|
| Status |
Public on Dec 30, 2011 |
| Title |
epithelium Alt, rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Lung epithelium transcripts 24hr after Alternaria challenge
|
| Organism |
Mus musculus |
| Characteristics |
tissue: bronchial epithelium
strain: C57/B6
age: 6 weeks
|
| Treatment protocol |
Prior to performing epithelial brushing, BAL was performed to remove BAL cells. The bronchial brushing was performed using a sterile plastic feeding tube (Solomon Scientific) modified by removal of the rubber bulb, sanding to create roughness, and autoclaving. The tube was inserted into the right main and left main bronchus with gentle brushing and immediately placed in RNAlater (Qiagen).
|
| Growth protocol |
Mice were housed in university vivarium and fed normal diet
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Airway epithelial cells obtained by bronchial brushing were lysed by multiple passages through an 18G needle. RNA was then extracted according to manufacturer’s protocol (Qiagen). Isolated epithelial RNA with sufficient purity (A260/280 = 1.97-2.12) and yield (8.99-12.66 ng/ul) was used for microarray analysis (GeneChip Mouse Gene 1.0 ST, Affymetrix).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Gene 1.0 ST. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
Gene expression data from lung epithelium 24 hours after Alternaria allergen challenge
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
|
| |
|
| Submission date |
Dec 29, 2011 |
| Last update date |
Dec 30, 2011 |
| Contact name |
Taylor Doherty |
| Organization name |
UC San Diego
|
| Street address |
9500 Gilman Dr 0635
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92078 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE34764 |
Expression data from mouse lung epithelium after allergen challenge |
|
