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Sample GSM489047 Query DataSets for GSM489047
Status Public on Dec 23, 2009
Title clock-675
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: no treatment
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, no treatment
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
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
VALUE rank invariant normalized (BeadStudio v3) signal intensity

Data table
ILMN_2896528 1464.262
ILMN_2721178 198.7113
ILMN_3033922 128.5401
ILMN_3092673 2497.122
ILMN_2816356 16.39314
ILMN_2808939 392.5875
ILMN_2634564 271.1067
ILMN_2737647 29.68393
ILMN_2734484 206.9449
ILMN_2952292 99.11658
ILMN_2699078 22.58257
ILMN_1213681 125.6673
ILMN_2735413 12.59578
ILMN_2735415 17.89155
ILMN_2891688 501.1448
ILMN_2637698 815.8765
ILMN_2674228 116.1252
ILMN_2601546 19.24133
ILMN_1230831 10.11677
ILMN_2848071 24.64291

Total number of rows: 25697

Table truncated, full table size 549 Kbytes.

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

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