Note: includes annotations on GRCh38.p12 patch sequences
This track provides an integrated display of DNase hypersensitivity in multiple
cell types using overlapping colored graphs of signal density with graph colors
assigned to cell types based on similarity of signal. The track is based on
results of experiments performed by the John Stamatoyannapoulos lab at the
University of Washington from September 2007 to January 2011 as part of the
ENCODE project first production phase.
The signal graphs displayed here are also included in the comprehensive
DNaseI HS track,
which also provides peak and region calls and uses the same coloring based on
similiarity of cell types (please note there is different coloring on the ENCODE hg38
Layered H3K4Me1 track,
Layered H3K4Me3 track, and
Layered H3K27Ac track,
which match the coloring used in their previous versions lifted from the hg19 assembly).
Raw sequence data files were processed by the UCSC ENCODE DNase analysis pipeline
described in the
Signal graphs were normalized so the average value genome-wide is 1.
Colors for the signal graphs were assigned by the UCSC BigWigCluster tool.
The cell types were clustered into a binary tree, a rainbow was cast to the leaf nodes providing coloring based on similarity.
Credit: Chris Eisenhart, J. Kent lab
The processed data for this track were generated at UCSC.
Credits for the primary data underlying this track are included in the
Miga KH, Eisenhart C, Kent WJ.
Utilizing mapping targets of sequences underrepresented in the reference assembly to reduce false
Nucleic Acids Res. 2015 Nov 16;43(20):e133.
Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang
H, Vernot B et al.
The accessible chromatin landscape of the human genome.
Nature. 2012 Sep 6;489(7414):75-82.
PMID: 22955617; PMC: PMC3721348
See also the references in the