ChIP-seq advice needed

[bcm]

We did a ChIP-seq recently. Although the data looked OK, there is only ~2million tags mapped to the human genome, about 20% of the passed tags (per lane). Our bioinformatics guy did some analysis and found a lot tags matched with the adaptor sequences. For the library construction, we did size selection of 200-500bp fragments before 18cycles PCR amplication.

I am wondering what we can do to increase the mappable tags. Would it help if we repeat size selection and PCR amplification?

Thank you very much.

[james hadfield]

How much material did you start with? If possible put more DNA into thte PCR and do fewer cycles. Did you adjust the amount of adapter to match input DNA? If you put too much adapter in you will get lots of adapter dimer products.

[elaney_k]

I reckon it's adapter dimer products related to the amount of adapter you used in the ligation step. I generally dilute the adapter 1:30 for use in the ChIP-seq prep protocol which stopped any adapter-dimers coming through.