Investigate the Mechanism of Epigenetic Reprogramming

The Yamanaka factors are proved to be able to able to rejuvenate the old mice and improve their cognitive abilities. But its mechanism remains a question for us. In this study, I want to look at the mechanism at the transcriptomics level in the process of rejuvenation.

Using RNA-seq data, I found there is a large discrepency among the same group, which causes a little differential expression genes. However, these groups are supposed to have some change as we have induced transcriptional factors.

The problem is caused by the high expression of these genes in the brain of WT. So how do we deal with this problem? How can we get meaningful results from our data? Is this problem caused by the mistaken group name of our samples?