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DNase-seq tracks

Track collection: Roadmap data by assay

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  Sample Type adrenal gland  B cell  brain  CD14-positive monocyte  CD4-positive, alpha-beta T cell  CD8-positive, alpha-beta T cell  common myeloid progenitor, CD34-positive  fibroblast of skin of abdomen  fibroblast of skin of back  fibroblast of skin of left biceps  fibroblast of skin of left quadriceps  fibroblast of skin of right biceps  fibroblast of skin of right quadriceps  fibroblast of skin of scalp  fibroblast of upper back skin  forelimb muscle  foreskin fibroblast  foreskin keratinocyte  foreskin melanocyte  heart  hematopoietic multipotent progenitor cell  hindlimb muscle  IMR-90  iPS DF 19.11  iPS DF 19.7  iPS DF 4.7  iPS DF 6.9  kidney  large intestine  left kidney  left lung  left renal cortex interstitium  left renal pelvis  lung  mammary epithelial cell  mesenchymal stem cell  mesendoderm  muscle of arm  muscle of back  muscle of leg  muscle of trunk  natural killer cell  neuronal stem cell  ovary  pancreas  placenta  psoas muscle  renal cortex interstitium  renal pelvis  right kidney  right lung  right renal cortex interstitium  right renal pelvis  skin of body  small intestine  spinal cord  spleen  stomach  T-cell  testis  thymus  trophoblast cell Sample Type  
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Assembly: Human Dec. 2013 (GRCh38/hg38)

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

Description

The track files were processed and hosted by ENCODE project.

This track displays the genomic maps based on the assay type. Data were generated using various assay methods across many different sample types for the Roadmap project.

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:

Protocols are located at the bottom of each experiment page. The list of the experiments can be found here: ChIP-seq   polyA plus RNA-seq   microRNA-seq   small RNA-seq   total RNA-seq   DNase   WGBS .

Pipeline overview: follow this link for pipeline overview.

Credits

These data were generated in the following labs which are listed in alphabetical order:

Bing Ren, UCSD
Bradley Bernstein, Broad Institute
Joe Ecker Lab, Salk Institute for Biological Studies
John Stamatoyannopoulos Lab, University of Washington
Joseph Costello, UCSF