|
| Status |
Public on Jun 25, 2013 |
| Title |
BP patient 79_biological replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
medicated bipolar patient
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: leukocytes from whole blood
genotype: bipolar patient
age: 24
gender: male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from leukocytes using the QIAamp RNA Blood Mini Kit (Qiagen), with an off-collumn Dnase (Qiagen) treatment followed by purification using an RNeasy MinElute column (Qiagen). All procedures were performed according to the manufacturer's instructions (Qiagen).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA was hybridized to an Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400, using standard procedures.
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner 3000 with Autoloader
|
| Data processing |
The data were analyzed using BRB-Array Tools versions: 3.8.1 (as described in the manuscript) and 4.2.1 (the processed matrix GEO data). Cell files were imported into the BRBArray Tools package, and converted to normalized intensity values using the Almost RMA (aRMA) algorithm. A total of 199 cel files were imported into the project, including expression data obtained from patients with other psychiatric disorders. Normalized intensity values reflect the a-RMA parameters employed across the entire sample dataset. Analyses were performed on the sub-set of samples relevent to the study hypothesis. Cel files and processed matrix data for those samples are uploaded here.
|
| |
|
| Submission date |
Apr 29, 2013 |
| Last update date |
Jun 25, 2013 |
| Contact name |
Catherine Clelland |
| E-mail(s) |
[email protected]
|
| Organization name |
Columbia University Medical Center
|
| Street address |
630 West 168th Street, P&S 12-461A
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE46449 |
Expression data from Patients with Bipolar (BP) Disorder and Matched Control Subjects |
|
