|
| Status |
Public on Feb 04, 2013 |
| Title |
Normal prostate NP_331 |
| Sample type |
genomic |
| |
|
| Source name |
Normal Prostate
|
| Organism |
Homo sapiens |
| Characteristics |
tissue site: Prostate
tissue type: Normal
sample id (short form for plotting): NP_331
description: Normal prostate
|
| Treatment protocol |
For MBD-SNP, samples were enriched for methylated DNA using magnetic-bead immobilized methyl-binding domain polypeptides as described previously (Yegnasubramanian et al., Nucl Acids Res, 2006; Yegnasubramanian et al., BMC Genomics, 2011). A unenriched total input sample that was otherwise treated the same, was used as a reference for each sample and was used to derive copy number estimates.
|
| Growth protocol |
DNA was obtained from metastatic prostate cancer tissues from the PELICAN rapid autopsy program at Johns Hopkins University, and from normal prostate tissues from organ donors.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using the manufacturer's recommended protocol
|
| Label |
Cy3 and Cy5
|
| Label protocol |
Standard Illumina protocol for Human Methylation450k DNA Analysis bead chip
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina Infinium Human Methylation450k Beadchip using the standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using a BeadArray Reader
|
| Data processing |
Data was normalized using the 'minfi' R package (Scale normalization, No background subtraction).
|
| |
|
| Submission date |
May 25, 2012 |
| Last update date |
Feb 04, 2013 |
| Contact name |
Martin Aryee |
| E-mail(s) |
aryee.martin@mgh.harvard.edu
|
| Organization name |
Massachusetts General Hospital
|
| Department |
Pathology
|
| Street address |
149 13th Street
|
| City |
Charlestown |
| State/province |
MA |
| ZIP/Postal code |
02129 |
| Country |
USA |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE38240 |
DNA methylation profiling of normal prostates and prostate cancer metastases [Illumina] |
| GSE38242 |
DNA methylation alterations exhibit striking intra-individual stability and inter-individual heterogeneity across metastatic dissemination |
|
