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Xenbase | Current Xine

Xine Volume 9 - number 1, June 2009


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

Dear fellow Xenopus researchers,



It is time to once again write a White Paper for community resources for Xenopus. As a first step in this process, a group of us is discussing plans for the next white paper this upcoming Friday (6/26/09). Join the discussion here
http://www.facebook.com/inbox/readmessage.php?t=1157518783488&mbox_pos=0#/topic.php?uid=64447883400&topic=9180
If people have additional/alternate ideas regarding contents that should be included, please send them to Kris Kroll by email (kkroll@wustl.edu) and she will pass them along to the group. In addition, it would be useful to know what you consider the highest priority items below, since we may solicit funds from the NIH more effectively if we can offer a prioritized list that reflects the needs of our community. Proposed topics:

--Xenopus laevis Genome Sequencing
--Xenopus tropicalis Genome Sequence improvements
--Arrayed Full length genome-wide Xenopus cDNA expression library/Gateway
expression system
--Xenopus Stock Center/Training Center at MBL
--Xenbase
--Xenopus TILLING resource
--Antibody stock center and generation of antibodies.
--Xenopus proteome network
--Xenopus Molecular Resource
--Genome wide MO library
--Xenopus specific RFAs and Pas

As a draft of the proposed White Paper is developed, it will be circulated for comment via Xine and Xenbase so that everyone will have a chance for significant input. We are likely to approach some of you for detailed input to specific areas and hope that you might be willing to help out.

Best wishes,
Rob Grainger
Richard Harland
Mustafa Khokha
Kris Kroll
John Wallingford
Aaron Zorn

Xenopus Facebook group



A Community of Xenopus Researchers page has been set up on Facebook. Get up to the minute news, keep in touch with friends and colleagues.

http://www.facebook.com/home.php?#/group.php?gid=64447883400

From Don Brown

I am in the process of giving away our population of transgenic
Xenopus laevis. Following is a description of our collection.
Some of these will be gone by the time that the list is
publicized but the new owners will have promised to breed them and
distribute progeny.

Best regards,
Don

TRANSGENIC  FROG  LIST (4.29.09)

* means we are pretty confident of their identity

TANK    # 5        #6    Recovering Inducible pCAR::TRDN-GFP*

TANK    # 6        #5    Inducible pCAR::TRDN-GFP (10.9.04)*
                                           ( #2 females / #2 males / #1 small damaged male)

TANK    # 7        #9   Inducible NßT::TRDN-GFP *
                                          (from 8.29.02 progeny)

*TANK    # 8          #1(M)(L.Toe.4)     NßT  alpha  (?)
                                     #1(M)(R.Toe.5)     TRß     (?)
                                     #1(F) / #2(M)       NßT: 12(a)(f0) + ?-cryst. (?)

*TANK    # 9        #8   pCAR::GFP2 (f1)  (8.14.01)  *
                                          (#3 females / #5 males) all  =>?-cryst  (-)

TANK    #10        #1   Tubulin alpha (front leg defect) *
                                   #1   NßT:tau:GFP  (remaining line 11)(f1) *

*TANK    #11                #2 males       pcs:MT-TR +  ?-cryst  (PCR +) *

*TANK    #12    #2      HSP::GFP.luc  (+ ?-cryst)  (line 5)(f1) (3 . 99) *
            #1       Keratin:GFP (f1) (line 9) (3 .99) (no  ?-cryst) *

TANK    #13        #12   Elastase:: TRDN-GFP (10.11.06) *

TANK    #14        #8    Tubulin.alpha1::GFP (4.16.03) *

TANK    #15        #2    NßT:tau:GFP  (remaining line 6)(3.99) *

TANK    #16        #14    Inducible Collagen::TRDN-GFP *
                                          >> from 1 male (4.17.03) fertilized  9.9.04

TANK    #19        #4     Keratin::TRDN-GFP (2.4.04) *

TANK    #20        #13    Elastase::GFP  (pancreatic prom.)(4.26.05) *

*TANK    #21        #10    CMV::GFP (line 16) *

TANK    #35        #4    5kb Insulin::GFP  (PCR+)(.?-cryst +)(11.6.07) *

*TANK    #36        #9    7kb Insulin::GFP (PCR+)(.?-cryst +)   (11.6.07) *

TANK    #40        #5   pcs2::Insulin::TRDN-GFP3 (1.24.08)(3.211.08) *
                                           (.?-cryst -)(PCR +)

A request from Mike Klymkowsky

klym@spot.colorado.edu
I discover that I have one "orphan" first generation Affymetrix
Xenopus laevis microarray; YET if find that I want to do another
experiment (an analysis of the molecular phenotype of twist morphant
embryos rescued by twist RNA, slug RNA or (not rescued) by GFP RNA.
Does anyone have "orphan" first generation Affymetrix microarrays
that need a good home? If so, please let me know.

From Mike Gilchrist

Many of you who attended the Xenopus meeting in Leiwen will have seen the
Xenopus image search engine that I presented
(http://informatics.gurdon.cam.ac.uk/apps/quickImage/)
and the plan to annotate the expression patterns of the in situ images in our collection. Listening to the other talks, it is clear that there are probably thousands of other high quality in situs in the community, most of them now published, but still representing very useful data. It would be great to make these original images accessible online, and annotate them as well.

If you can send them to me I will add them to the search engine and the annotation project. A few minutes work from a large number of people will make a big improvement to the data set.
To keep it simple, send an e-mail to me attaching your images and giving me the minimal information for each image that we need to make the search engine work.

The information we need is:
lab name (1)
species
image file name (2)
stage (3)
view (4)
accession number (5)
gene (6)

notes:
(1) e.g. Papalopulu Lab or Group, so that we can give credit appropriately.
(2) any image format is fine, we prefer medium resolution images to very high resolution originals, if you have a choice. Optimal is about half a screen width at native resolution, or about 100kb.
(3) precise N&F numerical stage preferred, otherwise stage range (10 - 12) or descriptive stage (Gastrula) if you're not sure.
(4) more important for early stages, when it may not be obvious.
(5) accession number of the sequence the probe was designed from.
(6) gene symbol (i.e. sox2) preferred.
If you have not got the accession number but are pretty sure about the gene, we can work with that.

If you want to send quite a lot of images, then it's probably best to attach no more than about 10 per e-mail. Alternatively, let me know, and we may be able to work out a better way of managing the data for larger numbers.

With your permission, we will be happy to share this data with Xenbase.
Thanks for your help.

Best wishes,
mike

Dr. Mike Gilchrist
Core Bioinformatics Group
The Wellcome Trust/Cancer Research UK Gurdon Institute
Cambridge CB2 1QN
tel: (44-1223-7) 67210
fax: (44-1223-3) 34089
mjg39@mole.bio.cam.ac.uk

News about availability of antibodies....

Dear DSHB User,

Since our last catalog mailing, we have obtained many new hybridomas that may be of interest to you. We also alert you to new hybridomas now being generated by the National Cancer Institute Clinical Proteomic Technologies for Cancer Initiative that will be distributed by the DSHB. When finished, the collection will cover 25% of the human genome. We will maintain our low prices as this collection and other collections are banked in and distributed by the DSHB.

We invite you to visit our new website, browse the new catalog and check out new products.

<http://dshb.biology.uiowa.edu/>

With best regards,
David R. Soll
Director, Developmental Studies Hybridoma Bank
University of Iowa

Email: dshb@uiowa.edu <mailto:dshb@uiowa.edu>
Email: david-soll@uiowa.edu <mailto:david-soll@uiowa.edu>

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.jsp
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 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