|
| Status |
Public on Dec 23, 2014 |
| Title |
6264509130_2_Tumor_prostate_cancer_Gleason6_HM450K |
| Sample type |
genomic |
| |
|
| Source name |
Prostate 3
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
disease state: Gleason 6 prostate cancer
tissue: prostate cancer tumor
|
| Growth protocol |
Patients undergoing radical prostatectomy for prostate cancer had fresh frozen samples of cancer as well as adjacent benign prostate tissue prospectively stored in a cancer biorepository program (http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/pubmed/22406482)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from the homogenized samples using the Allprep Micro Kit (Qiagen, CA, USA) following manufacturer’s instructions and bisulfite converted using the Zymo EZ DNA Methylation kit (Zymo Research Corporation, CA, USA). The resulting libraries were hybridized onto the Illumina HumanMethylation450 BeadChip.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 (HM450K bead array) Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
Gleason 6 cancer
|
| Data processing |
Raw intensity data was generated using an iScan microarray reader (Illumina).
|
| |
|
| Submission date |
Jun 13, 2013 |
| Last update date |
Dec 23, 2014 |
| Contact name |
Haroon Naeem |
| Organization name |
Monash University
|
| Department |
Monash Bioinformatics Platform
|
| Street address |
15 Innovation Walk (Room G98), Wellington Road
|
| City |
Melbourne |
| State/province |
Clayton, VIC |
| ZIP/Postal code |
3800 |
| Country |
Australia |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE47915 |
Human Prostate Cancer Illumina Infinium Human Methylation450 (HM450K bead array) BeadChip samples (benign vs tumor) |
|
