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Sample GSM1253288 Query DataSets for GSM1253288
Status Public on Dec 31, 2014
Title 1444-11H_3310
Sample type genomic
 
Source name ovarian cancer
Organism Homo sapiens
Characteristics gender: female
histologic type: clear cell
Growth protocol Samples were embedded in optimal cutting temperature medium and stored at -80 degrees celsius prior to use. All sections were cut and mounted on slides to confirm ≥60% tumor content with ≤20% necrosis.
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from frozen tissues using the AllPrep DNA/RNA/Protein Mini Kit (Qiagen).
Label Cy3, Cy5
Label protocol Standard Illumina Protocol
 
Hybridization protocol Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
Scan protocol Arrays were imaged using HiScan using standard recommended Illumina scanner setting
Data processing Please note that raw data (beta values) was used for data analysis. Normalization or filtering was not performed since there was excellent correlation between the beta values for a substantial number of CpG sites and the methylation % for these same CpGs obtained by bisulfite pyrosequencing. The beta values were taken directly from Illumina's Genome Studio v2010.3 software.
The non_normalized.txt contains unmethylated and methylated signal intensities.
 
Submission date Oct 28, 2013
Last update date Dec 31, 2014
Contact name Susan K. Murphy
Organization name Duke University Medical Center
Department Obstetrics and Gynecology
Street address B226 LSRC B Wing, Research Drive, Box 91012
City Durham
State/province NC
ZIP/Postal code 27708
Country USA
 
Platform ID GPL13534
Series (1)
GSE51820 DNA methylation profiles of primary ovarian cancers

Data table header descriptions
ID_REF
VALUE Average Beta
Detection Pval

Data table
ID_REF VALUE Detection Pval
cg00000029 0.1767442 0.00
cg00000108 0.8983687 0.00
cg00000109 0.8593631 0.00
cg00000165 0.6201336 0.00
cg00000236 0.7644458 0.00
cg00000289 0.6528066 0.00
cg00000292 0.821927 0.00
cg00000321 0.5829039 0.00
cg00000363 0.1734639 0.00
cg00000622 0.03059571 0.00
cg00000658 0.7988197 0.00
cg00000714 0.3298271 0.00
cg00000721 0.8747616 0.00
cg00000734 0.09478544 0.00
cg00000769 0.07568827 0.00
cg00000807 0.7792499 0.00
cg00000884 0.7821906 0.00
cg00000905 0.1550288 0.00
cg00000924 0.3395042 0.00
cg00000948 0.8298347 0.00

Total number of rows: 485577

Table truncated, full table size 12383 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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