|
| Status |
Public on Apr 24, 2009 |
| Title |
BL307 |
| Sample type |
RNA |
| |
|
| Source name |
Bronchial biopsies from lung tissue
|
| Organism |
Homo sapiens |
| Characteristics |
age: adult
gender: female
tissue: lung
|
| Treatment protocol |
The tissue samples were immediately placed in RNAlater (Ambion) to stabilize intracellular RNA during transport.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Biopsies were obtained from the sub-segmental and segmental bronchial carinae of the lower (3–5 biopsies) and upper (1–2 biopsies) lobes, as well as the lobar carinae of the middle (2 biopsies) and upper (1–2 biopsies) lobes to provide adequate samples of the large airways (3rd to 5th bronchial generation). When bronchoscopy was repeated after ICS treatment, biopsies were taken from the left lung at similar bronchial levels. The samples were mechanically homogenized (Rotor/Stator homogeniser, PowerGen) and total RNA was extracted using the RNEasy kit (Qiagen) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated probe was prepared from the entire cDNA reaction mixture with the ENZO bioarray high-yield RNA transcript labeling kit (ENZO diagnostics).
|
| |
|
| Hybridization protocol |
Following fragmentation, 5 ug of cRNA were hybridized at 45C overnight (16–20 hours). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
Following washing, the specifically bound probe was detected by incubating the arrays with SAPE (streptavidin phycoerthryin, Molecular Probes) and scanning the chips using a Gene Array Scanner (Agilent).
|
| Description |
allergic asthma 02, post ICS treatment
DV020808HGA12.CEL
|
| Data processing |
The scanned images were analyzed using the Microarray Analysis Suite 5.0 (MAS5, Affymetrix). Data was extracted using MAS5 and filtered to exclude genes that were not expressed (taken to be equivalent to a MAS5 absent call) in all samples.
|
| |
|
| Submission date |
Apr 24, 2009 |
| Last update date |
Jun 26, 2012 |
| Contact name |
Catherine Laprise |
| Organization name |
Université du Québec à Chicoutimi
|
| Street address |
555 Boul. Université
|
| City |
Chicoutimi |
| State/province |
Qc |
| ZIP/Postal code |
G7H 2B1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL8300 |
| Series (1) |
| GSE15823 |
Functional classes of bronchial mucosa genes that are differentially expressed in asthma |
|
