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Sample GSM345358 Query DataSets for GSM345358
Status Public on Nov 26, 2008
Title Sham; 1740174049_D
Sample type RNA
 
Source name Lung homogenate, 2h Sham treatment
Organism Mus musculus
Characteristics C57BL/6
Treatment protocol The NTHi cell pellet was washed and resuspended in 20 ml 0.9% sodium chloride solution. This suspension was passed three times through an EmulsiFlex C5 cell disruptor (Avestin) at greater then 10,000 psi, then diluted to 4-5 mg/ml in 0.9% sodium chloride solution by bicinchoninic assay (Pierce) and centrifuged at 15,000 x g for 10 min. The supernatant was collected, the protein concentration was adjusted to 2.5 mg/ml, and the lysate was sterilized by passage through a 0.2 µm filter and frozen in 8 ml aliquots at -80ºC. For treatment, a thawed aliquot was placed in an AeroMist CA-209 nebulizer driven by 10 l/min 5% CO2 in air for 20 min, resulting in aerosolization of 4 ml of lysate, with the protein concentration in residual lysate
Growth protocol Frozen stock (1 x 107 CFU/ml) of non-typeable Haemophilus influenzae (NTHi) was grown on chocolate agar at 300 ul per 10 cm plate (Remel) for 24 h at 37ºC in 5% CO2, then harvested and incubated for 16 h in 1 l brain-heart infusion broth (Acumedia) supplemented with 3.5 ug/ml NAD (Sigma-Adrich).
Extracted molecule total RNA
Extraction protocol total RNA extracted using Qiagen Rneasy per manufacturers instructions. cRNA amplification using Ambion total prep kit per manufacturers instructions.
Label Cy3
Label protocol 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 Gene expression in C57BL/6 mouse lungs after exposure to aerosolized NTHi lysate
Data processing Data was processed using Illumina BeadStudio v3. Data generated both with rank invariant normalization, using sham group as the reference group.
 
Submission date Nov 25, 2008
Last update date Nov 25, 2008
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 GPL6105
Series (1)
GSE13740 Gene expression in C57BL/6 mouse lungs after exposure to aerosolized NTHi lysate

Data table header descriptions
ID_REF
VALUE Values reported were derived using Illumina BeadStudio v3 and are relative signal intensity normalized to background.
Detection Pval
Avg_NBEADS
BEAD_STDERR

Data table
ID_REF VALUE Detection Pval Avg_NBEADS BEAD_STDERR
ILMN_2417611 222.6 0.53254 50 9.099
ILMN_1238136 203 0.79036 48 10.806
ILMN_2721178 528.1 0.00125 54 19.131
ILMN_2458840 203.4 0.78786 38 10.701
ILMN_1230777 2520.9 0 42 79.201
ILMN_2537239 1578.7 0 44 61.061
ILMN_1246069 454.9 0.0025 45 23.942
ILMN_2524361 247.5 0.26408 51 13.235
ILMN_1243193 724.2 0 59 26.508
ILMN_1232042 199.3 0.82728 50 8.834
ILMN_1242440 332.4 0.03755 49 14.204
ILMN_2543689 2593 0 55 86.011
ILMN_1233188 427.2 0.0025 50 19.632
ILMN_1224596 343.8 0.02691 45 16.656
ILMN_1233643 225.9 0.48561 43 12.195
ILMN_1222139 301.9 0.07196 58 12.028
ILMN_1259789 232.1 0.41302 43 10.105
ILMN_2773981 985 0 40 43.926
ILMN_2771349 401.9 0.00375 59 16.44
ILMN_2634566 1073.9 0 43 39.278

Total number of rows: 44505

Table truncated, full table size 1556 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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