Description
This track displays 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 Line | Classification | Isolated From |
BE(2)-C | neuroblastoma | brain (metastatic, from bone marrow) |
CRL-1690™ | hybridoma | B lymphocyte |
HCT 116 | colorectal carcinoma | colon |
HT-1080 | fibrosarcoma | connective tissue |
HepG2 | hepatocellular carcinoma | liver |
JEG-3 | choriocarcinoma | placenta |
SNU-182 | hepatocellular carcinoma | liver |
U-87 MG | glioblastoma-astrocytoma | brain |
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 value given
for each array probe is the transformed mean ratio of
undigested:digested genomic DNA.
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.
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