UCSD Histone Track Settings
 
Histone Modifications by ChIP-seq from REMC/UCSD

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Assay Type
H2AK5ac
H2BK120ac
H2BK12ac
H2BK15ac
H2BK20ac
H2BK5ac
H3K14ac
H3K18ac
H3K23ac
H3K23me2
H3K27ac
H3K27me3
H3K36me3
H3K4ac
H3K4me1
H3K4me2
H3K4me3
H3K56ac
H3K79me1
H3K79me2
H3K9ac
H3K9me1
H3K9me3
H4K20me1
H4K5ac
H4K8ac
H4K91ac
Input
H2A.Z
H3T11ph
H2AK9ac
H4K12ac
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Sample Type
H1 BMP4 Derived Mesendoderm Cultured Cells   H1 BMP4 Derived Mesendoderm Cultured Cells
H1 BMP4 Derived Trophoblast Cultured Cells   H1 BMP4 Derived Trophoblast Cultured Cells
H1 Derived Mesenchymal Stem Cells   H1 Derived Mesenchymal Stem Cells
H1 Derived Neuronal Progenitor Cultured Cells   H1 Derived Neuronal Progenitor Cultured Cells
H1   H1
H9   H9
IMR90   IMR90
iPS DF 19.11   iPS DF 19.11
iPS DF 6.9   iPS DF 6.9
Left Ventricle   Left Ventricle
Sigmoid Colon   Sigmoid Colon
Adrenal Gland   Adrenal Gland
Psoas Muscle   Psoas Muscle
Bladder   Bladder
Pancreas   Pancreas
Gastric   Gastric
Spleen   Spleen
Right Atrium   Right Atrium
Aorta   Aorta
Small Intestine   Small Intestine
Adipose Tissue   Adipose Tissue
Lung   Lung
Right Ventricle   Right Ventricle
Esophagus   Esophagus
Thymus   Thymus
Adult Liver   Adult Liver
Ovary   Ovary
Sample Type































Sample Type
 All
Assay Type
H2AK5ac
H2BK120ac
H2BK12ac
H2BK15ac
H2BK20ac
H2BK5ac
H3K14ac
H3K18ac
H3K23ac
H3K23me2
H3K27ac
H3K27me3
H3K36me3
H3K4ac
H3K4me1
H3K4me2
H3K4me3
H3K56ac
H3K79me1
H3K79me2
H3K9ac
H3K9me1
H3K9me3
H4K20me1
H4K5ac
H4K8ac
H4K91ac
Input
H2A.Z
H3T11ph
H2AK9ac
H4K12ac
Assay Type
All 
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  Assay Type↓1 Sample Type↓2 Donor/Library↓3   Track Name↓4  
dense
 Configure 		 H3K27ac  IMR90  YL58  IMR90 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.7 Pcnt=83 Library:YL58)    Data format 
dense
 Configure 		 H3K27me3  IMR90  LL223  IMR90 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.386 Pcnt=96 Library:LL223)    Data format 
dense
 Configure 		 H3K36me3  IMR90  LL225  IMR90 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4615 Pcnt=98 Library:LL225)    Data format 
dense
 Configure 		 H3K4me1  IMR90  LL222  IMR90 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5529 Pcnt=88 Library:LL222)    Data format 
dense
 Configure 		 H3K4me3  IMR90  LL221  IMR90 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.8482 Pcnt=100 Library:LL221)    Data format 
dense
 Configure 		 H3K9me3  IMR90  SK06  IMR90 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1913 Pcnt=64 Library:SK06)    Data format 
dense
 Configure 		 Input  IMR90  IMR90-05-I1  IMR90 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2108 Pcnt=89 Library:IMR90-05-I1)    Data format 
    
Assembly: Human Feb. 2009 (GRCh37/hg19)

Vizhub @ Wash U built this track, and Roadmap Epigenomics Consortium is responsible for its contents.

Description

This track displays histone modification maps generated by University of California at San Diego using ChIP-Seq. Experiments include various histone marks over a number of normal sample types. 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

This track 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. The subtracks can be displayed and configured individually. See instructions .

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 all ChIP-Seq experiments of this type (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 the Bin Ren lab at UCSD. Ren lab is part of Roadmap Epigenomics Project.

Useful links