Xine Volume 9 - number 5, November 2009Welcome 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 . <http://www.xenbase.org/other/static/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: http://www.xenbase.org/common/submitData.do <http://xlaevis.cpsc.ucalgary.ca/common/submitData.do?> or by contacting us at : xenbase@ucalgary.ca <mailto:xenbase@ucalgary.ca> -- 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. <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 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 |
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