## Description

This track displays DNaseI-hypersensitive sites identified using DNase-chip from three different human cell lines (primary CD4+ T cells, GM06990 lymphoblastoid cell line, and HeLa S3 cervical carcinoma cell line). DNaseI-hypersensitive sites are associated with all types of gene regulatory regions, including promoters, enhancers, silencers, and locus control regions.

RAW data represents averaged log2 ratio data from three biological replicates and three different DNase concentrations.

PVAL data represents significant regions that likely represent valid DNase I hypersensitive sites. Values represent -log10 p values as determined by the ACME (Algorithm for Capturing Microarray Enrichment) program (Scacheri, Crawford, and Davis, 2006). The higher the -log10 p values, the darker the region (and more likely the site is to be hypersensitive). Only regions that have p value < 0.001 are shown.

## Methods

DNaseI hypersensitive sites were isolated using a method called DNase-chip (Crawford et al., 2006). Briefly, DNaseI digested ends from intact chromatin were captured using three different DNase concentrations as well as three biological replicates. This material was amplified, labeled, and hybridized to NimbleGen ENCODE tiled microarrays.

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## References

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.

Scacheri PC, Crawford GE, Davis S. Analysis of ChIP-chip and DNase-chip data obtained from tiled microarrays. Methods Enzymol. 2006;411:270-82.