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Sample GSM489039 Query DataSets for GSM489039
Status Public on Dec 23, 2009
Title clock-428
Sample type RNA
 
Source name LR-CC
Organism Mus musculus
Characteristics tissue: whole lung
genome/variation: LR-CC (a Clara cell-targeted K-ras mutant)
treatment group: NTHi treated
treatment time: 1 d after last treatment
Treatment protocol WT or CC-LR mice were either challenged with NTHi lysate or sensitized to ovalbumin by intraperitoneal injection weekly for two weeks, then challenged for 30 min to an aerosol of ovalbumin in 0.9% saline weekly for eight weeks. Mice from each group were euthanized on day one after the last exposure for comparison. To reduce the lung leukocyte burden, the pulmonary vasculature was perfused and the airways lavaged with PBS.
Extracted molecule total RNA
Extraction protocol The lungs were mechanically homogenized, then total RNA was isolated from lung homogenates using the RNeasy system (Qiagen, Valencia, CA), and cRNA was synthesized and amplified from equal masses of total RNA using the Ilumina TotalPrep RNA amplification kit (Ambion, Austin, TX).
Label Cy3
Label protocol cRNA was hybridized to BeadChips prior to labeling with Cy3-Streptavidin per Illumina instructions.
 
Hybridization protocol cRNA was hybridized to BeadChips per Illumina instructions.
Scan protocol Chips were scanned using level 3 signal using a BeadStation 500 scanner.
Description k-ras, NTHi treated
Data processing Data was processed using Illumina BeadStudio v3. Matrix tables were generated both without normalization and with rank invariant normalization, using sham group as the reference group. Values reported were derived using Illumina BeadStudio v3 and are relative signal intensity normalized to background.
 
Submission date Dec 22, 2009
Last update date Dec 22, 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 - Box 403
Street address 1400 Holcombe Blvd
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL6885
Series (1)
GSE19605 Specificity for the Nature of Inflammation in Lung Cancer Promotion in Mice

Data table header descriptions
ID_REF
VALUE rank invariant normalized (BeadStudio v3) signal intensity

Data table
ID_REF VALUE
ILMN_2896528 1245.717
ILMN_2721178 406.9802
ILMN_3033922 613.1931
ILMN_3092673 2453.487
ILMN_2816356 13.93355
ILMN_2808939 354.5725
ILMN_2634564 197.1705
ILMN_2737647 9.173214
ILMN_2734484 472.7626
ILMN_2952292 96.03866
ILMN_2699078 -2.262156
ILMN_1213681 126.2036
ILMN_2735413 2.067329
ILMN_2735415 -3.473026
ILMN_2891688 318.2379
ILMN_2637698 864.162
ILMN_2674228 205.2406
ILMN_2601546 8.350698
ILMN_1230831 0.6744647
ILMN_2848071 18.45404

Total number of rows: 25697

Table truncated, full table size 555 Kbytes.




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

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