Hello everyone! I am working with several cell lines in 2 conditions each: control and treatment. I have transcriptome data for them and I would like to choose a panel of genes that distinguish one cell line (treatment vs control) from the others for further PCR validation. There are several genes that suit desired changes, but they may be expressed at different levels in cells. As I am looking for candidates to validation, I tend to choose genes with higher overall expression (in TPM). However, what is an optimal cutoff in TPM for gene to be detected in PCR? Would it be possible to validate differences between 200 and 80 TPM (treatment vs control), while in other cell lines this gene is being expressed at levels of about 2000 TPM?
Thank you in advance!
