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Track collection: Roadmap data by assay

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Brain Angular Gyrus
Placenta Chorion Smooth
Gastric
CD14 Primary Cells
IMR90
Brain Hippocampus Middle
CD4+ CD25- IL17 PMA-Ionomcyin stimulated Th17 Primary Cells
Adrenal Gland
HUES48
Brain Hippocampus Middle
Fetal Intestine Small
Left Ventricle
CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells
Pancreatic Islets
CD4+ CD25- CD45RO Memory Primary Cells
iPS20b
Brain Mid Frontal Lobe
Lung
Aorta
Duodenum Smooth Muscle
CD4+ CD25- Th Primary Cells
hESC Derived CD56+ Ectoderm Cultured Cells
Ovary
CD19 Primary Cells
Colonic Mucosa
Adult Liver
Peripheral Blood Mononuclear Primary Cells
Esophagus
Fetal Muscle Trunk
CD8 Memory Primary Cells
Thymus
H9 Cell line
Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells
Duodenum Mucosa
Penis Foreskin Fibroblast Primary Cells
hESC Derived CD56+ Mesoderm Cultured Cells
Sigmoid Colon
Brain Substantia Nigra
hESC Derived CD184+ Endoderm Cultured Cells
Brain Inferior Temporal Lobe
Stomach Smooth Muscle
CD4+ CD25- CD45RA Naive Primary Cells
Penis Foreskin Keratinocyte Primary Cells
Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells
CD4+ CD25+ CD127- Treg Primary Cells
Right Ventricle
Rectal Smooth Muscle
Mobiled CD34
H1 Derived Neuronal Progenitor Cultured Cells
Fetal Thymus
iPS18a
CD3 Primary Cells
Fetal Placenta
H1Es
Adult Kidney
CD56 Primary Cells
H1 Derived Neuronal Progenitor Cultured Cells
Right Atrium
Fetal Adrenal Gland
H1 BMP4 Derived Mesendoderm Cultured Cells
Brain Anterior Caudate
Adipose Nuclei
Brain Inferior Temporal Lobe
Brain Cingulate Gyrus
iPS DF 19.11
CD4 Naive Primary Cells
CD4 Memory Primary Cells
CD8 Primary Cells
HUES64
iPS DF 6.9
Brain Anterior Caudate
CD4+ CD25int CD127+ Tmem Primary Cells
Brain Mid Frontal Lobe
Spleen
Small Intestine
Bladder
Fetal Stomach
Skeletal Muscle
Adipose Tissue
CD8 Naive Primary Cells
Rectal Mucosa
Breast Fibroblast Primary Cells
Psoas Muscle
Neurosphere Cultured Cells Ganglionic Eminence Derived
H1 Derived Mesenchymal Stem Cells
Pancreas
Placenta Amnion
Colon Smooth Muscle
CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells
Fetal Muscle Leg
H1 BMP4 Derived Trophoblast Cultured Cells
Fetal Intestine Large
Brain Angular Gyrus
HUES6
Brain Cingulate Gyrus
Penis Foreskin Melanocyte Primary Cells
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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