[Xenopus] Please voice your preferences regarding XenCAt: A single cell Xenopus Cell Atlas

[Leon Peshkin]

Dear Xenopus researchers,

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.

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 !
I would appreciate if people shared their thoughts on:
1. what is your personal favorite dev. stage/ tissue to include into the
initial round of XenCAt. How about adult tissues ?
2. what dev.stage/tissue would be most useful to the wide community
3. what kind of data access/browsing functionality would you like to have
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 ?
5. should we focus on X.laevis or X.tropicalis ? why ?
6. should there be a perturbation component - profiling abnormal,
manipulated animal ?  What kind would be most useful for a wide community
?
7. What kind of functionality would you want to see for federated single
cell resources and re-processing pipelines ?

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 ?

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.

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

Template Letter,  XenCAt funding:

Dear Dr. Peshkin,

  *   Express your support for the XenCAt creation.
  *   Mention how creation of XenCAt was identified as an
essential Resource needed by the Xenopus Research Community in the 2020
Xenopus White Paper<https://www.xenbase.org/entry/doNewsRead.do?id=699>.
  *   Briefly, describe your research (listing previous and current NIH
grants).
  *   Explain how important having XenCAt would be to your research,
perhaps even transformative
  *   Describe how your lab currently uses Xenbase (yes) and how you would
see Xenbase-XenCAt integration.
  *   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.
        Signature, Position, Institute/Affiliation, Contact details


THANK YOU,

  -Leon Peshkin

P.S.
*From the Xenopus 2020 white paper: *
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.

For more details please see white paper here
http://www.xenbase.org/moxiemanager/tinymce/plugins/moxiemanager/data/files/slider%20images/documents/2020_whitepaper_Final.pdf
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