Sanger ChIP Track Settings
 
Sanger ChIP-chip (histones H3,H4 ab in GM06990, K562, HeLa, and other cells)   (Sanger ChIP-chip)

This track is part of a parent called 'Sanger ChIP-chip'. To show other tracks of this parent, go to the Sanger ChIP-chip configuration page.

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Track height: pixels (range: 16 to 128)
Data view scaling: Always include zero: 
Vertical viewing range: min:  max:   (range: -46.1 to 75)
Transform function:Transform data points by: 
Windowing function: Smoothing window:  pixels
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Select subtracks:
    All                    
    Cell_Type
            GM06990
            K562
            HeLa
            HFL-1
            MOLT4
            PTR8
    Factor
            H3K4me1
            H3K4me2
            H3K4me3
            H3ac
            H4ac
            H3K9me3
            H3K27me3
            H3K36me3
            H3K79me3
            CTCF
List subtracks: only selected/visible    all    ()  
dense
 SI H3K4m1 GM6990  Sanger Institute ChIP-chip (H3K4me1 ab, GM06990 cells)   schema 
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 SI H3K4m2 GM6990  Sanger Institute ChIP-chip (H3K4me2 ab, GM06990 cells)   schema 
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 SI H3K4m3 GM6990  Sanger Institute ChIP-chip (H3K4me3 ab, GM06990 cells)   schema 
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 SI H3ac GM06990  Sanger Institute ChIP-chip (H3ac ab, GM06990 cells)   schema 
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 SI H4ac GM06990  Sanger Institute ChIP-chip (H4ac ab, GM06990 cells)   schema 
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 SI H3K9me3 GM06990  Sanger Institute ChIP-chip (H3K9me3 ab, GM06990 cells)   schema 
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 SI H3K27me3 GM06990  Sanger Institute ChIP-chip (H3K27me3 ab, GM06990 cells)   schema 
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 SI H3K36me3 GM06990  Sanger Institute ChIP-chip (H3K36me3 ab, GM06990 cells)   schema 
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 SI H3K79me3 GM06990  Sanger Institute ChIP-chip (H3K79me3 ab, GM06990 cells)   schema 
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 SI CTCF GM06990  Sanger Institute ChIP-chip (CTCF ab, GM06990 cells)   schema 
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 SI H3K4me2 K562  Sanger Institute ChIP-chip (H3K4me2 ab, K562 cells)   schema 
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 SI H3K4me3 K562  Sanger Institute ChIP-chip (H3K4me3 ab, K562 cells)   schema 
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 SI H3ac K562  Sanger Institute ChIP-chip (H3ac ab, K562 cells)   schema 
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 SI H4ac K562  Sanger Institute ChIP-chip (H4ac ab, K562 cells)   schema 
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 SI H3K4me1 HeLa  Sanger Institute ChIP-chip (H3K4me1 ab, HeLa cells)   schema 
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 SI H3K4me2 HeLa  Sanger Institute ChIP-chip (H3K4me2 ab, HeLa cells)   schema 
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 SI H3K4me3 HeLa  Sanger Institute ChIP-chip (H3K4me3 ab, HeLa cells)   schema 
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 SI H3ac HeLa  Sanger Institute ChIP-chip (H3ac ab, HeLa cells)   schema 
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 SI H4ac HeLa  Sanger Institute ChIP-chip (H4ac ab, HeLa cells)   schema 
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 SI H3K4me1 HFL-1  Sanger Institute ChIP-chip (H3K4me1 ab, HFL-1 cells)   schema 
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 SI H3K4me2 HFL-1  Sanger Institute ChIP-chip (H3K4me2 ab, HFL-1 cells)   schema 
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 SI H3K4me3 HFL-1  Sanger Institute ChIP-chip (H3K4me3 ab, HFL-1 cells)   schema 
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 SI H3ac HFL-1  Sanger Institute ChIP-chip (H3ac ab, HFL-1 cells)   schema 
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 SI H4ac HFL-1  Sanger Institute ChIP-chip (H4ac ab, HFL-1 cells)   schema 
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 SI H3K4me1 MOLT4  Sanger Institute ChIP-chip (H3K4me1 ab, MOLT4 cells)   schema 
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 SI H3K4me2 MOLT4  Sanger Institute ChIP-chip (H3K4me2 ab, MOLT4 cells)   schema 
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 SI H3K4me3 MOLT4  Sanger Institute ChIP-chip (H3K4me3 ab, MOLT4 cells)   schema 
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 SI H3ac MOLT4  Sanger Institute ChIP-chip (H3ac ab, MOLT4 cells)   schema 
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 SI H4ac MOLT4  Sanger Institute ChIP-chip (H4ac ab, MOLT4 cells)   schema 
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 SI H3K4me1 PTR8  Sanger Institute ChIP-chip (H3K4me1 ab, PTR8 cells)   schema 
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 SI H3K4me2 PTR8  Sanger Institute ChIP-chip (H3K4me2 ab, PTR8 cells)   schema 
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 SI H3K4me3 PTR8  Sanger Institute ChIP-chip (H3K4me3 ab, PTR8 cells)   schema 
    
Data version: ENCODE June & Oct 2005 Freezes, Aug 2006 & Jan 2007 data

Description

ENCODE region-wide location analysis of H3 and H4 histones was conducted employing ChIP-chip using chromatin extracted from GM06990 (lymphoblastoid), K562 (myeloid leukemia-derived), HeLaS3 (cervix carcinoma), HFL-1 (embryonic lung fibroblast), MOLT-4 (lymphoblastic leukemia), and PTR8 cells. Experiments were conducted with antibodies to the following histones: H3K4me1, H3K4me2, H3K4me3, H3K9me3, H3K27me3, H3K36me3, H3K79me3, H3ac, H4ac, and CTCF.

Histone methylation and acetylation serves as a stable genomic imprint that regulates gene expression and other epigenetic phenomena. These histones are found in transcriptionally active domains called euchromatin.

Display Conventions and Configuration

This annotation follows the display conventions for composite "wiggle" tracks. The subtracks within this annotation may be configured in a variety of ways to highlight different aspects of the displayed data. The graphical configuration options are shown at the top of the track description page, followed by a list of subtracks. To display only selected subtracks, uncheck the boxes next to the tracks you wish to hide. For more information about the graphical configuration options, click the Graph configuration help link.

Methods

Chromatin from the cell line was cross-linked with 1% formaldehyde, precipitated with antibody binding to the histone, and sheared and hybridized to the Sanger ENCODE3.1.1 DNA microarray. DNA was not amplified prior to hybridization.

The raw and transformed data files reflect fold enrichment over background, averaged over six replicates.

Verification

There are six replicates: two technical replicates (immunoprecipitations) for each of the three biological replicates (cell cultures).

Raw and transformed (averaged) data can be downloaded from the Wellcome Trust Sanger Institute via the ENCODE data access web site or the ENCODE FTP site.

Credits

The data for this track were generated by the ENCODE investigators at the Wellcome Trust Sanger Institute, Hinxton, UK.