Hello all,
I am planning experiments on stimulated T cells (with anti-CD3/CD28) and I am wondering if anyone has experience with RNA seq on T cells after culture and stimulation.
I am afraid to induce culture-effects that might screw up my gene expression profiles and I couldn't find a clear answer in literature.
Any help is much appreciated :) thanks
Best,
Fleur
Yes, that stimulation will strongly affect gene expression profiles in your T cell populations.
@Noah, Thank you, do you think it still makes sense to do RNAseq on cultured cells or are the effects to strong to detect any differences? I am comparing cells from healthy and sick donors.
You may still detect differences between your condition, and If you're stimulating cells from both healthy and sick conditions then you might be ok, unless the CD3/CD28 interacts with whatever "sick" means and produces changes unique to the sick condition, but unrelated to the actual sickness. With RNAseq it's very easy to detect a difference between any two conditions, the objective is to detect meaningful differences, which can really only be evaluated by looking at functional categories enriched for your differentially expressed genes.
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