Single cell data clustering by TRBV type

Question

[dioscorea.bulbifera]

Hi all,

I'm currently working with some single cell data from which I've isolated and reclustered all of the T cells into a new dataset, and I'm seeing two clusters that separate from the rest of the cells and contain within them some kind of gradient from CD4 naive to CD4 activated to CD8 activated - essentially they're like miniature forms of the rest of the data that have separated out.

They have very limited transcriptomic differences from the rest of the data, but in one of them, every single cell expresses TRBV20-1 and in the other, TRBV5-1.

These clusters are a few thousand cells from multiple patients and are mostly not clonal and persist in UMAPs/clustering at multiple resolutions and number of included principle components. Any idea what might be causing this?

Thanks!

[Chenzhen Zhang]

Hi, I am experiencing the same problem. Have you found an explanation for this?