DNA Methylation Track Settings
 
DNA Methylation from REMC

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Adult Kidney 
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CD34 Primary Cells 
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H1 Derived Embryoid Body Cultured Cells 
H1 Derived Neuronal Progenitor Cultured Cells 
H1 Derived Neuronal Progenitor Cultured Cells r1a 
H1 Derived Neuronal Progenitor Cultured Cells r1b 
H1 Derived Neuronal Progenitor Cultured Cells r1c 
H1 Derived Neuronal Progenitor Cultured Cells r2a 
H1 Derived Neuronal Progenitor Cultured Cells r2b 
H1Es 
H9 Derived Embryoid Body Cultured Cells 
H9 Derived Neuronal Progenitor Cultured Cells 
H9 Cell line 
hESC Derived CD184 Endoderm Cultured Cells 
H9 Derived Neuron Cultured Cells 
HUES13 
HUES1 Derived Embryoid Body Cultured Cells 
HUES1 
HUES28 
HUES3 Derived Embryoid Body Cultured Cells 
HUES3 
HUES44 
HUES45 Derived Embryoid Body Cultured Cells 
HUES45 
HUES48 
HUES49 
HUES53 
HUES62 
HUES63 
HUES64 
HUES65 
HUES66 
HUES6 Derived Embryoid Body Cultured Cells 
HUES6 
HUES8 
HUES9 
IMR90 
iPS11a 
iPS11b 
iPS11c 
iPS15b 
iPS17a 
iPS17b 
iPS18a 
iPS18b 
iPS18c 
iPS20b 
iPS27b 
iPS27e 
iPS-DF.19.11 
iPS-DF.6.9 
Mobiled CD34 
Neurosphere Cultured Cells Cortex Derived 
Neurosphere Cultured Cells Ganglionic Eminence Derived 
Peripheral Blood Mononuclear Primary Cells 
Penis Foreskin Fibroblast Primary Cells 
Penis Foreskin Keratinocyte Primary Cells 
Penis Foreskin Melanocyte Primary Cells 
Primary Fibroblast 
Pancreatic Islets 
Rectal Mucosa 
Rectal Smooth Muscle 
Skeletal Muscle 
Stomach Mucosa 
Stomach Smooth Muscle 
H1 BMP4 Mesendoderm 
H1DMSC 
Brain Cingulate Gyrus 
Brain Inferior Temporal Lobe 
Mobilized CD34 Primary Cells 
Brain Mid Frontal Lobe 
Brain Hippocampus Middle 
Brain Angular Gyrus 
hESC Derived CD184+ Endoderm Cultured Cells 
Adult Liver 
Brain Anterior Caudate 
Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells 
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Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells 
Testis Spermatozoa Primary Cells 
Left Ventricle 
Adrenal Gland 
Spleen 
Psoas Muscle 
Pancreas 
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hESC Derived CD56+ Ectoderm Cultured Cells 
Right Atrium 
Thymus 
UCSF-4star 
hESC Derived CD56+ Mesoderm Cultured Cells 
Ovary 
Fetal Muscle Leg 
Aorta 
Small Intestine 
Adipose Tissue 
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Sample Type
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dense
 Configure 		 Bisulfite-Seq  IMR90  methylC-seq imr90 r1a  IMR90 Cell Line DNA Methylation by Bisulfite-seq Signal from REMC/UCSD (Library:methylC-seq_imr90_r1a)    Data format 
    
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 DNA methylation maps generated by Roadmap Epigenomics Project. Each track is collection of DNA methylation experiment data on one sample type.

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 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. .

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. Different y-axis range applies to each experiment types (MeDIP-Seq, MRE-Seq, MethylC-Seq) and can be controled in each view type.

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 MeDIP-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 MeDIP-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 the Roadmap Epigenomics Project.

Useful links