|
| Status |
Public on Dec 31, 2011 |
| Title |
PBMCs_Control_2 [IS] |
| Sample type |
RNA |
| |
|
| Source name |
peripheral blood mononuclear cells
|
| Organism |
Homo sapiens |
| Characteristics |
affected status (disease state): control
gender: female
age-at-examination: 68
age-at-onset: n/a
geographical origin: Mirandela
clinical characteristics: Hypertension
|
| Treatment protocol |
Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the GeneChip scanner 3000 – 7G.
|
| Description |
group A of hybridized samples
|
| Data processing |
Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were performed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, performs quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin) in CORRECTED column.
|
| |
|
| Submission date |
Jun 09, 2010 |
| Last update date |
Jan 19, 2012 |
| Contact name |
Sofia A Oliveira |
| E-mail(s) |
[email protected]
|
| Phone |
+351 217 999 411
|
| Fax |
+351 217 999 412
|
| Organization name |
Instituto de Medicina Molecular
|
| Department |
Edificio Egas Moniz
|
| Lab |
P1C-76
|
| Street address |
Av. Prof Egas Moniz
|
| City |
Lisbon |
| State/province |
Portugal |
| ZIP/Postal code |
1649-028 |
| Country |
Portugal |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE22255 |
Blood genomic expression profile for ischemic stroke (IS) |
|
