How to check for incorporation of plasmid DNA into human genomic DNA (ChIP-seq)?
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3 months ago
tss243 • 0

I have data from a human ChIP-Seq-like experiment where some samples were treated with a drug in combination with a synthetic plasmid. Now, I'd like to check if the plasmid was incorporated (partial or total) somehow into the human DNA. I have the plasmid sequence but I'm not sure how to do this. Any suggestions? Technical aspects: Sequencing platform: Illumina NextSeq 2000 Paired-end Sequencing length: 100bp

plasmid chipseq • 242 views
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Hi,

Nobody has answered you yet, probably because there are very basic things you assumed wrong, so I will try to comment on this.

The first thing you need to know is that ChIP-Seq is an assay of protein-bound DNA. You can only get the genomic region where your portion of interest is binding, against which you have an antibody, so your plasmid will not get into your pull.

Continuing with my previous point, plasmids are vectors/carriers and I don't think your plasmid will get inserted into the genome, instead, the insert (region of interest that you want to clone) might have a chance to get incorporated into the genome. And if your insert has a binding site of your target protein for which you have done immunoprecipitation then you may have a chance to get it in your ChIP-Seq data. You can get the insert sequence simply by aligning reads (from your ChiPSeq experiment) to it or searching it in your peaks.

On a separate note, If I am working with ChIP-Seq, I would prefer searching my insert in genomic input (it is a kind of background/control used in ChIP-Seq) rather than IP/pull.

Regards,

Nitin N.

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