Forum:Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization.

Question

[Sukhi Singh]

A nice paper about spiking method with respect to ChIP-Seq. Idea is to spike-in a foreign DNA (2.5%) of total ChiP'ed material, after sonication and then to sequence it. This foreign DNA serves as an internal control for signal normalization between two samples as opposed to the standard or widely used sequence depth normalization also called as scaling.

http://genome.cshlp.org/content/early/2014/04/07/gr.168260.113.abstract

My idea over the top is, one can spike-in two foreign DNA's, one for normalization and second for barcoding. For barcoding, you spike in certain foreign DNA in one type of samples ex. WT and not in condition. This is useful in the cases of sample swapping, which we experience a lot. Quickly go back and map to the reference genome of foreign DNA and see which sample has larger number of mapped reads, thats your WT

[Devon Ryan]

For those curious, the original article is here.

[Sukhi Singh]

Thanks, forgot to paste in the link!!

[Istvan Albert]

If I get your point correctly the goal of adding the second spike in is to protect against incorrect data labeling.

[Sukhi Singh]

Yes, I called it as internal barcoding.