|
| Status |
Public on Oct 18, 2012 |
| Title |
c.2 |
| Sample type |
RNA |
| |
|
| Source name |
control_bronchial biopsies
|
| Organism |
Homo sapiens |
| Characteristics |
disease status: non allergic non asthmatic subject, without any stimulation
tissue: bronchial biopsies
|
| Growth protocol |
Biopy protocol: 8 biopsies evaluated as acceptable by the research assistant were taken from bronchi of the right lung using alligator forceps (Olympus FB-15C-1). Biopsies were obtained from the ubsegmental and segmental bronchial carinae of the lower (3 to 5 biopsies) and upper (1 to 2 biopsies) lobes, as well as the lobar carinae of the middle (2 biopsies) and upper (1 to 2 biopsies) lobes to provide adequate samples of the large airways (3rd to 5th bronchial generation). The samples were immediately placed in RNAlater.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The samples were mechanically homogenized (Rotor/Stator homogenizer; PowerGen) and total RNA was extracted using the RNEasy kit (Qiagen) according to the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
Probe labelling was done at the McGill University and Genome Quebec Innovation Centre (www.genomequebec.mcgill.ca) and was performed in parallele for control and asthmatic samples.
|
| |
|
| Hybridization protocol |
Hybridation was done at the McGill University and Genome Quebec Innovation Centre (www.genomequebec.mcgill.ca) and was performed in parallele for control and asthmatic samples
|
| Scan protocol |
Scanning was done using a GeneArray Scanner at the McGill University and Genome Quebec Innovation Centre (www.genomequebec.mcgill.ca) and was performed in parallele for control and asthmatic samples
|
| Description |
SAMPLE 2
|
| Data processing |
The scanned images were analyzed using the Microarray Analysis Suite 5.0 (MAS5, Affymetrix) and the raw image fils obtained (.CEL) were used for statistical analyses. To calculate gene expression, the robust multiarray analysis (RMA) was used. To identify significant differences in gene expression, a pairwise comparison between control and allergic asthmatic subjects was performed with the microarray results, in the first case with the Limma package available in Bioconductor. However, no correction was applied when using the U133A GeneChips since the RMA method is more stringent. However, Smyth’s moderated t test was used.
|
| |
|
| Submission date |
Oct 17, 2012 |
| Last update date |
Oct 18, 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 |
GPL96 |
| Series (1) |
| GSE41649 |
Comparison of two sets of microarray experiments to define allergic asthma expression pattern |
|
