Should one use cell cycle regression on single-cell data from PBMCs?

Question

[hamarillo]

Hello,

can anyone tell me if the PBMCs datasets from 10x should undergo cell-cycle regression?

I read that PBMCs are not supposed to be cycling, but I don't know if that is only when a specific preparation has occurred (e.g. FACS sorting).

I thank you for any information.

Answer 1

[ATpoint]

It's like with every "should I" question, it depends. If you see evidence, for example in the clustering that cell cycle (or any other factor) drives unwanted cluster creation/separation and you feel that this is something you do not want then you may consider strategies to remove it. Else, don't.

[ATpoint]

See also for a great read: http://bioconductor.org/books/3.14/OSCA.advanced/cell-cycle-assignment.html