|
| Status |
Public on May 27, 2010 |
| Title |
whole blood, control replicate 4, test set, batch 3 |
| Sample type |
RNA |
| |
|
| Source name |
whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
dyt1 mutation status: WT
dystonia: control
hybridization batch: 3
dataset: test set
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole blood was collected in BD PAXgene Blood RNA Tubes (BD Diagnostics) according the recommendations of the manufacturer. RNA was extracted with PAXGene Blood RNA Kit (Qiagen) according to the manfacturer.
|
| Label |
biotin
|
| Label protocol |
Samples were enzymatically amplified, fragmented and biotinylated using GeneChip® Whole Transcript (WT) Sense Target Labeling Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip HuGene 1.0 ST v1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with fluidics protocol FS450_0001.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GCS3000 gene chip scanner using GCOS version 1.4 software with default settings.
|
| Description |
none
|
| Data processing |
Raw CEL-files were imported into Expression Console 1.0 (Affymetrix). PLIER was used for array normalization and signal calculation independently for each hybridization batch. Normalized signal values were imported into Genespring GX 7.3 (Agilent Technologies) and gene wise Z-score normalization across all samples of each hybridization batch was applied.
|
| |
|
| Submission date |
Dec 10, 2009 |
| Last update date |
May 27, 2010 |
| Contact name |
Michael H. Walter |
| E-mail(s) |
michael.walter@agilent.com
|
| Organization name |
University of Tuebingen
|
| Department |
Department of Medical Genetics
|
| Lab |
The Microarray Facility Tübingen
|
| Street address |
Calwer Str. 7
|
| City |
Tuebingen |
| ZIP/Postal code |
72076 |
| Country |
Germany |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE19419 |
Blood expression profiles define penetrance in DYT1 dystonia patients |
|
