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Histone Modifications by ChIP-seq from REMC/UCSD

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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
*Sample Type*																																		*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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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

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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

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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

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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

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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

Roadmap Consortium project home page
NCBI Epigenomics Gateway portal to all project data in GEO database
Epigenome Data and Analysis Coordination Center/EDACC