|
| Status |
Public on Oct 08, 2007 |
| Title |
Wtepi_infect_24h_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
WT epithelium, Pseudomonas aeruginosa infected, 24h
|
| Organism |
Mus musculus |
| Characteristics |
Strain: C57BL/6, Tissue: Airway Epithlium, Culture: Organotypic Air Liquid Interface
|
| Treatment protocol |
Pseudomonas aeruginosa (PA51673) was exposed to cells at a MOI of 5 for 1 to 24 h
|
| Growth protocol |
Primary mouse airway epithelial cells were cultured at an air liquid interface
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen Rneasy total RNA extraction was performed according to manufacturer's specifications
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2-8 ug total RNA by the Center for Array Technologies at the University of Washington (Seattle, WA)
|
| |
|
| Hybridization protocol |
cRNA were hybridized overnight to Mouse 430 2.0 Arrays then washed in the Affymetrix Fluidics Station.
|
| Scan protocol |
Chips were treated with phycoerythyrin-conjugated streptavidin and scnned for hybridized targets with the GeneChip Scanner 3000
|
| Description |
Gene expression data for airway epithlium exposed to Pseudomonas aeruginosa
|
| Data processing |
The data were inspected visually and with the Affymetrix quality control metrics in the GeneChip Operating Software. Two replicates were discarded from futher analysis (WT-24h-rep1 and M10-24h-rep2) due to high background and high scale factor. Cel files were extracted using GCOS and normalized in Bioconductor in the R environment. All samples were normalized using RMA and mean centered by genotype using the RMA function in the Affymetrix package and the scale function of the base R environment.
|
| |
|
| Submission date |
May 30, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Sean Y Kassim |
| E-mail(s) |
seanyk@u.washington.edu
|
| Phone |
206-897-1307
|
| Organization name |
University of Washington
|
| Department |
Medicine, PCCM
|
| Lab |
Center for Lung Biology
|
| Street address |
815 Mercer St
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98105 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE7957 |
Expression data from Pseudomonas aeruginosa exposed airway epithelium from C57Bl6 and MMP-7 and MMP-10 deficient mice. |
|
| Relations |
| Reanalyzed by |
GSE119085 |
