Description

This track is produced as part of the ENCODE project. The track displays the methylation status of specific CpG dinucleotides in the given cell types as identified by the Illumina Infinium Human Methylation 450 Bead Array platform. In general, methylation of CpG sites within a promoter causes silencing of the gene associated with that promoter.

The Infinium Human Methylation 450 platform uses bisulfite treated genomic DNA to assay the methylation status of more than 450,000 CpG sites covering all designatable RefSeq genes, including promoter, 5' and 3' regions, without bias against those lacking CpG islands. Additionally, the assay includes CpG islands and shores, CpG sites outside of CpG islands, non-CpG methylated sites identified in human stem cells, differentially methylated sites identified in tumor versus normal (multiple forms of cancer) and across several tissue types, CpG islands outside of coding regions, miRNA promoter regions, and disease-associated regions identified through GWAS.

The detailed protocol, information for CpG targets, and beta values are available from the supplemental directory.

Display Conventions and Configuration

Scores associated with each site are beta values (see Methods) multiplied by 1000. Methylation status is color-coded as:

• orange = methylated (score >= 600)
• purple = partially methylated (200 < score < 600)
• bright blue = unmethylated (0 < score <= 200)
• black = NA (score = 0)

Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.

Methods

Cells were grown according to the approved ENCODE cell culture protocols.

Genomic DNA was isolated from each cell line with the QIAGEN DNeasy Blood & Tissue Kit according to the instructions provided by the manufacturer. DNA concentrations and a level of quality of each preparation was determined by fluorescence with the Qubit Fluorometer (Invitrogen). Genomic DNA was treated with sodium bisulfite, converting unmethylated cytosines of CpG dinucleotides into uracils; methylated cytosines did not get converted. After bisulfite treatment, the methylation status of a site was assayed by single base-pair extension with a Cy3 or Cy5 labeled nucleotide on oligo-beads specific for the methylated or unmethylated state.

The bisulfite conversion reaction was done using the Zymo Research EZ-96 DNA Methylation^TM Kit. One step of the protocol was modified. During the incubation, a 30 second 95^oC denaturing step every hour was included to increase reaction efficiency as recommended by the Illumina Infinium Human Methylation27 protocol.

The bead arrays were run according to the protocol provided by Illumina.

A beta value was calculated for each CpG target with Illumina's Bead Studio software with the Methylation Module v3.2. Beta-value = intensity value from the methylated bead type/(intensity values from the methylated + intensity value from unmethylated bead types + 100). The data was then quality-filtered using p-values. Beta values with p-value greater than 0.01 are considered to fall below the minimum intensity and threshold are displayed as "NA".

Any beta value equal to or greater than 0.6 was considered fully methylated. Any beta value equal to or less than 0.2 was considered to be fully unmethylated. Beta values between 0.2 and 0.6 were considered to be partially methylated.

Release Notes

This is Release 1 (Dec 2011) of the 450K bead array data, with data corrections applied to the displayed data tables in May 2012. A perl script to correct coordinates in the download files has been included in the download directory.

The initial release had incorrect probe mappings. The data providers also requested these annotations be limited to the first nucleotide in the probe, so the single CpG assayed is displayed instead of the full probe. When the Infinium platform was first released, it was thought that methylation states of CpG's within the 50 bp window could be assigned by assaying a single nucleotide, but it has since been determined that methylation states vary even at close distances.

Credits

These data were produced by the Dr. Richard Myers Lab and the Dr. Devin Absher lab at the HudsonAlpha Institute for Biotechnology.

Cells were grown by the Myers Lab and other ENCODE production groups.

Data Release Policy

Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here.