I'm working on a project currently aimed at identifying transcriptional signatures of a specific murine gene knock out across many tissues. We've done some more weakly powered pilot work which found some stronger changes in some tissues, but mostly no significant change in others. Our expectation was that this mutation should have broader impacts based on the importance of the protein's pathway across the tissues examined, but we're just not seeing many significant changes.
I've recently been reading through GTEx publications and I stumbled across this passage in Melé, 2015 :
"Tissue transcription is generally dominated by the expression of a relatively small number of genes. Indeed, we found that for most tissues, about 50% of the transcription is accounted for by a few hundred genes... Because RNA samples are generally sequenced to the same depth, in tissues where a few genes dominate expression, fewer RNA-seq reads are comparatively available to estimate the expression of the remaining genes, decreasing the power to estimate expression variation."
Given this logic, I'm wondering if we would have seen more significant gene expression if we had sequenced more deeply in some of the tissues. My question is thus, are there any published guidelines for calculating appropriate sequencing depth using tissue/sample complexity for bulk RNA-Seq? I'm only aware of and have been instructed of general guidelines for appropriate read depth for such an experiment.
