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Sample GSM398361 Query DataSets for GSM398361
Status Public on Apr 29, 2009
Title 1519111021_B [18h training; Pseudomonas infected]
Sample type RNA
 
Source name lung 18h after challenge
Organism Mus musculus
Characteristics strain: BALB/c
tissue: lung
age: 5-8 wk old
Extracted molecule total RNA
Extraction protocol At designated timepoints after the infectious challenge, the mice were anesthetized and sacrificed. To reduce the gene expression signal of circulating leukocytes in the pulmonary vasculature, the pulmonary vasculature was exsanguinated and the pulmonary arterial system was flushed with PBS. The lungs were also submitted to repeated BAL to reduce the leukocyte burden of the airspaces. The lungs were then excised, homogenized, and total RNA was isolated using the RNeasy system (Qiagen, Valencia, CA). cRNA was synthesized, then amplified, from equal masses of total RNA extracted from the lungs of infected/sham challenged mice using the Ilumina TotalPrep RNA amplification kit (Ambion, Austin, TX).
Label Cy3
Label protocol Hybridized cRNA was labeled for 10 minutes with Cy3.
 
Hybridization protocol Amplified cRNA was then hybridized and labeled on Sentrix Mouse-6 Expression BeadChips (Illumina, Inc., San Diego, CA).
Scan protocol All microarrays were scanned on a BeadStation 500 (Illumina).
Description Pa 1: pseudomonas infected
Data processing Data were background corrected using the RMA method, then transformed by taking the base-two logarithm, and quantile normalized. Analysis of the microarray output was performed using a one-way ANOVA to identify infection-induced changes. P values were modeled using a beta-uniform mixture (BUM) model (30), and combined with false discover rate to determine a cutoff of p values. The analysis program was written in R (R Foundation for Statistical Computing, Vienna, Austria), utilizing the Illumina library developed by Simon Lin and Pan Du, Northwestern University.
 
Submission date Apr 28, 2009
Last update date Apr 28, 2009
Contact name Scott E Evans
E-mail(s) seevans@mdanderson.org
Organization name University of Texas-M.D. Anderson Cancer Center
Department Pulmonary Medicine - Unit 1462
Street address 1400 Holcombe Blvd
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL6099
Series (1)
GSE15869 Host lung gene expression patterns predict the etiology of infectious pneumonias

Data table header descriptions
ID_REF
VALUE Processed data were normalized using a rank invariant strategy in Illumina BeadStudio software.
BEAD_STDERR
Avg_NBEADS
Detection Pval

Data table
ID_REF VALUE BEAD_STDERR Avg_NBEADS Detection Pval
105290026 10.82493 3.587865 63 0.5639752
610369 26.8057 4.078808 53 0.1552795
1450014 -9.710875 3.968248 49 0.9863354
380019 36.92268 7.734995 42 0.08198757
100430441 10.11729 4.012269 34 0.5900621
610088 50.61744 5.912528 41 0.04285714
870181 5.773894 4.863706 38 0.7360249
103060390 8.954506 4.624493 44 0.6279503
4480390 4.846859 4.478804 31 0.7695652
101940014 4.03546 3.480411 48 0.7962733
103290520 5.349839 3.693536 56 0.7509317
102810300 13.35297 5.517816 34 0.4745342
104850707 7.193389 3.461404 46 0.684472
102100279 37.28646 5.104343 50 0.07826087
3360075 67.57446 6.728399 59 0.01304348
4610433 44.10514 7.001081 38 0.06024845
2230451 11.67725 4.361809 50 0.5403727
5360687 10.83309 4.843952 42 0.5639752
450537 390.4994 20.39817 52 0
5860368 0.8824235 5.237316 44 0.8795031

Total number of rows: 45988

Table truncated, full table size 1736 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record

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