## Description

This track shows genome-wide DNaseI hypersensitive (HS) sites as determined in human CD4+ T-cells. DNaseI HS sites identify regions of open chromatin believed to be largely 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

In full and pack display modes, DNaseI HS scores are displayed as a "wiggle" (histogram), where the height reflects the size of the score. In dense display mode, DNaseI HS is shown in grayscale using darker values to indicate higher levels of overall hypersensitivity.

The DNaseI HS wiggle can be configured in a variety of ways to highlight different aspects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options.

## 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. Resulting scores above 0 are considered hypersensitive.

## 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, Margulies EH, Weng Z, Furey TS, Crawford GE. High-resolution mapping and characterization of open chromatin across the genome. Cell. 2008 Jan 25;132(2):311-22.

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, Zhou D, Luo S, Vasicek TJ, Daly MJ, Wolfsberg TG, Collins FS. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res. 2006 Jan;16(1):123-31.