The measurement of ChIP-DNA sample concentration on a NanoDrop tends to be very inaccurate due to the high percent of background measured in the A260 wavelength in dilute concentrations of nucleic acid.
The Qubit fluorometer (Invitrogen) uses the Quant-iT dsDNA HS Assay Kit is used to measureDNA concentration. This assay uses PicoGreen to discriminate between various nucleic acid contributors in the sample and provide an accurate measurement of the concentration of dsDNA in the sample. This assay can quantitate samples that range from 10 pg/μl to 100 ng/μl.
ChIP-DNA samples typically require this more-sensitive pico-green based assay to provide an accurate of assessment of the DNA concentration. ChIP-DNA samples are typically observed to have a concentration that is less than 1 ng/ul.
A minimum of 10 μl of each sample should be provided for measurement. Ideally, only 1 μl of sample will be used for the measurement and the remainder will be returned. However, many ChIP-DNA samples are severely dilute and the assay may take as much as 5-8 μl of sample.