Con. By Assay DNase hypersensitivity Track Settings
 
DNase hypersensitivity tracks from Roadmap

Track collection: Roadmap Consolidated Analysis hub organized by assay

+  Description
+  All tracks in this collection (35)

Maximum display mode:       Reset to defaults   
Select views (Help):
macs2signal pval ▾       Signal ▾       macs2signal foldChange ▾      
Select subtracks by views and sample type:

  Data Type: Real Imputed
 All views macs2signal pval  Signal  macs2signal foldChange 
Sample Type
Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells 
CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells 
Lung 
Ovary 
Thymus 
CD4 Naive Primary cells 
CD4+ CD25- CD45RA+ Naive Primary Cells 
CD8 Naive Primary cells 
CD4 Memory Primary cells 
Mobilized CD34 Primary cells 
CD3 Primary cells 
CD15 Primary cells 
CD19 Primary cells 
Penis Foreskin Fibroblast Primary Cells 
Penis Foreskin Melanocyte Primary Cells 
H9 
HUES48 
HUES64 
H1 
hES-I3 
WA-7 
CD14 primary cells 
HUVEC 
Dnd41 
Adult Liver 
Bone Marrow Derived Mesenchymal Stem cell 
Adipose Nuclei 
Colonic Mucosa 
Rectal Mucosa 
Aorta 
Peripheral Blood Mononuclear Primary cells 
CD34 Primary cells 
CD8 Memory Primary Cells 
CD4+ CD25int CD127+ Tmem Primary Cells 
Brain Germinal Matrix 
CD4+ CD25+ CD127- Treg Primary Cells 
CD4+ CD25- Th Primary Cells 
Esophagus 
Right Atrium 
Brain Angular Gyrus 
Duodenum Smooth Muscle 
Duodenum Mucosa 
iPS DF 19.11 
iPS DF 6.9 
Breast vHMEC 
Breast Myoepithelial cells 
Rectal Smooth Muscle 
Skeletal Muscle 
Stomach Smooth Muscle 
Muscle Satellite Cultured Cells 
hiPS-15b 
hiPS-20b 
CD4+ CD25- CD45RO+ Memory Primary Cells 
hiPS-18b 
PanIslets 
Fetal Lung 
Fetal Kidney 
Monocytes-CD14+ 
Fetal Placenta 
Fetal Intestine Small 
Fetal Muscle Trunk 
Fetal Muscle Leg 
HeLa-S3 
Fetal Adrenal Gland 
Fetal Intestine Large 
Fetal Thymus 
NH-A 
NHDF-Ad 
NHEK 
NHLF 
HSMM 
HSMMtube 
Psoas Muscle 
H1 Derived Neuronal Progenitor Cultured Cells 
Placenta Amnion 
Stomach Mucosa 
Right Ventricle 
Gastric 
Osteobl 
Sigmoid Colon 
Left Ventricle 
Colon Smooth Muscle 
CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells 
Spleen 
A549 
K562 
Brain Inferior Temporal Lobe 
Brain Hippocampus Middle 
Brain Cingulate Gyrus 
Brain Anterior Caudate 
H9 Derived Neuron Cultured Cells 
CD34 cultured cells 
Brain Substantia Nigra 
Brain Mid Frontal Lobe 
Adipose Derived Mesenchymal Stem Cell Cultured Cells 
Mesenchymal Stem Cell Derived Adipocyte Cultured Cells 
hESC Derived CD184+ Endoderm Cultured Cells 
HepG2 
H1 BMP4 Derived Mesendoderm Cultured Cells 
IMR90 
H1 Derived Mesenchymal Stem Cells 
H1 BMP4 Derived Trophoblast Cultured Cells 
Penis Foreskin Keratinocyte Primary Cells 
Small Intestine 
HUES6 
UCSF-4star 
GM12878 
Fetal Brain 
Fetal Heart 
Pancreas 
H9 Derived Neuronal Progenitor Cultured Cells 
hESC Derived CD56+ Mesoderm Cultured Cells 
hESC Derived CD56+ Ectoderm Cultured Cells 
CD56 primary cells 
Fetal Stomach 
Neurospheres, Cortex Derived 
Neurospheres, Ganglionic Eminence Derived 
HMEC 
Sample Type
 All views macs2signal pval  Signal  macs2signal foldChange 
List subtracks: only selected/visible    all    ()
  Sample Type↓1 views↓2   Track Name↓3  
    
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 from Roadmap Epigenomics Integrative Analysis Hub, and are organized by assay types.
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)
  • State 21 -  PaleTurquoise  - Het (Heterochromatin)
  • State 22 -  Light Purple  - PromP (Poised Promoter)
  • State 23 -  Purple  - PromBiv (Bivalent Promoter)
  • State 24 -  Silver  - ReprPC (Repressed PolyComb)
  • State 25 -  White  - Quies (Quiescent/Low)

Methods

Experimental protocols: follow this link for experimental protocols.

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 .

Release Notes

Please follow the link for Roadmap Epigenomics data access policy

Credits

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. Nature 518, 317–330 (19 February 2015)

Useful links

Contacts

Please email Ting Wang for questions.