Annotation Refinement

[batson]

As people dig deeper into this dataset, they invariably come across interesting subpopulations below the granularity of the existing resolution. This issue is to track them.

• IgJ+ subpopulation of 'hematopoetic precursor cells'. May be plasmacytoid DCs, usually present at about 0.5% of pbmcs.

[jacobkimmel]

In the droplet-Lung data, there are distinct populations of stromal cells.

One of these subpopulations is likely pericytes.

It is marked by expression of Gucy1a3, and expresses canonical pericyte markers Cspg4 (i.e. Ng2 for the dev. biologists among us) and Pdgfrb.

See Fig. 4 in this great review for a reference on these markers.

http://dev.biologists.org/content/develop/141/3/502.full.pdf

Thanks for the amazing resource! Please let me know if a PR of some sort is a better way to contribute this information.

[aopisco]

hi @jacobkimmel, thanks for the reference! We're currently working on a larger data release and I'll make sure this point is addressed. As part of the new data release we will also introduce a way for community contributions towards improved annotations so please stay tuned :)

[jacobkimmel]

Thanks @aopisco!

Cataloging here in case it's helpful in the future, I also think there's an unannotated cluster of oligodendrocytes in the Limb Muscle droplet data set.

The cells are marked by Sox10, Plp1, Mbp, and Mpz -- all markers of oligodendrocytes and their associated precursors.

See the reference below:

https://docs.abcam.com/pdf/neuroscience/neural-markers-guide-web.pdf

[jacobkimmel]

If I can add a final note, there's another unlabeled population marked by Gucy1a3 that co-expresses Pdgfrb, Cspg4, and Mcam in the Limb Muscle droplet data set.

I have a strong hunch these are also pericytes, though the literature in skeletal muscle on pericyte markers isn't quite as robust as elsewhere.

See below for references that some of the common markers (Cpsg4 et al) are still valid in the skeletal muscle.

https://www.ncbi.nlm.nih.gov/pubmed/23517218 .
https://www.ncbi.nlm.nih.gov/pubmed/23128780