This track, produced as part of the 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. Sequencing these next-generation-sequencing DNase samples to significantly higher depths of 300-fold or greater 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.
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:
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.
Results were validated by conventional DNaseI hypersensitivity assays using end-labeling/Southern blotting methods.
This is Release 2 (April 2011) of this track, which includes 7 additional experiments.
A number of previously released Peaks have been replaced by updated versions. The affected database tables and files include 'V2' in the name, and metadata is marked with "submittedDataVersion=V2", followed by the reason for replacement, "Fixed bug in peak calls that artificially reduced the number of peaks".
Previous versions of files are available for download from the FTP site
These data were generated by the UW ENCODE group.
Contact: Richard Sandstrom
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.
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. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16837-42.
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.