|
| Status |
Public on Aug 29, 2011 |
| Title |
prostate cancer_sample_2 [aCGH] |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
prostate cancer_recurrence, castration-resistant
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Castration-resistant prostate cancer
treatment: Orchiectomy, Androcur
tissue: prostate cancer tumor
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from the samples after overnight proteinase K treatment using standard protocols.
|
| Label |
Cy5
|
| Label protocol |
12 µg of genomic DNA was digested overnight with AluI and RsaI, followed by standard phenol-chloroform purification. 3 µg of digested tumor DNA and reference DNA was labeled with Cy5-dUTP and Cy3-dUTP (PerkinElmer, Waltham, MA), respectively, in a random priming reaction using Bioprime Array CGH Genomic Labeling Module (Invitrogen).
|
| |
|
| Channel 2 |
| Source name |
Male genomic DNA, Promega, Cat# G1471
|
| Organism |
Homo sapiens |
| Characteristics |
reference: Promega normal male genomic DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from the samples after overnight proteinase K treatment using standard protocols.
|
| Label |
Cy3
|
| Label protocol |
12 µg of genomic DNA was digested overnight with AluI and RsaI, followed by standard phenol-chloroform purification. 3 µg of digested tumor DNA and reference DNA was labeled with Cy5-dUTP and Cy3-dUTP (PerkinElmer, Waltham, MA), respectively, in a random priming reaction using Bioprime Array CGH Genomic Labeling Module (Invitrogen).
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed according to the protocol (oligonucleotide array-based CGH for genomic DNA analysis, protocol version 2.0, August 2005, Agilent Technologies).
|
| Scan protocol |
Arrays were scanned with a laser confocal scanner (Agilent Technologies).
|
| Data processing |
Feature Extraction software (version 8.1.1.1, Agilent Technologies) was used for image analysis using manufacturer’s recommended settings (44K_CGH_0605).
|
| |
|
| Submission date |
Apr 06, 2011 |
| Last update date |
Aug 29, 2011 |
| Contact name |
Maija K Wolf |
| E-mail(s) |
maija.wolf@helsinki.fi
|
| Organization name |
Institute for Molecular Medicine Finland (FIMM)
|
| Street address |
Biomedicum Helsinki 2U, Tukholmankatu 8,
|
| City |
Helsinki |
| ZIP/Postal code |
FIN-00290 |
| Country |
Finland |
| |
|
| Platform ID |
GPL2873 |
| Series (1) |
| GSE28403 |
Integrative genomic, transcriptomic and RNAi analysis indicates a potential oncogenic role for FAM110B in castration-resistant prostate cancer. |
|
