This track displays DNaseI sensitivity/hypersensitivity (log[2] scale) mapped over ENCODE regions in lymphoblastoid cells (GM06990) using the Chromatin Accessibility Profiling (CAP) methodology (P. Sabo, J. Stamatoyannopoulos et al, in preparation). DNaseI "hyperaccessibility" or "hypersensitivity" is a universal feature of active cis-regulatory sequences in vivo. Peaks in CAP signal represent DNaseI hypersensitive sites.
CAP comprises a novel method for isolating DNA segments corresponding to specific DNaseI cleavage events on individual nuclear chromatin templates. Following purification, sample DNA is labeled and hybridized directly to a Nimblegen ENCODE tiling array, without amplification. Signal ratios are determined relative to a control sample comprising naked DNaseI-treated DNA. The quantitative DNaseI cutting (= DNaseI sensitivity) pattern is then readily reconstructed from the signal. All values above the log(2)=0 baseline (error-corrected) are highly statistically significant. Signal peaks correspond with DNaseI hypersensitive sites.
The data have been extensively validated by conventional DNaseI hypersensitivity assays (indirect end-label + Southern blotting method).
The data were generated and validated by the Seattle ENCODE investigators in collaboration with R. Green's group at Nimblegen (Madison, WI).