visualization tracks are available at our web site:
<http://www.ncmls.nl/gertjanveenstra/genomedata.asp>

The raw data have been deposited at NCBI GEO:
<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14025>

In addition the data will be available at Xenbase.
To upload the tracks in the UCSC browser go to the X. tropicalis Genome Browser Gateway:
<http://genome.ucsc.edu/cgi-bin/hgGateway?org=X.+tropicalis&pix=1200>
Click the button: [Add custom tracks]

Then either browse to a locally stored (downloaded) track, or simply copy-paste one of the download links from our webpage (right-click, select [Copy shortcut] or [Copy link location]), and click [Submit].

Best regards,
Gert
___________________________________________________

___________________________________________________
Call for content

Xine could be used to disseminate information and
protocols of general utility to the research community. In order for
this to occur, please send any such contributions to the editor who
will include them in a future (or special) issue of Xine.
_________________________________________________________
If you wish to read Xine in html format and/or see back issues,
they are available at the following places

http://blumberg-lab.bio.uci.edu/xine/index.htm
http://blumberg.bio.uci.edu/xine/index.htm
http://www.xenbase.org/xine/xine.html
_________________________________________________________
Links to useful sources of information for Xenopus (in no particular order)

general interest and utility
<http://www.nih.gov/science/models/xenopus/> Trans NIH Xenopus
initiative
<http://tropicalis.berkeley.edu/home/> - Harland lab X. tropicalis site
<http://faculty.virginia.edu/xtropicalis/> - Grainger lab X. tropicalis site
<http://tropmap.biology.uh.edu/> - Amy Sater's X. tropicalis genetic map
<https://list.mail.virginia.edu/mailman/listinfo/troplist> - Information on the
X. tropicalis listserver
<http://list.mail.virginia.edu/pipermail/troplist/> - Troplist archives.
Lots of good information here.
<http://www.xenbase.org/> - Peter Vize's Xenopus ´┐Żber database
<http://www.nimr.mrc.ac.uk/devbiol/zimmerman/> - Zimmerman Lab
X. tropicalis website, database of mutants

genomic resources
<http://xenopus.nibb.ac.jp/> - XDB at NIBB - Naoto Ueno's
X. laevis EST database <http://xgc.nci.nih.gov/> - Xenopus gene collection
<http://informatics.gurdon.cam.ac.uk/online/xt-fl-db.html> - full length
collection at the Gurdon Institute
<http://genome.jgi-psf.org/Xentr4/Xentr4.home.html> - JGI X. tropicalis
genome site with browser and other info
<http://www.dkfz-heidelberg.de/molecular_embryology/axeldb.htm>
AXELDB - Christof Niehrs' Xenopus database
___________________________________________________________
Subscription information

I have constructed the Xine mailing list from serveral sources. As
always, if you are not on the list and wish to be, want to update your
e-mail address or would rather not receive it at all, please contact
Bruce Blumberg (mailto:blumberg@uci.edu).

Until next time,

Bruce



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