|
| Status |
Public on Apr 17, 2008 |
| Title |
Prachatice child 16 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
human whole blood collected into PAXgene RNA vacutainer by venapuntcure in the inner elbow
|
| Organism |
Homo sapiens |
| Characteristics |
whole blood collected into PAXgene RNA vacutainer by venapuntcure in the inner elbow from Prachatice individual
|
| Treatment protocol |
Blood collection into PAXgene RNA vacutainers.
|
| Growth protocol |
No growth protocols were used as RNA was extracted from blood without any ex vivo performances.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolation with PAXgene Blood RNA system according to manufacturer's instructions. Additional DNAse treatment and concentration of material with Qiagens MinElute system according to manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
Agilent Low RNA Input Linear Amplification system according to the manufacturer's instructions.
|
| |
|
| Channel 2 |
| Source name |
common reference sample compsed of total RNAs isolated from whole blood from 20 Prachatice children
|
| Organism |
Homo sapiens |
| Characteristics |
whole blood collected into PAXgene RNA vacutainer by venapuntcure in the inner elbow
|
| Treatment protocol |
Blood collection into PAXgene RNA vacutainers.
|
| Growth protocol |
No growth protocols were used as RNA was extracted from blood without any ex vivo performances.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolation with PAXgene Blood RNA system according to manufacturer's instructions. Additional DNAse treatment and concentration of material with Qiagens MinElute system according to manufacturer's instructions.
|
| 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 ScanArrayExpress (Perkin Elmer). All slides were scanned with set laser power at 100% and photomultiplier gain at 55% for Cy5 and 60% for Cy3 channel based on previous establishment of ideal scan settings
|
| Description |
Blood collected from Prachatice children which live in an area with low levels of air pollution
|
| 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 |
Apr 18, 2007 |
| Last update date |
Apr 20, 2007 |
| Contact name |
Danitsja Maria van Leeuwen |
| Organization name |
Maastricht University
|
| Department |
Health Risk Analysis and Toxicology
|
| Street address |
PO Box 616
|
| City |
Maastricht |
| ZIP/Postal code |
6200 MD |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL887 |
| Series (1) |
| GSE7543 |
Differential gene expression between individuals exposed to different levels of air pollution |
|
