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Sample GSM196078 Query DataSets for GSM196078
Status Public on Oct 08, 2007
Title M7KOepi_infect_24h_rep3
Sample type RNA
 
Source name Mmp7-/- 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

Data table header descriptions
ID_REF
VALUE mean-centered log2 RMA data

Data table
ID_REF VALUE
1415670_at 0.148218889
1415671_at -0.094150045
1415672_at 0.260340949
1415673_at 0.052984927
1415674_a_at 0.199673581
1415675_at -0.374307013
1415676_a_at -0.126913143
1415677_at -0.227486678
1415678_at -0.246642245
1415679_at -0.027246562
1415680_at 0.081822616
1415681_at -0.244202487
1415682_at -0.279699418
1415683_at 0.327870101
1415684_at -0.203586831
1415685_at -0.687180724
1415686_at 0.088992608
1415687_a_at -0.243771976
1415688_at -0.000507928
1415689_s_at -0.307409496

Total number of rows: 45101

Table truncated, full table size 1047 Kbytes.




Supplementary file Size Download File type/resource
GSM196078.CEL.gz 3.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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