These tracks are from Roadmap Epigenomics Integrative Analysis Hub, and are organized by assay types.
Unconsolidated data is basically all the ChIP-seq and DNase Release 9 data at the EDACC as it was except filtered for 36 bp read length mappability and processed to create peak calls and signal tracks.
Chip-seq is used primarily to determine how transcription factors and other chromatin-associated proteins influence phenotype-affecting mechanisms. Determining how proteins interact with DNA to regulate gene expression is essential for fully understanding many biological processes and disease states.
DNA methylation of human DNA mostly happens on cytosine bases of CpG dinucleotides.
The methylated DNA usually prevent accessibility of regulatory proteins thus hampering transcription,
while unmethylated DNA is usually associated with 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.
BS-seq (whole genome Bisulfite sequencing) applies routine sequencing methods on bisulfite-treated genomic DNA to determine methylation status at CpG dinucleotides.
RRBS (reduced representation bisulfite sequencing) is analogous to the reduced representation shotgun sequencing used for single nucleotide polymorphism (SNP) discovery. The method is based on size selection of restriction fragments to generate a 'reduced representation' of the genome of a strain, tissue or cell type. Then the 'reduced representation' was treated by bisulfite and sequencing.
Display conventions
Each track can be turned on/off individually.
All tracks displays read density data in form of wiggle plots.
For Histone/DNase, there also enrichment signal tracks using MACS based on pvalue or fold Change.
Data processing:
EDACC
carried out data processing and quality assessment.
Details are fully explained
here
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
.
US Server