|
| Status |
Public on Nov 01, 2008 |
| Title |
HRV-infected, asthmatic S16 (U133 Plus 2.0 Array) |
| Sample type |
RNA |
| |
|
| Source name |
HRV-infected PBE cells, asthmatic S16
|
| Organism |
Homo sapiens |
| Characteristics |
Human primary bronchial epithelial cells from patients with mild asthma, cultured in monolayers, passage 3
16 hours p.i.
|
| Treatment protocol |
One 6-well plate of PBE cells from every subject was either infected with 0.4 ml/well of rhinovirus dilution (10 PFU / cell), or incubated with medium alone for 1 hour at 34°C. After addition of 1.6 ml of growth medium to each well, cells were incubated for 15 hrs at 37°C.
|
| Growth protocol |
Frozen stocks of human PBE cells obtained from the bronchial brushings were grown in collagen-coated 75 cm2 flasks containing 10 ml of BEGM (Lonza) at 37°C, 5% CO2. When cells were about 80% confluent (usually 5-6 day intervals), they were seeded at 4-5 x 10e4 cells/well on collagen-coated 6-well plates and grown in 2 ml BEGM, for 3-4 days (37°C, 5% CO2).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA from adherent cells was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA, after overnight incubation at 37C (Expression Analysis Technical Manual).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C to Human Genome U133 Plus 2.0 GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the GeneChip® Scanner 3000 (Affymetrix).
|
| Description |
Gene expression data from HRV-infected PBE cells from asthmatic individual
|
| Data processing |
Fluorescent signal intensities were extracted from scanned images using Affymetrix default analysis settings of the GCOS version 1.4 software. A scaling factor of 1000 was applied to each array to bring the average signal intensity to the same level. HG U133 Plus 2.0 GeneChip quality control parameters for all samples were within recommended range. Log2-transformed expression values across all the chips were extracted using the Robust Multichip Average (RMA) method. Processing with RMA involved background correction, probe level quantile normalization across all the 22 chips and expression summarization.
|
| |
|
| Submission date |
Oct 29, 2008 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Yury A Bochkov |
| E-mail(s) |
yabochkov@wisc.edu
|
| Phone |
608-263-8553
|
| Organization name |
University Of Wisconsin-Madison
|
| Department |
Pediatrics
|
| Street address |
600 Highland Ave, K4/945 CSC
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53792-9988 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE13396 |
Rhinovirus-induced modulation of gene expression in bronchial epithelial cells from subjects with asthma |
|
| Relations |
| Reanalyzed by |
GSE119087 |
