We are attempting Hi-ChIP and following the Hi-C and ChIP (including RNA Pol II) we have very little DNA. Our aim was to use Tn5 transposase and PCR amplification of the library but several of the protocols indicate a requirement for 15-50ng of DNA. We certainly are not getting this although our 3C and ChIP diagnostics show significant enrichment. We are currently using the Q-bit spectrometer from Invitrogen very little DNA is being read.

Any suggestions on quantification of ChIP material or advice on low yield Tn5 reactions would be appreciated.