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Genomic Footprinting from REMC/UW

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 All Assay Type Digital Genomic Footprinting 
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Fetal Brain 
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IMR90 
Mobilized CD34 Primary Cells 
iPS DF 19 
Penis Foreskin Fibroblast Primary Cells 
H1 BMP4 Derived Trophoblast Cultured Cells 
H1 Derived Mesenchymal Stem Cells 
H1 BMP4 Derived Mesendoderm Cultured Cells 
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CD8 Primary Cells 
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Fetal Thymus 
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 All Assay Type Digital Genomic Footprinting 
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  Assay Type↓1 Sample Type↓2 Donor/Library↓3   Track Name↓4  
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 Digital Genomic Footprinting  Breast vHMEC  DS18406  UW Breast vHMEC Digital Genomic Footprinting Donor RM035 Library DGF.DS18406 EA Release 9    Schema 
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 Digital Genomic Footprinting  CD3 Primary Cells  DS17198  UW CD3 Primary Cells Digital Genomic Footprinting Donor RO 01679 Library DGF.DS17198 EA Release 9    Schema 
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 Digital Genomic Footprinting  CD4 Primary Cells  DS17881  UW CD4 Primary Cells Digital Genomic Footprinting Donor RO 01701 Library DGF.DS17881 EA Release 9    Schema 
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 Digital Genomic Footprinting  CD56 Primary Cells  DS17189  UW CD56 Primary Cells Digital Genomic Footprinting Donor RO 01679 Library DGF.DS17189 EA Release 9    Schema 
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 Digital Genomic Footprinting  CD8 Primary Cells  DS17203  UW CD8 Primary Cells Digital Genomic Footprinting Donor RO 01679 Library DGF.DS17203 EA Release 9    Schema 
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 Digital Genomic Footprinting  Fetal Brain  H-22510  Fetal Brain Digital Genomic Footprinting (HOTSPOT_SCORE=0.6871 Pcnt=10)    Schema 
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 Digital Genomic Footprinting  Fetal Heart  H-22662  Fetal Heart Digital Genomic Footprinting (HOTSPOT_SCORE=0.5269 Pcnt=40)    Schema 
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 Digital Genomic Footprinting  Fetal Intestine Large  DS17313  UW Fetal Intestine Large Digital Genomic Footprinting Donor H-23769 Library DGF.DS17313 EA Release 9    Schema 
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 Digital Genomic Footprinting  Fetal Intestine Small  DS17317  UW Fetal Intestine Small Digital Genomic Footprinting Donor H-23769 Library DGF.DS17317 EA Release 9    Schema 
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 Digital Genomic Footprinting  Fetal Lung  H-23266  Fetal Lung Digital Genomic Footprinting (HOTSPOT_SCORE=0.6416 Pcnt=60)    Schema 
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 Digital Genomic Footprinting  Fetal Muscle Arm  DS17765  UW Fetal Muscle Arm Digital Genomic Footprinting Donor H-23914 Library DGF.DS17765 EA Release 9    Schema 
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 Digital Genomic Footprinting  Fetal Thymus  DS20341  UW Fetal Thymus Digital Genomic Footprinting Donor H-24409 Library DGF.DS20341 EA Release 9    Schema 
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 Digital Genomic Footprinting  H1 BMP4 Derived Mesendoderm Cultured Cells  DS19310  UW H1 BMP4 Derived Mesendoderm Cultured Cells Digital Genomic Footprinting Library DGF.DS19310 EA Release 8    Schema 
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 Digital Genomic Footprinting  H1 BMP4 Derived Trophoblast Cultured Cells  DS19317  UW H1 BMP4 Derived Trophoblast Cultured Cells Digital Genomic Footprinting Library DGF.DS19317 EA Release 8    Schema 
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 Digital Genomic Footprinting  H1 Derived Mesenchymal Stem Cells  DS21042  UW H1 Derived Mesenchymal Stem Cells Digital Genomic Footprinting Library DGF.DS21042 EA Release 8    Schema 
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 Digital Genomic Footprinting  iPS DF 19  DS15153  UW iPS DF 19.11 Cell Line Digital Genomic Footprinting Library DGF.DS15153 EA Release 8    Schema 
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 Digital Genomic Footprinting  IMR90  DS13219  IMR90 Digital Genomic Footprinting (HOTSPOT_SCORE=0.5004 Pcnt=20)    Schema 
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 Digital Genomic Footprinting  Mobilized CD34 Primary Cells  RO-01535  Mobilized CD34 Primary Cells Digital Genomic Footprinting (HOTSPOT_SCORE=0.6652 Pcnt=80)    Schema 
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 Digital Genomic Footprinting  Penis Foreskin Fibroblast Primary Cells  DS18224  UW Penis Foreskin Fibroblast Primary Cells Digital Genomic Footprinting Donor skin01 Library DGF.DS18224 EA Release 8    Schema 
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 Digital Genomic Footprinting  Penis Foreskin Keratinocyte Primary Cells  DS18692  UW Penis Foreskin Keratinocyte Primary Cells Digital Genomic Footprinting Donor skin01 Library DGF.DS18692 EA Release 9    Schema 
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 Digital Genomic Footprinting  Penis Foreskin Melanocyte Primary Cells  DS18590  UW Penis Foreskin Melanocyte Primary Cells Digital Genomic Footprinting Donor skin01 Library DGF.DS18590 EA Release 9    Schema 
    

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 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