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.