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Sample GSM345359 Query DataSets for GSM345359
Status Public on Nov 26, 2008
Title NTHi 2h; 1740174013_B
Sample type RNA
 
Source name Lung homogenate, 2h NTHi 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 238.3 0.43742 45 8.731
ILMN_1238136 241.3 0.398 53 8.182
ILMN_2721178 661.3 0 44 20.301
ILMN_2458840 238.5 0.43554 47 8.69
ILMN_1230777 2958.3 0 34 125.65
ILMN_2537239 2060.2 0 46 67.28
ILMN_1246069 962.7 0 46 31.927
ILMN_2524361 247.2 0.31414 47 10.082
ILMN_1243193 1164.8 0 34 36.103
ILMN_1232042 255.7 0.21089 34 9.976
ILMN_1242440 296.4 0.04506 56 7.945
ILMN_2543689 2716 0 51 78.78
ILMN_1233188 443 0.00188 41 16.183
ILMN_1224596 344.1 0.00751 38 11.899
ILMN_1233643 231.5 0.56446 38 8.659
ILMN_1222139 281.7 0.07697 48 8.189
ILMN_1259789 254.9 0.21902 50 8.106
ILMN_2773981 753.1 0 41 21.544
ILMN_2771349 556.4 0.00125 61 17.506
ILMN_2634566 790.6 0 47 17.698

Total number of rows: 44505

Table truncated, full table size 1535 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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