## Description

This track shows a discretized version of genome-wide DNaseI hypersensitive (HS) sites as determined in human CD4+ T-cells. DNaseI HS sites identify regions of open chromatin believed to largely be free of nucleosomes and have been shown to accurately identify the locations of genetic regulatory elements, including promoters, enhancers, silencers, insulators, and locus control regions. DNaseI HS sites are believed to differ in degree of openness. Scores shown in this annotation reflect an estimate of this openness.

## Display Conventions and Configuration

DNaseI HS sites are represented as gray or black boxes. The intensity of the box reflects the HS score and represents the estimated degree of hypersensitivity of the site.

## Methods

DNaseI HS were determined for human CD4+ T-cells using DNase-sequencing and DNase-chip. Over 12.5 million uniquely aligned DNase sequence tags were generated using Illumina (Solexa) and 454 Life Sciences (Roche) sequencers from the same biological sample. Each base was assigned a score using Parzen windows kernal density estimation. The Nimblegen 38-array whole genome platform was used to generate data from 2 biological replicates. Ratio scores for the two were averaged. These data were combined by re-scaling each using Z-scores and then summing. This annotation reflects those contiguous regions with combined scores above zero. Each record contains the maximum base pair score within each identified region.

## Credits

This annotation was created by Alan Boyle, Terry Furey, and Greg Crawford at Duke University's Institute for Genome Sciences & Policy (IGSP).

## References

Boyle AP, Davis S, Shulha HP, Meltzer P, Weng Z, Furey TS, Crawford GE. High-resolution mapping and characterization of open chromatin across the genome. Submitted. 2007.

Crawford GE, Davis S, Scacheri PC, Renaud G, Halawi MJ, Erdos MR, Green R, Meltzer PS, Wolfsberg TG, Collins FS. DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat Methods. 2006 Jul;3(7):503-9.

Crawford GE, Holt IE, Whittle J, Webb BD, Tai D, Davis S, Margulies EH, Chen Y, Bernat JA, Ginsburg D et al. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res. 2006 Jan;16(1):123-31.