Description

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 for the ENCODE Project during the period September 2007 through January 2011. The signal graphs displayed here are also included in the comprehensive UW DnaseI HS track, which also provides peak and region calls.

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 mitochondrial sequence. Results from all replicates were pooled, and further processed by the Hotspot program. (Colors assigned by BigWigCluster). 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. 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.