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ENCODE Univ. Washington DNaseI Hypersensitivity by Digital DNaseI   (All Regulation tracks)

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 Configure 		 GM12878  1st  Hot Spots  ENCODE UW Digital DNaseI Hotspots - 1st (in GM12878 cells)    Data format   2010-04-01 
 
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 Configure 		 K562  1st  Hot Spots  ENCODE UW Digital DNaseI Hotspots - 1st (in K562 cells)    Data format   2009-09-09 
 
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     Restriction Policy
Source data version: through the ENCODE Jan 2010 Freeze
Assembly: Human Mar. 2006 (NCBI36/hg18)

Description

This track is produced as part of the ENCODE Project. This track shows DNaseI sensitivity measured genome-wide in different cell lines using the Digital DNaseI methodology (see below), and DNaseI hypersensitive sites. DNaseI has long been used to map general chromatin accessibility and DNaseI hypersensitivity is a universal feature of active cis-regulatory sequences. The use of this method has led to the discovery of functional regulatory elements that include enhancers, insulators, promotors, locus control regions and novel elements. For each experiment (cell type) this track shows DNaseI hypersensitive zones (HotSpots) and hypersensitive sites (Peaks) based on the sequencing tag density (Signal).

Display Conventions and Configuration

This track is a multi-view composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here.

For each cell type, this track contains the following views:

HotSpots
DNaseI hypersensitive zones identified using the HotSpot algorithm.
Peaks
DNaseI hypersensitive sites (DHSs) identified as signal peaks within FDR 0.5% hypersensitive zones.
Raw Signal
Density graph (wiggle) of signal enrichment based on aligned read density.

DNaseI sensitivity is shown as the absolute density of in vivo cleavage sites across the genome mapped using the Digital DNaseI methodology (see below). Data have been normalized to 25 million reads per cell type.

Methods

Cells were grown according to the approved ENCODE cell culture protocols. Digital DNaseI was performed by performing DNaseI digestion of intact nuclei, isolating DNaseI 'double-hit' fragments as described in Sabo et al. (2006), and direct sequencing of fragment ends (which correspond to in vivo DNaseI cleavage sites) using the Solexa platform (27 bp reads). Uniquely mapping high-quality reads were mapped to the genome. DNaseI sensitivity is directly reflected in raw tag density (Signal), which is shown in the track as density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome). DNaseI hypersensitive zones (HotSpots) were identified using the HotSpot algorithm described in Sabo et al. (2004). 0.5% false discovery rate thresholds (FDR 0.005) were computed for each cell type by applying the HotSpot algorithm to an equivalent number of random uniquely mapping 27mers. DNaseI hypersensitive sites (DHSs or Peaks) were identified as signal peaks within FDR 0.5% hypersensitive zones using a peak-finding algorithm.

Verification

Data were verified by sequencing biological replicates displaying correlation coefficient > 0.9. Results are extensively validated by conventional DNaseI hypersensitivity assays using end-labeling/Southern blotting methods. Multiple cell type Southern blotting methods are available in supplemental materials.

Release Notes

This is release 5 (Oct 2011) of the UW DNaseI HS track. Southern blot validation images have been added. The files corresponding to tables that have been revoked or replaced in previous releases are still available for download from the FTP site.

Credits

These data were generated by the UW ENCODE group.

Contact: Richard Sandstrom

References

Sabo PJ, Hawrylycz M, Wallace JC, Humbert R, Yu M, Shafer A, Kawamoto J, Hall R, Mack J, Dorschner M et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. PNAS. 2004 Nov 30;101(48):16837-42.

Sabo PJ, Kuehn MS, Thurman R, Johnson BE, Johnson EM, Cao H, Yu M, Rosenzweig E, Goldy J, Haydock A et al. Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nature Methods. 2006 Jul;3(7):511-8.

Data Release Policy

Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here.