I am trying to find papers on anything related to T Cells being activated ex vivo with CD3/CD28 beads (e.g. Dynabeads) and subsequently profiled using scRNA-seq. Any papers with flow cytometry analysis would help too (I have read some papers reporting on the kinetics of cytokine expression using flow cytometry after activation, but the authors seem to use plate-bound CD3/CD28, not beads).
There are a few things I am hoping to optimize for my own experiments, such as the duration of activating my T Cells. For example, I find that I get T-cell activation (staining for CD69 in flow cytometry) at 24h, but I do lose a lot of cells in the process since the cells still are attached to the beads at t=24h (manufacturer says that the cells begin unsticking to the beads around 72h). On the other hand, I don't know if "activating for too long" would alter my cell populations (isolated CD4+ cells) too much. Another concern is not being able to detect things like CD69, which are only unregulated at “earlier” time points (CD69 levels peak ~24h, from what I have read). I am thinking about running a time-course experiment (comparing @24h, 48h, 72h, etc.), but that would be quite costly. Some studies activate for 72h, while others do 24h and 48h. So in short: it’d be very informative to see a paper that shows how expression levels change depending on how long T Cells are activated for with these CD3/CD28 beads.
If you could direct me to any relevant research, that'd be much appreciated!
Relevant papers that I have found so far:
Article Genome-Wide Analysis of Immune Activation in Human T and B C...
https://www.cell.com/cell/pdf/S0092-8674(17)30596-2.pdf
https://www.pnas.org/content/114/31/E6400
https://www.nature.com/articles/s41467-019-12464-3
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