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Series GSE40700 Query DataSets for GSE40700
Status Public on Sep 07, 2012
Title CpG Methylation by Illumina Methyl27 Bead Arrays from ENCODE/HAIB
Project ENCODE
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Florencia Pauli mailto:[email protected]). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:[email protected]).
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 HumanMethylation27 BeadArray platform (http://www.illumina.com/pages.ilmn?ID=243). In general, methylation of CpG sites within a promoter causes silencing of the gene associated with that promoter.
Detailed information for the CpG targets is in an XLS formatted spreadsheet on the Myers' lab protocols website (http://hudsonalpha.org/myers-lab/protocols).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
 
Overall design Cells were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell).
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).
The Methyl27K platform uses bisulfite treated genomic DNA to assay the methylation status of 27,578 CpG sites within more than 14,000 genes. When genomic DNA is treated with sodium bisulfite, unmethylated cytosine of CpG dinucleotides are converted into uracils; methylated cytosines do not get converted. After bisulfite treatment, the methylation status of a site is assayed by single base-pair extension with a Cy3 or Cy5 labeled nucleotide on oligo-beads specific for the methylated or unmethylated state. A beta value is calculated by Illumina's Bead Studio software for each CpG target. This value represents the intensity value from the methylated bead type divided by the sum of the intensity values from the methylated and unmethylated bead types for any given CpG target.
Bisulfite conversion reaction was done using the Zymo Research EZ-96 DNA Methylation Kit (http://www.zymoresearch.com/epigenetics/dna-methylation/ez-96-dna-methylation-kit). One step of the protocol was modified. During the incubation, a 30 sec 95oC 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 (http://www.illumina.com/pagesnrn.ilmn?ID=275).
The intensity data from the BeadArray was processed using Illumina's BeadStudio software with the Methylation Module v3.2. The data was then quality-filtered using p-values.
Any beta value equal to or greater than 0.6 is considered fully methylated. Any beta value equal to or less than 0.2 is considered to be fully unmethylated. Beta values between 0.2 and 0.6 are considered to be partially methylated. Beta-values are quality filtered and spots that fall below the minimum intensity threshold are displayed as "NA".
Score in the bed files is beta value x 1000
Web link http://genome-preview.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeHaibMethylArray
 
Contributor(s) Myers R, Absher D, Pauli F
Citation missing Has this study been published? Please login to update or notify GEO.
BioProject PRJNA63443
Submission date Sep 07, 2012
Last update date Jan 02, 2015
Contact name ENCODE DCC
E-mail(s) [email protected]
Organization name ENCODE DCC
Street address 300 Pasteur Dr
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
 
Platforms (1)
GPL8490 Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2)
Samples (63)
GSM999397 HudsonAlpha_MethylArray_H1-hESC_Methyl27
GSM999398 HudsonAlpha_MethylArray_GM12892_Methyl27
GSM999399 HudsonAlpha_MethylArray_GM12891_Methyl27

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE40700_RAW.tar 40.7 Mb (http)(custom) TAR (of BED, BED9)
Processed data provided as supplementary file
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