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Sample GSM345354 Query DataSets for GSM345354
Status Public on Nov 26, 2008
Title Sham; 1740174013_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 230.3 0.66145 51 7.815
ILMN_1238136 235.8 0.5582 50 7.998
ILMN_2721178 618.1 0 33 15.765
ILMN_2458840 239.9 0.47872 46 8.056
ILMN_1230777 3472.3 0 36 102.452
ILMN_2537239 2247.3 0 51 66.585
ILMN_1246069 908.8 0 36 30.57
ILMN_2524361 252.7 0.296 53 8.81
ILMN_1243193 857.3 0 42 27.718
ILMN_1232042 221.7 0.7985 63 6.725
ILMN_1242440 334.5 0.01314 44 9.836
ILMN_2543689 3057.1 0 52 74.342
ILMN_1233188 507.9 0.00125 47 18.362
ILMN_1224596 347.1 0.00814 35 17.888
ILMN_1233643 226.8 0.7209 51 6.392
ILMN_1222139 296.9 0.05632 42 9.458
ILMN_1259789 256.4 0.26158 51 9.063
ILMN_2773981 982 0 42 32.136
ILMN_2771349 551.4 0 63 13.44
ILMN_2634566 771.4 0 43 30.981

Total number of rows: 44505

Table truncated, full table size 1534 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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