I'm planning to sequence a bunch of cancer cells using Smart-Seq. Apart from distinguishing subtypes of the cancer cells (which is the main goal) I also want to see how much they differ from regular cells.
Therefore I'm going to sequence several control cells. However not in the same quantity as cancer cells i.e. ~ 200 cancer cells and 20 regular cells. I'm aware of the disproportion but still the regular cells are the matter of secondary importance.
To reduce the possible imbalance within regular cells (getting kind of average transcriptome) I'm thinking of pooling/mixing 5 regular cells before sequencing and threat such pool as one cell i.e. from total 100 isolated regular cells I would get 20 pooled cells.
Would it be beneficial or quite the opposite?
If you mix you lose the per-cell resolution and the ability to see how the per-cell expression profiles are. I do not see the benefit at all.
In such way I could sequence 20 "artificial cells" instead of 100 regular cells (not enough resources to sequence all of 100 regular cells). I thought that pooling could possibly provide more robust expression profiles of control cells. Anyway, so you say that the best solution would be to take the 20 ot 100 regular cells and discard the rest?