This track, produced as part of the mouse ENCODE Project, contains deep sequencing DNase data
that will be used to identify sites where regulatory factors bind to the genome
(footprints).
Footprinting is a technique used to define the DNA sequences that interact
with and bind DNA-binding proteins, such as transcription factors,
zinc-finger proteins, hormone-receptor complexes, and other
chromatin-modulating factors like CTCF. The technique depends upon the
strength and tight nature of protein-DNA interactions. In their native chromatin
state, DNA sequences that interact directly with DNA-binding proteins are
relatively protected from DNA degrading endonucleases, while the exposed/unbound
portions are readily degraded by such endonucleases. A massively parallel
next-generation sequencing technique to define the DNase hypersensitive sites
in the genome was adopted. The DNase samples were sequenced using next-generation
sequencing machines to significantly higher depths of 300-fold or greater. This produces
a base-pair level resolution of the DNase susceptibility maps of the native
chromatin state. These base-pair resolution maps represent and are dependent
upon the nature and the specificity of interaction of the DNA with the
regulatory/modulatory proteins binding at specific loci in the genome; thus
they represent the native chromatin state of the genome under investigation.
The deep sequencing approach has been used to define the footprint landscape of
the genome by identifying DNA motifs that interact with known or novel DNA
binding proteins.
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 1.0% hypersensitive zones.
Signal
Per-base count of sequence reads whose 5' end (corresponding to a
DNaseI-induced DNA cut) coincides with the given position.
Raw Signal
The density of tags mapping within a 150 bp sliding window
(at a 20 bp step across the genome).
NOTE: The names of the signal views in this track are reversed from conventions used in
other ENCODE tracks, where the less processed signal is termed "Raw".
DNaseI sensitivity is shown as the absolute density of in vivo
cleavage sites across the genome mapped using the Digital DNaseI methodology
(see below).
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. Digital DNaseI was performed by DNaseI digestion of
intact nuclei, followed by isolating DNaseI "double-hit" fragments (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). High-quality reads were
mapped to the NCBI37/mm9 mouse genome using Bowtie 0.12.5;
only unique mappings were kept. DNaseI sensitivity is directly reflected
in raw tag density (Raw 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 (Sabo et al., 2004).
False discovery rate thresholds of 1.0% (FDR 0.01) were computed for each cell type by applying
the HotSpot algorithm to an equivalent number of random uniquely
mapping 36-mers. DNaseI hypersensitive sites (DHSs or Peaks)
were identified as signal peaks within 1.0% (FDR 0.01) hypersensitive zones
using a peak-finding algorithm. Only DNase Solexa libraries from unique
cell types producing the highest quality data, as defined by Percent
Tags in Hotspots (PTIH ~40%), were designated for deep sequencing to a depth
of over 200 million tags.
Verification
Results were validated by
conventional DNaseI hypersensitivity assays using end-labeling/Southern
blotting methods.
Release Notes
This is Release 1 (Aug 2012) of this track, which contains a total of 22 DNaseI
Digital Genomic Footprinting (DNaseI DGF) experiments.
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.
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