|
| Status |
Public on May 01, 2010 |
| Title |
SCO_11_c |
| Sample type |
RNA |
| |
|
| Source name |
testicular biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
deletion: AZFc
histology: SCO
|
| Treatment protocol |
Testicular biopsies were obtained from open surgery and classified based on homogeneous histology with no discrepancy to paralle biopsies and test-TESE.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Biopsies were homogeneized in RNApure (Peqlab, Germany) with an Ultra-Thurrax and total RNA repurified on RNeasy columns (Qiagen, Germany). Quality control was done with a Bioanalyzer (Agilent, USA).
|
| Label |
Cy5
|
| Label protocol |
total RNA was amplified with the MessageAmp III Kit (Ambion, USA) and Biotin-UTP incorporated as a label.
|
| |
|
| Hybridization protocol |
Hybridization was conducted for 20h at 37°C and arrays washed in 1x TNT (10 min, RT) and 1x TNT (60 min, 46°C). Staining with Cy5-Streptavidin was done for 30 min at RT. Then, arrays were washed 2 times with 1x TNT for 10 min and 0.2x SSPE for 30s. They were spin-dried in a centrifuge at 2000 rpm for 2 min.
|
| Scan protocol |
Scanning was done on an Affymetrix 428 Scanner (Affymetrix, USA) at PMT 70 settings using the Jaguar 2.0 software for image acquisition.
|
| Description |
Patient with Sertoli-cell only syndrome and AZFc deletion #4
|
| Data processing |
Scan images were converted to raw values by the CodeLink Expression analysis software (GE Healthcare, USA) and these normalized by quantile normalization using the Bioconducter package 'affy'.
|
| |
|
| Submission date |
Apr 30, 2010 |
| Last update date |
Apr 30, 2010 |
| Contact name |
Andrej-Nikolai Spiess |
| E-mail(s) |
a.spiess@uke.uni-hamburg.de
|
| Phone |
+49-40-42803-1585
|
| Fax |
+49-40-42803-1554
|
| URL |
http://www.dr-spiess.de
|
| Organization name |
University Hospital Hamburg-Eppendorf
|
| Department |
Andrology
|
| Lab |
Molecular Andrology
|
| Street address |
Martinistr. 52
|
| City |
20246 Hamburg |
| State/province |
n/a |
| ZIP/Postal code |
n/a |
| Country |
Germany |
| |
|
| Platform ID |
GPL2891 |
| Series (1) |
| GSE21613 |
Analysis of testicular transcriptome changes in the presence of Y-chromosomal microdeletions |
|
