|
| Status |
Public on May 09, 2009 |
| Title |
Pool 3 Acute stage |
| Sample type |
RNA |
| |
|
| Source name |
Acute samples
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: PBMC
disease state: Acute
|
| Treatment protocol |
Peripheral blood was collected during acute exacerbation post glucocorticoid treatment (inhaled salbutamol and ipratropium bromide at 20 min intervals for first hour, and oral prednisolone 1mg/kg) and at convalescence ≥ six weeks later and cryopreserved.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cryopreserved PBMCs using TRIzol followed by RNeasy as according to the manufacturer's instructions. Equal amounts of RNA from 5 subjects were pooled, either at acute exacerbation or convalescent stage, to give a total of 10 pools for analysis.
|
| Label |
Biotin
|
| Label protocol |
Labeled cRNA were prepared according to the standard Affymetrix protocol from 1 ug of total pooled RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 h at 45°C on Affymetrix U133Plus2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix Scanner 3000.
|
| Description |
n/a
|
| Data processing |
Microarray data were analysed in the open-source statistical software R employing the probe-level model (PLM) algorithm for background subtraction, normalization and summarization of probe set intensities.
|
| |
|
| Submission date |
May 08, 2009 |
| Last update date |
May 08, 2009 |
| Contact name |
Kathy Laura McKenna |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute for Child Health Research
|
| Street address |
100 Roberts Rd
|
| City |
Perth |
| State/province |
Western Australia |
| ZIP/Postal code |
6008 |
| Country |
Australia |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE16032 |
Gene expression data from severe asthmatic children: PBMC profiles during acute exacerbation versus convalescence |
|
