By Assay H3K9me3 Track Settings
 
H3K9me3 tracks for 127 sample type(s)

Track collection: Roadmap data by assay

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CD3 Primary Cells
Breast Luminal Epithelial Cells
Gastric
Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells
iPS15b
Treg Primary Cells
CD14 Primary Cells
Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells
ES-I3
CD4+ CD25- IL17 PMA-Ionomcyin stimulated Th17 Primary Cells
Adrenal Gland
HUES48
Penis Foreskin Keratinocyte Primary Cells
Brain Hippocampus Middle
Fetal Intestine Small
Left Ventricle
CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells
Adipose Derived Mesenchymal Stem Cell Cultured Cells
Fetal Heart
CD4+ CD25- CD45RO Memory Primary Cells
iPS20b
HUES64
Lung
CD4+ CD25- Th Primary Cells
Fetal Brain
Penis Foreskin Melanocyte Primary Cells
Duodenum Smooth Muscle
Aorta
hESC Derived CD56+ Ectoderm Cultured Cells
hESC Derived CD184+ Endoderm Cultured Cells
Fetal Lung
Th17 Primary Cells
CD19 Primary Cells
CD4+ CD25- CD45RO+ Memory Primary Cells
Adult Liver
CD34 Primary Cells
Peripheral Blood Mononuclear Primary Cells
H9 Derived Neuronal Progenitor Cultured Cells
Esophagus
Fetal Muscle Trunk
CD8 Memory Primary Cells
Neurosphere Cultured Cells Cortex Derived
IMR90
H9 Cell line
Neurosphere Cultured Cells Ganglionic Eminence Derived
CD15 Primary Cells
Ovary
UCSF-4Star
Rectal Smooth Muscle
Penis Foreskin Fibroblast Primary Cells
Mesenchymal Stem Cell Derived Adipocyte Cultured Cells
hESC Derived CD56+ Mesoderm Cultured Cells
Muscle Satellite Cultured Cells
Sigmoid Colon
hESC Derived CD184+ Endoderm Cultured Cells
CD4+ CD25+ CD127- Treg Primary Cells
Right Atrium
Fetal Brain
CD4+ CD25- CD45RA Naive Primary Cells
Penis Foreskin Keratinocyte Primary Cells
Breast vHMEC
CD4+ CD25- CD45RA+ Naive Primary Cells
CD4+ CD25+ CD127- Treg Primary Cells
Right Ventricle
Brain Substantia Nigra
Mobiled CD34
H1 Derived Neuronal Progenitor Cultured Cells
Fetal Thymus
Colon Smooth Muscle
iPS18a
CD3 Primary Cells
Fetal Placenta
H1Es
CD19 Primary Cells
H1 Derived Neuronal Progenitor Cultured Cells
H1 BMP4 Derived Trophoblast Cultured Cells
Fetal Adrenal Gland
Duodenum Mucosa
Thymus
Brain Inferior Temporal Lobe
Brain Cingulate Gyrus
iPS DF 19.11
Adipose Nuclei
CD4 Naive Primary Cells
CD4 Memory Primary Cells
CD8 Primary Cells
Peripheral Blood Mononuclear Primary Cells
Adult Kidney
CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells
H9 Derived Neuron Cultured Cells
iPS DF 6.9
Fetal Intestine Large
Brain Anterior Caudate
Adult Liver
iPS18c
CD4+ CD25int CD127+ Tmem Primary Cells
Stomach Mucosa
Brain Mid Frontal Lobe
Spleen
Small Intestine
Duodenum Smooth Muscle
Fetal Stomach
Fetal Kidney
Psoas Muscle
CD8 Naive Primary Cells
ES-WA7
CD4+ CD25- Th Primary Cells
Breast Myoepithelial Cells
CD34 Cultured Cells
Pancreatic Islets
Neurosphere Cultured Cells Ganglionic Eminence Derived
Pancreatic Islets
H1 Derived Mesenchymal Stem Cells
Pancreas
Stomach Smooth Muscle
Placenta Amnion
Colonic Mucosa
Colon Smooth Muscle
CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells
Fetal Muscle Leg
H1 BMP4 Derived Trophoblast Cultured Cells
Rectal Mucosa
Brain Angular Gyrus
HUES6
Penis Foreskin Melanocyte Primary Cells
Brain Germinal Matrix
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Assembly: Human Feb. 2009 (GRCh37/hg19)

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

Description

These tracks are genome-wide maps on epigenetic marks surveyed by Roadmap Epigenomics Project. Each track is about one type of epigenetic mark, and contains multiple experiments assayed for that mark type. DNA methylation and histone modification are two types of most important epigenetic marks.

DNA methylation of human DNA mostly happens on cytosine bases of CpG dinucleotides. The methylated DNA usually prevent accessibility of regulatory proteins and hampers transcription, while unmethylated DNA is usually indicative of open chromatin. The MeDIP-Seq and MRE-Seq experiments are usually performed on same sample to identify genome-wide DNA methylation pattern. MeDIP-Seq (methylated DNA immunoprecipitation and sequencing) is a ChIP-based approach utilizing antibody against methylated cytosine. This method enriches methylated DNA and high read count indicates high likelihood of underlying region is methylated. The MRE-Seq (methylation restriction enzyme sequencing) uses methylation-sensitive restriction enzymes to digest DNA, and only cut at unmethylated restriction sites. The cut restriction sites will be detected by sequencing where reads aligned to a restriction site on reference genome means the restriction site is unmethylated.

The MethylC-Seq (MethylC sequencing) uses bisulfite to convert methylated cytosines to thymines before sequencing. The percentage of reads with a T versus a C indicates the percentage methylation at the cytosine. Details can be found in this paper Lister R, et al., Nature. 2009 Nov 19;462(7271):315-22. .

RRBS (Reduced-Representation-Bisulfite-Sequencing) is similar to MethylC-seq except RRBS uses restriction enzyme to fragment the genome into fragments suitably-sized for sequencing. While RRBS produces percent methylation similar to MethylC-seq, it is limited to cytosines that are within restriction fragments of a suitable size and then tend to measure CpG dense regions only. Details can be found in this paper: Meissener, A. et al., Nucleic Acids Res. 2005; 33(18): 5868-5877. .

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

Each track can be turned on/off individually. Inside each track, sub-tracks are displayed in same vertical space and are overlayed with transparent colors for contrast. All tracks 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. Sub-tracks sharing same space use same scale.

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 this type of ChIP-Seq experiments (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 labs from participating institutions of Roadmap Epigenomics Project.

Useful links