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Sample GSM345370 Query DataSets for GSM345370
Status Public on Nov 26, 2008
Title NTHi 4h; 1740174049_F
Sample type RNA
 
Source name Lung homogenate, 4h 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 - Unit 1462
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 235 0.47247 56 8.806
ILMN_1238136 218 0.7791 28 11.584
ILMN_2721178 631.2 0 39 24.355
ILMN_2458840 227.2 0.60638 46 9.038
ILMN_1230777 2386.1 0 53 105.867
ILMN_2537239 1622 0 41 97.273
ILMN_1246069 682.6 0 34 36.167
ILMN_2524361 260.5 0.17835 57 9.548
ILMN_1243193 941.6 0 52 38.29
ILMN_1232042 233.1 0.51064 52 8.592
ILMN_1242440 286.2 0.0801 52 9.449
ILMN_2543689 1917.5 0 45 123.465
ILMN_1233188 429.7 0.0025 36 19.697
ILMN_1224596 352 0.00563 51 13.633
ILMN_1233643 231.5 0.53692 56 7.187
ILMN_1222139 285.3 0.0826 47 9.237
ILMN_1259789 231.7 0.53379 36 13.358
ILMN_2773981 860.8 0 44 34.284
ILMN_2771349 487.4 0.00125 49 18.624
ILMN_2634566 1161.8 0 32 66.247

Total number of rows: 44505

Table truncated, full table size 1544 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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