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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.
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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
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US Server