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

Ken Cho kwcho at uci.edu
Tue May 5 19:02:56 EDT 2020

Hi Leon
When do you need a support letter by? 
Where do I find your slack space?  I did search, but could not find it. 

> On Apr 22, 2020, at 8:17 PM, Leon Peshkin <peshkin at gmail.com> wrote:
> 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 <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
>   -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 <http://www.xenbase.org/moxiemanager/tinymce/plugins/moxiemanager/data/files/slider%20images/documents/2020_whitepaper_Final.pdf>
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