Broad Histone Track Settings
 
Histone Modifications by ChIP-seq from REMC/Broad

Maximum display mode:       Reset to defaults   
Select views (Help):
Coverage ▾      
Select subtracks by assay type and sample type:
 All Assay Type H3K27ac  H3K27me3  H3K36me3  H3K4me1  H3K4me2  H3K4me3  H3K9ac  H3K9me3  Input  H2A.Z Assay TypeAll 
Sample Type Sample Type
Adipose Derived Mesenchymal Stem Cell Cultured Cells   Adipose Derived Mesenchymal Stem Cell Cultured Cells
Adult Kidney   Adult Kidney
Adult Liver   Adult Liver
Adipose Nuclei   Adipose Nuclei
Brain Anterior Caudate   Brain Anterior Caudate
Brain Angular Gyrus   Brain Angular Gyrus
Brain Cingulate Gyrus   Brain Cingulate Gyrus
Brain Hippocampus Middle   Brain Hippocampus Middle
Brain Inferior Temporal Lobe   Brain Inferior Temporal Lobe
Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells   Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells
Brain Mid Frontal Lobe   Brain Mid Frontal Lobe
Brain Substantia Nigra   Brain Substantia Nigra
CD15 Primary Cells   CD15 Primary Cells
CD19 Primary Cells   CD19 Primary Cells
CD34 Cultured Cells   CD34 Cultured Cells
CD34 Primary Cells   CD34 Primary Cells
CD3 Primary Cells   CD3 Primary Cells
CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells   CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells
CD4+ CD25- CD45RO Memory Primary Cells   CD4+ CD25- CD45RO Memory Primary Cells
CD4+ CD25- CD45RA Naive Primary Cells   CD4+ CD25- CD45RA Naive Primary Cells
CD4+ CD25- IL17 PMA-Ionomcyin stimulated Th17 Primary Cells   CD4+ CD25- IL17 PMA-Ionomcyin stimulated Th17 Primary Cells
CD4+ CD25- Th Primary Cells   CD4+ CD25- Th Primary Cells
CD4+ CD25int CD127 Tmem Primary Cells   CD4+ CD25int CD127 Tmem Primary Cells
CD4+ CD25+ CD127- Treg Primary Cells   CD4+ CD25+ CD127- Treg Primary Cells
CD4 Memory Primary Cells   CD4 Memory Primary Cells
CD4 Naive Primary Cells   CD4 Naive Primary Cells
CD8 Memory Primary Cells   CD8 Memory Primary Cells
CD8 Naive Primary Cells   CD8 Naive Primary Cells
Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells   Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells
Colonic Mucosa   Colonic Mucosa
Colon Smooth Muscle   Colon Smooth Muscle
Duodenum Mucosa   Duodenum Mucosa
Duodenum Smooth Muscle   Duodenum Smooth Muscle
ES-I3   ES-I3
ES-WA7   ES-WA7
Fetal Brain   Fetal Brain
Fetal Heart   Fetal Heart
Fetal Kidney   Fetal Kidney
Fetal Lung   Fetal Lung
H1Es   H1Es
hESC Derived CD184+ Endoderm Cultured Cells   hESC Derived CD184+ Endoderm Cultured Cells
HUES48   HUES48
HUES64   HUES64
HUES6   HUES6
iPS-11a   iPS-11a
iPS-15b   iPS-15b
iPS-18a   iPS-18a
iPS-18b   iPS-18b
iPS-18c   iPS-18c
iPS-20b   iPS-20b
Mobilized CD34 Primary Cells   Mobilized CD34 Primary Cells
Mobilized CD4 Primary Cells   Mobilized CD4 Primary Cells
Mesenchymal Stem Cell Derived Adipocyte Cultured Cells   Mesenchymal Stem Cell Derived Adipocyte Cultured Cells
Muscle Satellite Cultured Cells   Muscle Satellite Cultured Cells
Pancreatic Islets   Pancreatic Islets
Rectal Mucosa   Rectal Mucosa
Rectal Smooth Muscle   Rectal Smooth Muscle
Skeletal Muscle   Skeletal Muscle
Stomach Smooth Muscle   Stomach Smooth Muscle
Stomach Mucosa   Stomach Mucosa
Th17 Primary Cells   Th17 Primary Cells
Treg Primary Cells   Treg Primary Cells
H9 Derived Neuronal Progenitor Cultured Cells   H9 Derived Neuronal Progenitor Cultured Cells
CD4+ CD25- CD45RA+ Naive Primary Cells   CD4+ CD25- CD45RA+ Naive Primary Cells
CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells   CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells
H9 Derived Neuron Cultured Cells   H9 Derived Neuron Cultured Cells
CD4+ CD25int CD127+ Tmem Primary Cells   CD4+ CD25int CD127+ Tmem Primary Cells
hESC Derived CD56+ Mesoderm Cultured Cells   hESC Derived CD56+ Mesoderm Cultured Cells
hESC Derived CD56+ Ectoderm Cultured Cells   hESC Derived CD56+ Ectoderm Cultured Cells
CD4+ CD25- CD45RO+ Memory Primary Cells   CD4+ CD25- CD45RO+ Memory Primary Cells
Sample Type Sample Type
 All Assay Type H3K27ac  H3K27me3  H3K36me3  H3K4me1  H3K4me2  H3K4me3  H3K9ac  H3K9me3  Input  H2A.Z Assay TypeAll 
List subtracks: only selected/visible    all    ()
  Assay Type↓1 Sample Type↓2 Donor/Library↓3   Track Name↓4  
    
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 histone modification maps generated by Broad Institute using ChIP-Seq. Experiments include various histone marks over a number of normal sample types. Histone marks are critical epigenetic components. They are covalent modifications of amino acid residues of histone proteins, which modify protein's biochemical property and affect transcription and chromatin state. The histone marks are measured by ChIP-Seq experiments (chromatin immunoprecipitation followed by sequencing).

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 ChIP-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 ChIP-Seq experiments of this type (e.g. all H3K4me3 ChIP-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 the Bradley E. Berstein lab at Broad Institute. Berstein lab is part of Roadmap Epigenomics Project.

Useful links