How many cell lines for RNA-seq comparisons?
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
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Arup Ghosh
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miller.time.716 •
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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).
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Minimum two biological replicates each are generally recommended. ~30 - 40 million reads per sample are sufficient in my experience.