ENCODE Regulation DNase HS Track Settings
 
DNase I Hypersensitivity in 95 cell types from ENCODE

Track collection:
Integrated Regulation from ENCODE

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  views↓1 Similarity↓2 Cell Type↓3 Tissue↓4   Track Name↓5  
 
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 Peaks      K562  bone marrow  K562 lymphoblast chronic myeloid leukemia cell line DNaseI Peaks from ENCODE   Schema 
 
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 Peaks      NHLF  lung  NHLF lung fibroblast DNaseI Peaks from ENCODE   Schema 
 
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 Peaks      HSMM  muscle  HSMM skeletal muscle myoblast DNaseI Peaks from ENCODE   Schema 
 
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 Peaks      HUVEC  blood vessel  HUVEC umbilical vein endothelial cell DNaseI Peaks from ENCODE   Schema 
 
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 Peaks      NHEK  skin  NHEK epidermal keratinocyte DNaseI Peaks from ENCODE   Schema 
 
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 Peaks      HepG2  liver  HepG2 hepatocellular carcinoma cell line DNaseI Peaks from ENCODE   Schema 
 
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 Peaks      GM12878  blood  GM12878 B-lymphocyte, lymphoblastoid cell line DNaseI Peaks from ENCODE   Schema 
 
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 Peaks      H7-hESC  embryo  H7-hESC embryonic stem cell DNaseI Peaks from ENCODE   Schema 
 
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 Peaks      HeLa-S3  cervix  HeLa-S3 cervical epithelial adenocarcinoma cell line DNaseI Peaks from ENCODE   Schema 
    


p12 Note: includes annotations on GRCh38.p12 patch sequences

Description

These tracks contain the results of DNase I hypersensitivity 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. Colors were assigned to cell types based on similarity of signal.

Other views of this data (along with additional documentation) are available from the hg19 ENCODE UW DNaseI HS track.

Display Conventions and Configuration

This track is a composite annotation track containing multiple subtracks, one for each cell type. The display mode and filtering of each subtrack can be individually controlled. For more information about track configuration, see Configuring Multi-View Tracks.

Methods

Raw sequence data files were processed by the UCSC ENCODE DNase analysis pipeline (July 2014 specification), diagrammed here:

ENCODE DNase Pipeline Credit: Qian Alvin Qin, X. Liu lab

Briefly, sequence files were aligned to the hg38 (GRCh38) genome assembly augmented with 'sponge' sequence (ref). Multi-mapped reads were removed, as were reads that aligned to 'sponge' or mitochondiral sequence. Results from all replicates were pooled, and further processed by the Hotspot program to call peaks as well as broader regions of activity ('hotspots'), and to create signal density graphs. Signal graphs were normalized so the average value genome-wide is 1.

The cell types were clustered into a binary tree, a rainbow was cast to the leaf nodes providing coloring based on similarity.

ENCODE cell clustering by similarity Credit: Chris Eisenhart, J. Kent lab
(Please note there is different coloring on the ENCODE hg38 Transcription track, Layered H3K4Me1 track, Layered H3K4Me3 track, and Layered H3K27Ac track, which match the coloring used in their previous versions lifted from the hg19 assembly).

Credits

The processed data for this track were produced by UCSC. Credits for the primary data underlying this track are included in the ENCODE UW DNaseI HS track description.

References

Miga KH, Eisenhart C, Kent WJ. Utilizing mapping targets of sequences underrepresented in the reference assembly to reduce false positive alignments. Nucleic Acids Res. 2015 Nov 16;43(20):e133. PMID: 26163063

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 ENCODE UW DNaseI HS track.