Description

These tracks contain the results of DNAse I hypersensitivity experiments performed by the John Stamatoyannapoulos lab at the University of Washington for the ENCODE Project during the period September 2007 through January 2011.

The primary data for this track (along with methods descriptions, credits and references) on which this track is based are available from the 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

The raw sequence data files were processed according to the ENCODE DNase analysis pipeline defined in July 2014 (need ref). 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.

Credits

The processed data for this track were generated at UCSC using the ENCODE Analysis Pipeline for DNase. CODE Analysis Working Group. Credits for the primary data underlying this track are included in track description pages listed in the Description section above.

References

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.

See also the references in the related ENCODE UW DnaseI HS track.