Sample Summary CD56 Primary Cells Summary Track Settings
 
Roadmap Epigenome CD56 Primary Cells Summary for 8 assay type(s)

Track collection: Sample Summary

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     CD56 DGF 79 89  UW CD56 Primary Cells Digital Genomic Footprinting Donor RO 01679 Library DGF.DS17189 EA Release 9    Data format 
     CD56 DNase 21 89  CD56 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6307 Pcnt=97)    Data format 
     CD56 DNase 36 43  CD56 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2282 Pcnt=2)    Data format 
     CD56 H3K27ac 01 16  UW CD56 Primary Cells Histone H3K27ac Donor RO 01701 Library Histone.DS21716 EA Release 9    Data format 
     CD56 H3K27me3 79 94  UW CD56 Primary Cells Histone H3K27me3 Donor RO 01679 Library Histone.DS22594 EA Release 9    Data format 
     CD56 H3K36me3 79 95  UW CD56 Primary Cells Histone H3K36me3 Donor RO 01679 Library Histone.DS22595 EA Release 9    Data format 
     CD56 H3K4me1 79 93  UW CD56 Primary Cells Histone H3K4me1 Donor RO 01679 Library Histone.DS22593 EA Release 9    Data format 
     CD56 H3K4me3 01 15  UW CD56 Primary Cells Histone H3K4me3 Donor RO 01701 Library Histone.DS21715 EA Release 9    Data format 
     CD56 Input 01 29  UW CD56 Primary Cells ChIP-Seq Input Donor RO 01701 Library Histone.DS21629 EA Release 9    Data format 
     MCD56 DNase 89 76  Mobilized CD56 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.266 Pcnt=8)    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

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 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 three institutions: UCSF, UBC, UCSD as part of Roadmap Epigenomics Project.

Useful links