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DNase Hypersensitivity Raw Signal from REMC/UW

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 Configure 		 ChromatinAccessibility  IMR90  DS11759  IMR90 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2914 Pcnt=5 Library:DS11759)    Data format 
    
Assembly: Human Feb. 2009 (GRCh37/hg19)

Vizhub @ Wash U built this track, and Roadmap Epigenomics Consortium is responsible for its contents.

Description

This track displays chromatin accessibility data generated by Univeristy of Washington using DNase-Seq. Experiments were done on various types of normal samples. The hypersensitive chromatin sites can be cut by DNase enzyme, and resulting DNA fragments are subjected to high-throughput sequencing for identification. By inferring that the DNA 'hyper-sensitive' sites are thus accessible to in-vivo trans-acting factors, these sites may indicate genomic locations with cis-regulatory roles.

Display conventions

This track displays read density data in form of wiggle plots. Number of aligned reads is counted at each base pair, and a summarized value is computed for each 20 bp interval for display. The subtracks can be displayed and configured individually. See instructions .

Methods

Experimental protocols: follow this link for experimental protocols.

Data processing: EDACC carried out data processing and quality assessment. Details are fully explained here . In brief, sequencing reads were aligned with 'Pash' program to derive read density data. The read density data is prepared into 'wiggle' format files with fixed step length of 20 bp. Data in wiggle and other formats have been deposited in NCBI Gene Expression Omnibus database for public access.

Quality control: the HotSpot was one of the methods used to assess quality of DNase-Seq experiments. The long track name includes a "Hotspot_Score" field indicates the percentage of sequencing reads found inside hotspot regions. The "Pcnt" field shows the percentile of current experiment score in all DNase-Seq experiments. This value is subject to change in next Data Release. The most comprehensive and up-to-date description on QC Metrics used by the consortium can be found here .

Release Notes

The data is combination of Release II, III, IV, V, VI, VII, VIII and IX which were mapped to human reference genome version hg19. The data is production of Roadmap Epigenomics Project.

Please follow the link for Roadmap Epigenomics data access policy

Credits

These data were generated in John Stamatoyannopoulos lab at University of Washington. Stamatoyannopoulos lab is part of Roadmap Epigenomics Project.

Useful links