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Xine Volume 9 - number 5, November 2009



Welcome to Xine, the source for Xenopus news and information. Here's
what's happening...


From Mustafa Khokha and John Wallingford,

Dear Colleagues,

There are three Community Goals for which we need your help and somewhat
urgently:

1. US Xenopus Resouce center (XRC) - The US stock center has passed a major
hurdle. We've just gotten word that funding of the P41 grant to establish
the center is likely to be approved by the NIH/NCRR. However, in order to
avoid a budget cut, we need your help to demonstrate community support. We
need the NICHD to provide some additional support in order to fund the grant
fully. To demonstrate Community support, please provide a letter of support
to James Coulombe <CoulombeJ@mail.nih.gov>. Attached to this email is a
draft letter, please edit the first few sentences describing why the XRC
would benefit you, generate a PDF with institutional letterhead, and email
to James Coulombe. It should only take a few minutes.

2. Xenbase - The grant funding Xenbase is also about to expire. Peter Vize
and Aaron Zorn have submitted a P41 grant as well that has received an
excellent score and is now under Council review at NIH/NICHD. Again, a
letter of support would likely sway NIH/NICHD to fund the grant fully and
allow all of the proposed aims in the grant to be implemented allowing
Xenbase to create much greater functionality. Another letter is attached to
this email as a draft. Please edit the first few sentences to address why
Xenbase is useful to you, generate a PDF with institutional letterhead, and
email to James Coulombe <CoulombeJ@mail.nih.gov>.

We realize that many of you have provided letters of support in the past for
these endeavors. We urge you to submit additional letter now. We are very
close to getting these two critical resources fully funded! Also so we can
track letters, please feel free to cc to rmg-lab@virginia.edu.

3. 2009 Xenopus White Paper - The White paper is nearly complete and we
anticipate submitting the letter to the NIH in the next two days. Over 130
investigators are currently signatories which lends considerable weight to
the White Paper. If the the above resources, Xenopus laevis genome
sequencing, an ORFeome, and other Community Resources would benefit you, we
urge you to become a signatory. We anticipate submitting the letter this
Wednesday before Thanksgiving and will be closing to signatories tomorrow -
11/24 by 5pm. If you have not already done so, please follow the
instructions below to provide your input:

A draft of the white paper can be found on Xenbase .
<static-xenbase/xine/xrd.jsp>

To SIGN the White Paper:
Send an email to SignXWP2009@Gmail.com


To COMMENT on and SIGN on the White Paper:
Send an email to CommentXWP2009@Gmail.com


To DISSENT from the White Paper:
Please tell us why you dissent and what could be changed in order to make
you re-consider.
send an email to DissentXWP2009@Gmail.com

Many thanks.
Mustafa Khokha
Yale University
John Wallingford
HHMI
University of Texas - Austin


From Jeff Bowes and Xenbase

Xenbase has recently added a gene expression search tool. This tool allows users to search for image or EST-based evidence of gene expression. Users can search expression by any combination of Gene/Clone id, development stage, anatomy terms, experimenter, assay type, experiment type and/or several other criteria. We will also soon be releasing an update that will allow theuser to search by sequence similarity as well.

Currently our gene expression data includes over 18,600 images from XDB3, 2,600 images from Axeldb and over 2,000 community submitted images. There are also over 1,000 images from recent articles in Cell, Current Biology, Development, Developmental Biology, Developmental Cell, Developmental Dynamics, Mechanisms of Development and Proceedings of the National Academy of Sciences. These journals have given Xenbase permission to reproduce images and captions describing Xenopus gene expression.

The expression search is located at:
http://www.xenbase.org/geneExpression/geneExpressionSearch.do?method=display <http://www.xenbase.org/geneExpression/geneExpressionSearch.do?method=display>

We would like to encourage further community data submissions. If you have data you would like to submit to Xenbase, gene expression or other, you cando so here:

submitData.do <http://xlaevis.cpsc.ucalgary.ca/common/submitData.do?>

or by contacting us at : xenbase@cchmc.org <mailto:xenbase@cchmc.org>

--
Jeff Bowes M.Sc.
Technical Director, Xenbase
Department of Biological Sciences
University of Calgary
Calgary, Alberta T2N 1N4
CANADA
Tel: (403) 220-2824
Fax: (403) 284-4707



From Gert Veenstra

Recently we published Xenopus gastrula chromatin state and transcriptome maps. These include ChIP-seq profiles of H3K4me3, H3K27me3 and RNA PolymeraseII, 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 Françoijs, 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.

<https://pubmed.ncbi.nlm.nih.gov/19758566

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
static-xenbase/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 onthe
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 über 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