UW DNaseI HS Track Settings
 
DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington   (All Expression and Regulation tracks)

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  Cell Line↓1 Strain↓2 Age↓3 Treatment↓4 Sex↓5 Replicate↓6 Views↓7   Track Name↓8    Restricted Until↓9
 
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 3134  RIII  Immortalized      M  1  Hotspots  3134 DNaseI HS Hotspots Rep 1 from ENCODE/UW    schema   2011-04-23 
 
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 3134  RIII  Immortalized      M  1  Peaks  3134 DNaseI HS Peaks Rep 1 from ENCODE/UW    schema   2011-04-23 
 
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 3134  RIII  Immortalized      M  1  Signal  3134 DNaseI HS Signal Rep 1 from ENCODE/UW    schema   2011-04-23 
 
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 B-cell (CD19+)  C57BL/6  Adult 8 Weeks      M  1  Hotspots  B-cell (CD19+) DNaseI HS Hotspots Rep 1 from ENCODE/UW    schema   2012-01-19 
 
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 B-cell (CD19+)  C57BL/6  Adult 8 Weeks      M  1  Peaks  B-cell (CD19+) DNaseI HS Peaks Rep 1 from ENCODE/UW    schema   2012-01-19 
 
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 B-cell (CD19+)  C57BL/6  Adult 8 Weeks      M  1  Signal  B-cell (CD19+) DNaseI HS Signal Rep 1 from ENCODE/UW    schema   2012-01-19 
 
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 Cerebellum  C57BL/6  Adult 8 Weeks      M  1  Hotspots  Cerebellum DNaseI HS Hotspots Rep 1 from ENCODE/UW    schema   2011-04-20 
 
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 Cerebellum  C57BL/6  Adult 8 Weeks      M  1  Peaks  Cerebellum DNaseI HS Peaks Rep 1 from ENCODE/UW    schema   2011-04-20 
 
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 Cerebellum  C57BL/6  Adult 8 Weeks      M  1  Signal  Cerebellum DNaseI HS Signal Rep 1 from ENCODE/UW    schema   2011-04-20 
 
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 Cerebrum  C57BL/6  Adult 8 Weeks      M  1  Hotspots  Cerebrum DNaseI HS Hotspots Rep 1 from ENCODE/UW    schema   2011-04-22 
 
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 Cerebrum  C57BL/6  Adult 8 Weeks      M  1  Peaks  Cerebrum DNaseI HS Peaks Rep 1 from ENCODE/UW    schema   2011-04-22 
 
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 Cerebrum  C57BL/6  Adult 8 Weeks      M  1  Signal  Cerebrum DNaseI HS Signal Rep 1 from ENCODE/UW    schema   2011-04-22 
 
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 ES-CJ7  129S1/SVImJ  Embryonic Day 0      M  1  Hotspots  ES-CJ7 DNaseI HS Hotspots Rep 1 from ENCODE/UW    schema   2011-04-28 
 
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 ES-CJ7  129S1/SVImJ  Embryonic Day 0      M  1  Peaks  ES-CJ7 DNaseI HS Peaks Rep 1 from ENCODE/UW    schema   2011-04-28 
 
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 ES-CJ7  129S1/SVImJ  Embryonic Day 0      M  1  Signal  ES-CJ7 DNaseI HS Signal Rep 1 from ENCODE/UW    schema   2011-04-28 
 
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 MEL  Unknown  Immortalized      M  1  Hotspots  MEL DNaseI HS Hotspots Rep 1 from ENCODE/UW    schema   2011-04-23 
 
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 MEL  Unknown  Immortalized      M  1  Peaks  MEL DNaseI HS Peaks Rep 1 from ENCODE/UW    schema   2011-04-23 
 
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 MEL  Unknown  Immortalized      M  1  Signal  MEL DNaseI HS Signal Rep 1 from ENCODE/UW    schema   2011-04-23 
 
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 Whole Brain  C57BL/6  Adult 8 Weeks      M  1  Hotspots  Whole Brain Adult 8 Weeks DNaseI HS Hotspots Rep 1 from ENCODE/UW    schema   2011-04-28 
 
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 Whole Brain  C57BL/6  Adult 8 Weeks      M  1  Peaks  Whole Brain Adult 8 Weeks DNaseI HS Peaks Rep 1 from ENCODE/UW    schema   2011-04-28 
 
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 Whole Brain  C57BL/6  Adult 8 Weeks      M  1  Signal  Whole Brain Adult 8 Weeks DNaseI HS Signal Rep 1 from ENCODE/UW    schema   2011-04-28 
 
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 Whole Brain  C57BL/6  Embryonic Day 14.5      M  1  Hotspots  Whole Brain Embryonic Day 14.5 DNaseI HS Hotspots Rep 1 from ENCODE/UW    schema   2011-04-28 
 
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 Whole Brain  C57BL/6  Embryonic Day 14.5      M  1  Peaks  Whole Brain Embryonic Day 14.5 DNaseI HS Peaks Rep 1 from ENCODE/UW    schema   2011-04-28 
 
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 Whole Brain  C57BL/6  Embryonic Day 14.5      M  1  Signal  Whole Brain Embryonic Day 14.5 DNaseI HS Signal Rep 1 from ENCODE/UW    schema   2011-04-28 
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Description

This track was produced as part of the mouse ENCODE Project. It shows DNaseI sensitivity measured genome-wide in mouse tissues and 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, promoters, locus control regions and novel elements. For each experiment (tissue/cell type), this track shows DNaseI sensitivity as a continuous function using sequencing tag density (Signal), and discrete loci of DNaseI sensitive zones (HotSpots) and hypersensitive sites (Peaks).

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. This track contains the following views:

HotSpots
DNaseI sensitive zones identified using the HotSpot algorithm.
Peaks
DNaseI hypersensitive sites (DHSs) identified as signal peaks within FDR 1.0% hypersensitive zones.
Signal
The density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome).

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.

Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.

Methods

Cells were grown according to the approved ENCODE cell culture protocols. Fresh tissues were harvested from mice and the nuclei prepared according to the tissue-appropriate protocol. Digital DNaseI was performed by 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 Illumina IIx (and Illumina HiSeq by early 2011) platform (36 bp reads). Uniquely-mapping high-quality reads were mapped to the genome using Bowtie. DNaseI sensitivity is directly reflected in raw tag density, 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 sensitive zones (HotSpots) were identified using the HotSpot algorithm described in Sabo et al. (2004). False discovery rate thresholds of 1.0% (FDR 1.0%) were computed for each cell type by applying the HotSpot algorithm to an equivalent number of random uniquely-mapping 36mers. DNaseI hypersensitive sites (DHSs or Peaks) were identified as signal peaks within FDR 1.0% hypersensitive zones using a peak-finding algorithm (I-max).

Verification

Data were verified by sequencing biological replicates displaying correlation coefficient > 0.9.

Release Notes

This is Release 2 (September 2012) of this track. It adds 32 new experiments including 22 new cell lines and 4 new treatments.

Credits

These data were generated by the UW ENCODE group.

Contact: Richard Sandstrom

References

John S, Sabo PJ, Thurman RE, Sung MH, Biddie SC, Johnson TA, Hager GL, Stamatoyannopoulos JA. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat Genet. 2011 Mar;43(3):264-8.

Sabo PJ, Hawrylycz M, Wallace JC, Humbert R, Yu M, Shafer A, Kawamoto J, Hall R, Mack J, Dorschner MO et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc Natl Acad Sci U S A. 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. Nat 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.