|
| Status |
Public on Jan 28, 2009 |
| Title |
Smoker 3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Spermatozoa obtained from frozen pure ejaculate
|
| Organism |
Homo sapiens |
| Characteristics |
Ejaculate collected by masturbation, pure ejaculate snap-frozen
|
| Treatment protocol |
Sperm collection into appropriate containers.
|
| Growth protocol |
No growth protocols were used as RNA was extracted from sperm without any ex vivo performances.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolation with Qiagen RNA MinElute RNA Isolation Kit according to manufacturer's instructions, including an additional DNAse treatment.
|
| Label |
Cy5
|
| Label protocol |
Agilent Low RNA Input Linear Amplification system according to the manufacturer's instructions.
|
| |
|
| Channel 2 |
| Source name |
common reference sample composed of spermatozoal total RNA isolated from one non-smoking subject
|
| Organism |
Homo sapiens |
| Characteristics |
n/a
|
| Treatment protocol |
Sperm collection into appropriate containers.
|
| Growth protocol |
No growth protocols were used as RNA was extracted from sperm without any ex vivo performances.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolation with Qiagen RNA MinElute RNA Isolation Kit according to manufacturer's instructions, including an additional DNAse treatment.
|
| Label |
Cy3
|
| Label protocol |
Agilent Low RNA Input Linear Amplification system according to the manufacturer's instructions.
|
| |
|
| |
| Hybridization protocol |
Hybridization according to Agilent instructions.
|
| Scan protocol |
Scanning on GenePix 4000B (Molecular Devices). All slides were scanned with set laser power at 100% and photomultiplier gain at 69,9% for Cy5 and 64,5% for Cy3 channel based on automatic establishment of ideal scan settings
|
| Description |
none
|
| Data processing |
Data preparations were performed in GeneSight software (BioDiscovery) andf included in chronological order: background subtraction, omission of bad spots (controls and irregularly shaped spots), LOWESS normalization, log (base=2) transformations, calculation of difference of Cy5 (test) with Cy3 (common reference) sample
|
| |
|
| Submission date |
Nov 13, 2008 |
| Last update date |
Jan 27, 2009 |
| Contact name |
Joost Linschooten |
| E-mail(s) |
Joost.Linschooten@GRAT.unimaas.nl
|
| Phone |
+31 (0)43 388 1088
|
| URL |
http://www.grat.nl
|
| Organization name |
Maastricht University
|
| Department |
Health Risk Analysis & Toxicology
|
| Street address |
Universiteitssingel 50
|
| City |
Maastricht |
| ZIP/Postal code |
PO Box 616, 6200 MD |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE13600 |
Use of spermatozoal total RNA profiles to study gene-environment interactions in human germ cells |
|
