These tracks are from Roadmap Epigenomics Integrative Analysis Hub, and are organized by complete epigenome ID (EID) assigned by Roadmap.
This is the complete set of Roadmap Epigenomics Integrative Analysis Hub. Consolidated refer to the 127 reference epigenomes that uses additional steps of pooling and subsampling and these are the ones used in the paper. All data types were reprocessed for the consolidated epigenomes.
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.
Peak calling
For histone marks, peaks were called using MACSv2 with a p-value threshold of 0.01.
The peaks are not optimally thresholded using IDR.
For the broad marks, the parameters are not optimal to call broad
domains. These peaks represent narrow regions of strong
enrichment. The broad domain calls are yet to be produced.
DNase*.narrowPeak calls were also called using MACS2 again with a
p-value threshold of 0.01.
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.
There are also imputed signal for segmentations tracks.
Primary Core Marks segmentation
State 1 - Red - TssA (Active_TSS)
State 2 - OrangeRed - TssAFlnk (Flanking_Active_TSS)
State 3 - LimeGreen - TxFlnk (Transcr_at_gene_5_and_3primer)
State 4 - Green - Tx (Strong_transcription)
State 5 - DarkGreen - TxWk (Weak_transcription)
State 6 - GreenYellow - EnhG (Genic_enhancers)
State 7 - Yellow - Enh (Enhancers)
State 8 - MediumAquamarine - ZNF/Rpts (ZNF_genes&repeats)
State 9 - PaleTurquoise - Het (Heterochromatin)
State 10 - IndianRed - TssBiv (Bivalent/Poised_TSS)
State 11 - DarkSalmon - BivFlnk (Flanking_Bivalent_TSS/Enh)
State 12 - DarkKhaki - EnhBiv (Bivalent_Enhancer)
State 13 - Silver - ReprPC (Repressed_PolyComb)
State 14 - Gainsboro - ReprPCWk (Weak_Repressed_PolyComb)
State 15 - White - Quies (Quiescent/Low)
Auxiliary Core Marks + K27ac segmentation
State 1 - Red - TssA (Active_TSS)
State 2 - Orange_Red - TssFlnk (Flanking_TSS)
State 3 - Orange_Red - TssFlnkU (Flanking_TSS_Upstream)
State 4 - Orange_Red - TssFlnkD (Flanking_TSS_Downstream)
State 5 - Green - Tx (Strong_transcription)
State 6 - DarkGreen - TxWk (Weak_transcription)
State 7 - GreenYellow - EnhG1 (Genic_enhancer1)
State 8 - GreenYellow - EnhG2 (Genic_enhancer2)
State 9 - Orange - EnhA1 (Active_Enhancer1)
State 10 - Orange - EnhA2 (Active_Enhancer2)
State 11 - Yellow - EnhWk (Weak_Enhancer)
State 12 - Medium_Aquamarine - ZNF/Rpts (ZNF_genes&repeats)
State 13 - PaleTurquoise - Het (Heterochromatin)
State 14 - IndianRed - TssBiv (Bivalent/Poised_TSS)
State 15 - DarkKhaki - EnhBiv (Bivalent_Enhancer)
State 16 - Silver - ReprPC (Repressed_PolyComb)
State 17 - Gainsboro - ReprPCWk (Weak_Repressed_PolyComb)
State 18 - White - Quies (Quiescent/Low)
Imputed Marks Segmentation
State 1 - Red - TssA (Active TSS)
State 2 - Orange Red - PromU (Promoter Upstream TSS)
State 3 - Orange Red - PromD1 (Promoter Downstream TSS with DNase)
State 4 - Orange Red - PromD2 (Promoter Downstream TSS)
State 5 - Green - Tx5' (Transcription 5')
State 6 - Green - Tx (Transcription)
State 7 - Green - Tx3' (Transcription 3')
State 8 - Light Green - TxWk (Weak transcription)
State 9 - GreenYellow - TxReg (Transcription Regulatory)
State 10 - GreenYellow - TxEnh5' (Transcription 5' Enhancer)
State 11 - GreenYellow - TxEnh3' (Transcription 3' Enhancer)
State 12 - GreenYellow - TxEnhW (Transcription Weak Enhancer)
State 13 - Orange - EnhA1 (Active Enhancer 1)
State 14 - Orange - EnhA2 (Active Enhancer 2)
State 15 - Orange - EnhAF (Active Enhancer Flank)
State 16 - Yellow - EnhW1 (Weak Enhancer 1)
State 17 - Yellow - EnhW2 (Weak Enhancer 2)
State 18 - Yellow - EnhAc (Enhancer Acetylation Only)
State 19 - Light Yellow - DNase (DNase only)
State 20 - Medium Aquamarine - ZNF/Rpts (ZNF genes & repeats)
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
.
These data were generated from Roadmap Epigenomics Project.
All track, plus peak, alignment tracks could be visualized at WashU EpiGenome Browser.
Roadmap Epigenomics Consortium et.al Integrative analysis of 111 reference human epigenomes. Nature518, 317–330 (19 February 2015)
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