RNA seq experiment design - two in house cell lines, data analysis with CCLE

Question

[zoeyn192666]

Hi,

I have two in house cell lines and I want to do RNAseq on them. At the end I would like to compare the DEGs and expressions of certain genes with commercial cell line RNA seq data obtained from CCLE. I am thinking to use Novaseq and to match the CCLE protocol as close as possible. I am wondering: to see how much batch effect there are, I am thinking about including a few commercial cell lines as well, would 2 or 3 be sufficient to represent? Also what are some plots people use to represent batch effects?

Thank you all so much in advance!!

Answer 1

[swbarnes2]

RNASeq is very susceptible to batch effect; if you compare your sample to someone else's, there will be no way to tell what differences are due to biology, and what differences are caused by technical artifacts from being prepped in two totally separate places.