select reference genes from transriptome data

Question

[sd.gamboa.t]

Hi!

I'm currently performing a transcriptome study. I got the differential expressed genes (DEG) from the data using edgeR. Now, I need to validate the transcriptome results by performing qRT-PCR of some of the transcripts. However, I'd like to select some reference genes from the transcriptome itself. Is it possible to achieve this using edgeR or is there any other tool that could help me?

Thanks in advance for your help!

Samuel

[GenoMax]

I'd like to select some reference genes from the transcriptome itself

What do you mean by that?

[sd.gamboa.t]

By comparing all the samples of the transcriptome, i want to select a couple of genes whose expression is stable among samples. Then, I intend to design primers based on such genes and use them as normalization reference for the qRT-PCR validation.

Answer 1

[glihm]

For this particular experiment that you want to conduct, I recommend you to don't use "stable" genes, selected from DEG. A better approach could be, depending on the organism/cell line you are working on, selecting the well known housekeeping gene.

If you still thinking about a selection of the "reference genes" from DEG, you can try to order you genes by log2FC and then by p-value. And from this hierarchy you can try to extract the "genes that seem to be very stable between your conditions in your experiment".