Forum: Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization.
4
gravatar for Sukhi Singh
6.7 years ago by
Sukhi Singh10k
Netherlands
Sukhi Singh10k wrote:

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. Quicky go back and map to the reference genome of foreign DNA and see which sample has larger number of mapped reads, thats your WT·

scalingimage

 

ADD COMMENTlink modified 6.7 years ago • written 6.7 years ago by Sukhi Singh10k

For those curious, the original article is here.

ADD REPLYlink written 6.7 years ago by Devon Ryan98k

Thanks, forgot to paste in the link!!

ADD REPLYlink written 6.7 years ago by Sukhi Singh10k

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

ADD REPLYlink written 6.7 years ago by Istvan Albert ♦♦ 86k

Yes, I called it as internal barcoding.

ADD REPLYlink written 6.7 years ago by Sukhi Singh10k
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