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Status |
Public on Oct 08, 2007 |
Title |
M10KOepi_infect_24h_rep1 |
Sample type |
RNA |
|
|
Source name |
Mmp10-/- 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.
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|
|
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 |