|
| Status |
Public on Dec 31, 2014 |
| Title |
1444-10C_3266 |
| Sample type |
genomic |
| |
|
| Source name |
ovarian cancer
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
histologic type: endometrioid
|
| 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 |
|
