confirmation RNA-seq's results

Question

[parviz Heidari]

We have RNA-seq data of tomato root and we wanted to confirm this data set with qRT-PCR so we selected some genes which involve in hormone pathway but some of these genes are not in DEGs (differential expression genes) list which were selected by DEseq.we found high correlation between RNA-seq and qRT-PCR results.

Could we report these results or we have to do qRT-PCR again with genes which have high DEG?

Thanks

Answer 1

[Renesh]

The RNA-Seq studies will give the idea to study overall genes in your given species. The results obtained by RNA-Seq and qRT-PCR must be analogous (high correlation), as the genes which are highly up-regulated under treatment will be presented more in RNA-Seq library.

The dense bands obtained from qRT-PCR results are the confirmation of the genes which you found up-regulated from RNA-Seq studies. So if you did already qRT-PCR of up-regulated genes selected from DESeq, you do not need to repeat it again.