GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM196076 Query DataSets for GSM196076
Status Public on Oct 08, 2007
Title M7KOepi_infect_24h_rep1
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
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.
Reanalyzed by GSE119085

Data table header descriptions
VALUE mean-centered log2 RMA data

Data table
1415670_at 0.370395039
1415671_at -0.248299138
1415672_at -0.026207197
1415673_at 0.552005721
1415674_a_at 0.272085932
1415675_at -0.417611718
1415676_a_at -0.03468967
1415677_at -0.123092622
1415678_at -0.267442356
1415679_at 0.148423586
1415680_at 0.081653282
1415681_at -0.05040256
1415682_at -0.248744112
1415683_at 0.371729497
1415684_at -0.287249948
1415685_at -0.499089402
1415686_at 0.011895637
1415687_a_at 0.015071908
1415688_at 0.023756818
1415689_s_at -0.860276039

Total number of rows: 45101

Table truncated, full table size 1048 Kbytes.

Supplementary file Size Download File type/resource
GSM196076.CEL.gz 3.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap