Footprinting Track Settings
 
Genomic Footprinting from REMC/UW

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 Configure 		 Digital Genomic Footprinting  Fetal Brain  H-22510  Fetal Brain Digital Genomic Footprinting (HOTSPOT_SCORE=0.6871 Pcnt=10)    Data format 
 
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 Configure 		 Digital Genomic Footprinting  Fetal Heart  H-22662  Fetal Heart Digital Genomic Footprinting (HOTSPOT_SCORE=0.5269 Pcnt=40)    Data format 
 
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 Configure 		 Digital Genomic Footprinting  Fetal Lung  H-23266  Fetal Lung Digital Genomic Footprinting (HOTSPOT_SCORE=0.6416 Pcnt=60)    Data format 
 
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 Configure 		 Digital Genomic Footprinting  IMR90  DS13219  IMR90 Digital Genomic Footprinting (HOTSPOT_SCORE=0.5004 Pcnt=20)    Data format 
 
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 Configure 		 Digital Genomic Footprinting  Mobilized CD34 Primary Cells  RO-01535  Mobilized CD34 Primary Cells Digital Genomic Footprinting (HOTSPOT_SCORE=0.6652 Pcnt=80)    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 digital genomic footprinting 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 were mapped to human reference genome version hg19 as part of Release IV (07/11/2011) 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