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<p>Hi all, <br>
</p>
<p>I think that it would be most useful to include X. laevis and
stages extending NF22, as much or the interesting organogenesis
many people study is happening then. Probably it does not need to
be dense in time points, but still, st25-45 should be well covered
IMO. <br>
</p>
<p>All the best and everyone stay healthy! <br>
</p>
<p>Peter<br>
</p>
<div class="moz-cite-prefix">Am 5/6/2020 um 1:02 AM schrieb Ken Cho:<br>
</div>
<blockquote type="cite"
cite="mid:A3B9D2ED-E845-4513-85E6-03E0F256C95E@uci.edu">
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Hi Leon
<div class="">When do you need a support letter by? </div>
<div class="">Where do I find your slack space? I did search, but
could not find it. </div>
<div class="">Ken<br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Apr 22, 2020, at 8:17 PM, Leon Peshkin <<a
href="mailto:peshkin@gmail.com" class=""
moz-do-not-send="true">peshkin@gmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">
<div dir="ltr" class="">
<div dir="ltr" class="">
<div dir="ltr" class="">
<div dir="ltr" class="">
<div dir="ltr" class="">
<div dir="ltr" class="">
<div dir="ltr" class="">
<div dir="ltr" class="">Dear Xenopus
researchers, </div>
<div dir="ltr" class=""><br class="">
</div>
<div class="">This post is to invite your
thoughts and support for the Xenopus
Cell Atlas. This echos my request at
"Xenopus Community" Slack space,
specifically #cell_atlas channel. Please
try to both respond there so we have a
discussion and to directly write to
me, whether it is a one-liner or a
generous message I can use as a letter
of support (see below). At the end of
this text I copy a Xenopus White Paper
2020 paragraph relevant to XenCAt. </div>
<div class=""><br class="">
</div>
<div class="">
<div class="">I am preparing an
application for an NIH funding of what
will mostly be a very careful
execution of established techniques to
deeply profile and characterize cell
types in Xenopus. To make sure we have
excellent reference where we see our
familiar cell types and genes in the
right place, but also a lot of new
high -confidence results, cell types,
marker genes. The X.trop 10.0 genome
looks really excellent by the way, it
is all coming together to celebrate
Xenopus !</div>
<div class="">I would appreciate if
people shared their thoughts on:</div>
<div class="">1. what is your personal
favorite dev. stage/ tissue to include
into the initial round of XenCAt. How
about adult tissues ? </div>
<div class="">2. what dev.stage/tissue
would be most useful to the wide
community</div>
<div class="">3. what kind of data
access/browsing functionality would
you like to have</div>
<div class="">4. what other than single
cell transcriptional profile would you
like to have and which technologies
you feel are mature enough to apply in
Xenopus: scATAC, sc-proteomics,
micro-CT, in-situ sequencing, anything
else ?</div>
<div class="">5. should we focus on
X.laevis or X.tropicalis ? why ?</div>
<div class="">6. should there be a
perturbation component - profiling
abnormal, manipulated animal ? What
kind would be most useful for a wide
community ? </div>
<div class="">7. What kind of
functionality would you want to see
for federated single cell resources
and re-processing pipelines ?</div>
</div>
<div class=""><br class="">
</div>
<div dir="ltr" class="">
<div class="">I would specifically
welcome thoughts on how to relate
CRISPR mutants to the Cell Atlas. On
one hand the Xenopus Cell Atlas should
be universally interesting and
describe canonical cell types, which
mutants are not. Yet, some mutations
would lead not to or not only to a
change of gene expression in a given
cell type, but also to changes in
proportional populations of cell types
(most obviously immune populations),
so that some cells of a very rare type
become suddenly well represented and
thus can be sampled and characterized
in a mutant not in normal animal. Can
people suggest such examples/cite
papers and specify specific
mutant situations of interest ? </div>
<div class=""><br class="">
</div>
<div class="">The way things look now, I
will be proposing to re-do what we
have published as our original Single
Cell in X.trop - stages NF10 - 22,
whole embryo, but have much more
closely and regularly spaces time
points to provide material for the
"trajectory inference", and then cover
a few select later stages in 40s and
50s. It's a complex organism and there
it makes sense to get away from whole
body to dissecting out some organs. <br
class="">
<br class="">
<div class="">I would also very much
appreciate if people send me a
formal email message which I can use
as a quick LOS for my application,
using some of the same ideas you
must have worded for Xenbase support
letters</div>
<div class=""><br class="">
</div>
<div class="">Template Letter, XenCAt
funding:</div>
<div class=""><br class="">
</div>
<div class="">Dear Dr. Peshkin,</div>
<div class=""><br class="">
</div>
<div class=""> * Express your
support for the XenCAt creation.</div>
<div class=""> * Mention how
creation of XenCAt was identified as
an essential Resource needed by the
Xenopus Research Community in the
2020 Xenopus White Paper<<a
href="https://www.xenbase.org/entry/doNewsRead.do?id=699"
class="" moz-do-not-send="true">https://www.xenbase.org/entry/doNewsRead.do?id=699</a>>.</div>
<div class=""> * Briefly, describe
your research (listing previous and
current NIH grants).</div>
<div class=""> * Explain how
important having XenCAt would be to
your research, perhaps even
transformative</div>
<div class=""> * Describe how your
lab currently uses Xenbase (yes) and
how you would see Xenbase-XenCAt
integration. </div>
<div class=""> * I hope you have
confidence that we can take this on,
please express why. Perhaps because
There is a history of producing
resources for the community in
collaboration with Xenbase - such as
proteomics expression Atlas, the
original work of X.laevis-tropicalis
mRNA expression comparison, the
expertise in co-organizing and
teaching Xenopus Bioinformatics
workshop at the MBL for almost a
decade, co-organizing and directing
the Xenopus Single Cell Jamboree
bootcamp at Janelia Farms in 2018. </div>
<div class=""> Signature,
Position, Institute/Affiliation,
Contact details</div>
<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">THANK YOU, </div>
<div class=""><br class="">
</div>
<div class=""> -Leon Peshkin </div>
<div class=""><br class="">
</div>
<div class="">P.S. </div>
<div class=""><b class="">From the
Xenopus 2020 white paper: </b></div>
<div class="">XenCAt: The single cell
atlas of Xenopus development: Science
magazine identified in toto -omic
analysis of embryos at the single cell
level -including in Xenopus- as the
Breakthrough of the Year for
2018. In this fast-accelerating field,
so called “single cell atlases” have
already been compared to a
“Facebook for cells” – providing a
“social” data structure that organizes
gene expression of individual
cells according to bipartite
similarity across cells and genes. The
value of such a resource to a wide
research community is comparable to
whole genome sequencing and annotation
earlier in the century.
Both demand and opportunity make the
Xenopus Cell Atlas (XenCAt) an
essential resource for the
community that is intimately connected
to both of the aforementioned
“Immediate Needs”. On the one
hand, Xenbase is a natural knowledge
portal to collect and host the XenCAt
effort and eventually to
provide a sophisticated browsing and
interrogation environment. On the
other, genome editing efforts will
be central for construction of the
atlas (through generation of tools for
lineage tracing, for example) but
will also benefit from such an atlas
as a detailed spatial and temporal
reference for gene expression and
function. <br class="">
</div>
<div class=""><br class="">
</div>
<div class="">For more details please
see white paper here</div>
<div class=""><a
href="http://www.xenbase.org/moxiemanager/tinymce/plugins/moxiemanager/data/files/slider%20images/documents/2020_whitepaper_Final.pdf"
class="" moz-do-not-send="true">http://www.xenbase.org/moxiemanager/tinymce/plugins/moxiemanager/data/files/slider%20images/documents/2020_whitepaper_Final.pdf</a><br
class="">
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
_______________________________________________<br
class="">
Xenopus mailing list<br class="">
<a href="mailto:Xenopus@lists.mbl.edu" class=""
moz-do-not-send="true">Xenopus@lists.mbl.edu</a><br
class="">
<a class="moz-txt-link-freetext" href="https://lists.mbl.edu/mailman/listinfo/xenopus">https://lists.mbl.edu/mailman/listinfo/xenopus</a><br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
<br>
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<pre class="moz-quote-pre" wrap="">_______________________________________________
Xenopus mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Xenopus@lists.mbl.edu">Xenopus@lists.mbl.edu</a>
<a class="moz-txt-link-freetext" href="https://lists.mbl.edu/mailman/listinfo/xenopus">https://lists.mbl.edu/mailman/listinfo/xenopus</a>
</pre>
</blockquote>
<pre class="moz-signature" cols="72">--
Universitätsklinikum Freiburg
Innere Medizin IV &
ZBSA - Center for Biological Systems Analysis
Dr. Peter Walentek
Emmy-Noether-Groupleader
Habsburger Str. 49 - 79104 Freiburg, Germany
Phone-Office: +49 761 203-97206
Phone-Lab: +49 761 203-97209
<a class="moz-txt-link-abbreviated" href="mailto:peter.walentek@medizin.uni-freiburg.de">peter.walentek@medizin.uni-freiburg.de</a>
<a class="moz-txt-link-abbreviated" href="http://www.uniklinik-freiburg.de/walentek-en.html">www.uniklinik-freiburg.de/walentek-en.html</a></pre>
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