By Assay Tracks
 
Roadmap data by assay tracks

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Bisulfite-Seq  Bisulfite-Seq tracks for 48 sample type(s)  
ChromatinAccessibility  ChromatinAccessibility tracks for 89 sample type(s)  
DGF  DGF tracks for 21 sample type(s)  
H2A.Z  H2A.Z tracks for 7 sample type(s)  
H2AK5ac  H2AK5ac tracks for 7 sample type(s)  
H2AK9ac  H2AK9ac tracks for 1 sample type(s)  
H2BK120ac  H2BK120ac tracks for 7 sample type(s)  
H2BK12ac  H2BK12ac tracks for 6 sample type(s)  
H2BK15ac  H2BK15ac tracks for 5 sample type(s)  
H2BK20ac  H2BK20ac tracks for 3 sample type(s)  
H2BK5ac  H2BK5ac tracks for 7 sample type(s)  
H3K14ac  H3K14ac tracks for 6 sample type(s)  
H3K18ac  H3K18ac tracks for 8 sample type(s)  
H3K23ac  H3K23ac tracks for 8 sample type(s)  
H3K23me2  H3K23me2 tracks for 2 sample type(s)  
H3K27ac  H3K27ac tracks for 96 sample type(s)  
H3K27me3  H3K27me3 tracks for 125 sample type(s)  
H3K36me3  H3K36me3 tracks for 130 sample type(s)  
H3K4ac  H3K4ac tracks for 8 sample type(s)  
H3K4me1  H3K4me1 tracks for 125 sample type(s)  
H3K4me2  H3K4me2 tracks for 8 sample type(s)  
H3K4me3  H3K4me3 tracks for 120 sample type(s)  
H3K56ac  H3K56ac tracks for 3 sample type(s)  
H3K79me1  H3K79me1 tracks for 7 sample type(s)  
H3K79me2  H3K79me2 tracks for 5 sample type(s)  
H3K9ac  H3K9ac tracks for 49 sample type(s)  
H3K9me1  H3K9me1 tracks for 1 sample type(s)  
H3K9me3  H3K9me3 tracks for 127 sample type(s)  
H3T11ph  H3T11ph tracks for 1 sample type(s)  
H4K12ac  H4K12ac tracks for 1 sample type(s)  
H4K20me1  H4K20me1 tracks for 3 sample type(s)  
H4K5ac  H4K5ac tracks for 3 sample type(s)  
H4K8ac  H4K8ac tracks for 7 sample type(s)  
H4K91ac  H4K91ac tracks for 6 sample type(s)  
Input  Input tracks for 138 sample type(s)  
MeDIP-Seq  MeDIP-Seq tracks for 19 sample type(s)  
MRE-Seq  MRE-Seq tracks for 18 sample type(s)  
mRNA-Seq  mRNA-Seq tracks for 80 sample type(s)  
RRBS  RRBS tracks for 70 sample type(s)  
smRNA-Seq  smRNA-Seq tracks for 15 sample type(s)  

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