|
| Status |
Public on Jul 01, 2012 |
| Title |
Ejaculate not resulting in oocyte fertilization, F46 |
| Sample type |
RNA |
| |
|
| Source name |
ejaculate after 30 min liquefaction
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: ejaculate
ivf outcome: no oocyte fertilization
motility (a+b) [%]: 42
ejaculate volume: 6.7
concentration [10e6/ml]: 46
oocytes in metaphase ii: 1
age of woman [years]: 25
fertilisation ratio [%] (2pn/mii): 0.0
cumulative embryo score: n.v.
pregnancies: n.v.
|
| Treatment protocol |
Human ejaculates were liquefied for 30 min at 37°C, and an aliquot of 1 mL was washed once by centrifugation in PBS (500 g).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from the ejaculates by a specially designed two-fold genomic DNA pre-elimination protocol (Rneasy Micro). Details are to be found under http://www.dr-spiess.de/supp/MHRCappallo2011/RNA.pdf.
|
| Label |
biotin
|
| Label protocol |
50 - 500 ng total RNA were amplified with the MessageAmp III Kit (Ambion, USA), and Biotin-UTP was incorporated as a label.
|
| |
|
| Hybridization protocol |
Hybridization was conducted for 20h at 37°C, and arrays were 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 a ScanArray Gx Scanner (Perkin Elmer) at PMT 70/LP 90% setting and 5um resolution. Images were acquired with the ScanArray Express 3.0 software (Perkin Elmer).
|
| Description |
F46
|
| Data processing |
Scan images were converted to raw values by the CodeLink Expression analysis software (GE Healthcare, USA). Genes with lower than 5th percentile expression values over all samples were removed. Normalization was by quantile normalization using the Bioconducter package 'affy'.
|
| |
|
| Submission date |
May 02, 2011 |
| Last update date |
Jul 01, 2012 |
| 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 |
GPL2895 |
| Series (1) |
| GSE29002 |
The transcriptome of ejaculates used for successful/failed in vitro-fertilization |
|
