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 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
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.
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) * 10These 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.
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.
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.