By Assay ChromatinAccessibility Track Settings
 
ChromatinAccessibility tracks for 89 sample type(s)

Track collection: Roadmap data by assay

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Sample Type
CD3 Primary Cells
Fibroblasts Fetal Skin Biceps Right
Mobilized CD3 Primary Cells
Fibroblasts Fetal Skin Upper Back
Fetal Renal Cortex Right
IMR90
Fetal Kidney Right
Fetal Intestine Small
Fetal Renal Cortex
Gastric
Fetal Heart
iPS DF 4.7
Fetal Lung Left
Fetal Brain
Fetal Muscle Arm
Fibroblasts Fetal Skin Scalp
Fetal Muscle Back
Fibroblasts Fetal Skin Biceps Left
CD56 Primary Cells
Ovary
Fetal Lung
Fetal Ovary
CD14 Primary Cells
Fetal Muscle Lower Limb Skeletal
Fetal Kidney Left
Fetal Renal Pelvis
Fetal Placenta
H9 Cell line
Fetal Thymus
Fetal Adrenal Gland
Fetal Kidney Right
Fibroblasts Fetal Skin Back
CD8 Primary Cells
Fetal Spinal Cord
Mobilized CD8 Primary Cells
Fibroblasts Fetal Skin Quadriceps Right
CD20 Primary Cells
Fetal Brain
Penis Foreskin Keratinocyte Primary Cells
Breast vHMEC
Fetal Muscle Leg
Fetal Muscle Arm
H1 BMP4 Derived Mesendoderm Cultured Cells
Fetal Renal Pelvis Left
Mobiled CD34
Fetal Thymus
Fetal Kidney
Fetal Stomach
Fetal Muscle Trunk
H1Es
Fetal Placenta
CD19 Primary Cells
H1 Derived Neuronal Progenitor Cultured Cells
Fetal Adrenal Gland
Fetal Intestine Large
Fetal Lung Right
Fetal Renal Cortex
Fibroblasts Fetal Skin Quadriceps Left
Fetal Testes
Fetal Stomach
Fetal Renal Cortex Left
iPS DF 19.11
Penis Foreskin Fibroblast Primary Cells
iPS DF 6.9
Fetal Spleen
H1 Derived Mesenchymal Stem Cells
Fetal Renal Pelvis
Small Intestine
Penis Foreskin Melanocyte Primary Cells
Fetal Kidney
Psoas Muscle
H1 Derived Neuronal Progenitor Cultured Cells
Fetal Muscle Back
Fetal Kidney Left
Fetal Skin
Mobilized CD4 Primary Cells
Fetal Muscle Upper Limb Skeletal
Fibroblasts Fetal Skin Abdomen
Fetal Lung Right
Pancreas
Heart
CD4 Primary Cells
iPS DF 19.7
Fetal Muscle Leg
H1 BMP4 Derived Trophoblast Cultured Cells
Fetal Renal Pelvis Right
Fetal Lung Left
Fetal Muscle Upper Trunk
Penis Foreskin Melanocyte Primary Cells
Sample Type
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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 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