Description

This track displays DNaseI sensitivity/hypersensitivity (log[2] scale) mapped over ENCODE regions in lymphoblastoid cells (GM06990) using the DNase/Array methodology (P.J. Sabo et al., submitted for publication). DNaseI "hyperaccessibility" or "hypersensitivity" is a universal feature of active cis-regulatory sequences in vivo. Peaks in DNaseI sensitivity signal measured using DNase/Array represent DNaseI hypersensitive sites.

Methods

DNase/Array 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 genomic DNA tiling array, without amplification. DNaseI sensitivity signal is expressed as a log[2] ratio relative to a control sample comprising DNaseI-treated naked DNA. The data are scaled so that log[2]=0 represents the 99% confidence bound on experimental noise; all values above the log[2]=0 baseline are highly statistically significant. Signal peaks correspond with DNaseI hypersensitive sites.

Validation

The data have been extensively validated by conventional DNaseI hypersensitivity assays (indirect end-label + Southern blotting method). The data have an overall sensitivity of 91.7%, and specificity of >99.5% for DNaseI hypersensitive sites.

Credits

The data were generated and validated by the UW ENCODE investigators in collaboration with R. Green's group at Nimblegen, Inc. (Madison, WI).