[Xenopus] Gathering Letters of Support for a grant to generate the second version of the Xenopus ORFeome

[Stukenberg, Peter Todd (pts7h)]

Dear Xenopus Community:
We will submit an NIH grant in early June to expand the Xenopus ORFeome project to include the ~15,000 cDNAs for which there are currently no X. laevis or X. tropicalis clones.  To be competitive we need to document community support.   This project was voted as the highest priority in the last Xenopus PI meeting and will be listed as such in the 2016 white paper.  As you probably know in the first version of the ORFeome we moved Open Reading Frames (ORFs) from all of the available cDNAs generated by the various EST projects into Gateway vectors.  This first set of Xenopus laevis clones is fully integrated into Xenbase (http://www.xenbase.org/reagents/static/orfeome.jsp) and has been available for over a year through the EXRC in Portsmouth, as well as through commercial vendors including GE Dharmacon.  We are putting the final touches to the first version of X. tropicalis ORFeome that was generated in a similar manner and it will be available soon.  This will complete the first version of the Xenopus ORFeome project.
We are writing a grant to obtain funds to generate Gateway entry clones for the remaining ~15,000 Xenopus tropicalis ORFs that are missing in the current ORFeome.  For most of the planned new new ORFs there are no commercially available cDNA clones for either X. tropicalis or X. laevis.  Thus the importance of this next version of the project is to not only greatly expand the ORFeome but also provide the first available cDNA clones for over 1/2 of the Xenopus ORFs.  Our plan is to employ bioinformatics to identify genes that are not represented in the current ORFeome and use the latest gene models and RNA-seq data to identify and validate the translational start and end sites of each ORF.  We will de novo clone each ORF from reverse transcribed RNA by PCR and use Gateway technology to put the clones in Gateway donor vectors.
What we need from you is evidence that the community views this second version of the ORFeome as an important extension to this resource.  What would be ideal is if you could write a short letter outlining why you think the second version of the ORFeome is a critical resource for the community (for example you often need to characterize clones that are not available from EST libraries), put this on letterhead and send it to Todd Stukenberg (pts7h at virginia.edu<mailto:pts7h at virginia.edu>).  At the very least please write a quick email to Todd simply stating that you strongly support the second version of the Xenopus ORFeome.  The number of supporting emails will be quantified and the letters included with the application. Please forward your letters of support by May 20th.
Thank you for your help in generating a competitive Xenopus resource proposal!

Sincerely,

Todd Stukenberg, Aaron Zorn, Mike Gilchrist and Dave Hill


Todd Stukenberg, Ph.D.
Professor
Department of Biochemistry and Molecular Genetics
University of Virginia School of Medicine
Charlottesville VA 22908

pts7h at virginia.edu<mailto:pts7h at virginia.edu>
(ph) 434-924-5252
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