Stanf Meth Score Track Settings
 
Stanford Methylation Digest Smoothed Score   (All ENCODE Chromosome, Chromatin and DNA Structure tracks)

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 Stan Meth Sc Be2C  Stanford Methylation Digest Smoothed Score (Be2C cells)   Data format 
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 Stan Meth Sc CRL1690  Stanford Methylation Digest Smoothed Score (CRL1690 cells)   Data format 
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 Stan Meth Sc HCT116  Stanford Methylation Digest Smoothed Score (HCT116 cells)   Data format 
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 Stan Meth Sc HT1080  Stanford Methylation Digest Smoothed Score (HT1080 cells)   Data format 
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 Stan Meth Sc HepG2  Stanford Methylation Digest Smoothed Score (HepG2 cells)   Data format 
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 Stan Meth Sc JEG3  Stanford Methylation Digest Smoothed Score (JEG3 cells)   Data format 
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 Stan Meth Sc Snu182  Stanford Methylation Digest Smoothed Score (Snu182 cells)   Data format 
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 Stan Meth Sc U87  Stanford Methylation Digest Smoothed Score (U87 cells)   Data format 
    
Source data version: ENCODE June 2005 Freeze
Assembly: Human May 2004 (NCBI35/hg17)
Data coordinates converted via liftOver from: July 2003 (NCBI34/hg16)

Description

This track displays smoothed (sliding-window mean) scores for experimentally determined regions of unmethylated CpGs in the ENCODE regions. These experiments were performed in eight cell lines, each of which is displayed as a separate subtrack:

Cell LineClassificationIsolated From
BE(2)-Cneuroblastomabrain (metastatic, from bone marrow)
CRL-1690™hybridomaB lymphocyte
HCT 116colorectal carcinomacolon
HT-1080fibrosarcomaconnective tissue
HepG2hepatocellular carcinomaliver
JEG-3choriocarcinomaplacenta
SNU-182hepatocellular carcinomaliver
U-87 MGglioblastoma-astrocytomabrain

Display Conventions and Configuration

This annotation follows the display conventions for composite 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

High molecular weight genomic DNA was prepared from each cell line. The genomic DNA was digested with a cocktail of six methyl-sensitive restriction enzymes (AciI, HhaI, BstUI, HpaII, HgaI, and HpyCH4IV) and size selected to deplete the genome of unmethylated regions. Digested and undigested DNA (control) were amplified, labeled, and hybridized to oligo tiling arrays produced by NimbleGen. The data for each array were median subtracted (log 2 ratios) and normalized (divided by the standard deviation).

The transformed mean ratios of undigested:digested genomic DNA for all probes were then smoothed by calculating a sliding-window mean. Windows of six neighboring probes (sliding two probes at a time) were used; within each window, the highest and lowest value were dropped, and the remaining four values were averaged. In order to increase the contrast between high and low values for visual display, the average was converted to a score by the formula:

score = 8^(average) * 10
These scores are for visualization purposes; for all analyses, the raw ratios, which are available in the Stanf Meth track, should be used.

Higher scores in this track indicate regions that are more strongly methylated, due to the greater difference between the undigested and digested hybridization signals.

Verification

Three biological replicates and two technical replicates were done for each of the eight cell lines. The Myers lab is currently testing the specificity and sensitivity using real-time PCR.

Credits

These data were generated in the Richard M. Myers lab at Stanford University (now at HudsonAlpha Institute for Biotechnology). Please contact David Johnson for further information regarding the methods and the data for this track.