How many cell lines for RNA-seq comparisons?

Question

[miller.time.716]

I have 2 cell lines which show a difference in growth advantage when implanted in immunocompromised mice. If I want to identify differences in gene expression between the 2 cell lines, how many replicates of each line would I need and how much read depth should I aim for? The cell lines are human neural stem cells that were infected with three lentiviral vectors

[Satyajeet Khare]

Minimum two biological replicates each are generally recommended. ~30 - 40 million reads per sample are sufficient in my experience.

Answer 1

[Arup Ghosh]

For transcript comparison b/w cell lines or differential gene expression analysis, it is recommended to have minimum two replicates and >30x coverage(paired end).

If you also want to check splice variants then coverage should be >50x (paired end).