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

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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!!


experimentdesign


RNAseq


batcheffect

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