Evaluating an RNA-Seq/ChIP-Seq Scientific finding

Question

[benjyrolls]

Hello

I would like to evaluate the robustness of my scientific findings done in RNA-Seq and ChIP-Seq. Assuming I found some genes (Gene1, Gene2,Gene3 etc) being targeted by p53 transcription factor. for the scientific findings I have thought about checking result with other experiments to make sure thy agree .

How can I evaluate my whole RNA-Seq/ Chip_seq experiment from data sets to scientific findings ?

Kind regards

benjy

Answer 1

[Devon Ryan]

There's no single answer to this. Generally validation falls into two groups:

1. Validating the finding itself, such as by using qPCR on additional samples.
2. Performing downstream wetlab experiments, which then demonstrate (hopefully) the relevance of the observed change. Options for you would be to knockdown some of the affected genes in the presence of up-regulated p53 and see if you get the expected cellular (or whatever) phenotype. Alternatively, over-express a couple of the genes and see if you get the expected phenotype. Exactly how this should be done is dependent on the exact story you want to tell.