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Sample GSM414798 Query DataSets for GSM414798
Status Public on Jun 09, 2009
Title lung_AIRmin_male_urethane_mice13
Sample type RNA
 
Source name lung from AIRmin male treated with urethane
Organism Mus musculus
Characteristics tissue: lung
strain: AIRmin
gender: M
agent: urethane
Treatment protocol two intraperitoneal injections of 1 mg/g body weight urethane or saline solution
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with RNeasy Midi kit (Qiagen, Valencia, CA) from normal lung parenchyma and purified with RNeasy MinElute CleanUP Kit (Qiagen). RNA concentration was determined with a Nanodrop spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA)
Label biotin
Label protocol Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description no additional information
Data processing The data were normalised using cubic spline normalization with Illumina's BeadStudio Gene Expression Module v3.4, July 2008 (see VALUE column below).
The data were then filtered by detection p-value (p<0.05). A matrix of the normalized, filtered data is linked as supplementary file at the foot of the Series record.
 
Submission date Jun 09, 2009
Last update date Jun 09, 2009
Contact name Loris De Cecco
E-mail(s) loris.dececco@istitutotumori.mi.it
Organization name IRCSS Istituto Nazionale Tumori
Street address via Venezian 1
City Milan
ZIP/Postal code 20133
Country Italy
 
Platform ID GPL6885
Series (1)
GSE16510 Normal lung transcriptome distinguishes mouse lines with different susceptibility to inflammation and to tumorigenesis

Data table header descriptions
ID_REF
VALUE Bead Studio calculated average signal (cubic spline normalized)
Detection Pval BeadStudio Detection p-value

Data table
ID_REF VALUE Detection Pval
ILMN_2896528 15901.51 0
ILMN_2721178 4156.568 0
ILMN_3033922 5384.252 0
ILMN_3092673 21781.22 0
ILMN_2816356 514.8244 0.007518797
ILMN_2808939 3713.459 0
ILMN_2634564 1697.067 0
ILMN_2737647 240.0604 0.2330827
ILMN_2734484 1128.087 0
ILMN_2952292 463.4992 0.007518797
ILMN_2699078 156.639 0.8270677
ILMN_1213681 1885.169 0
ILMN_2735413 245.4535 0.216792
ILMN_2735415 279.7285 0.131579
ILMN_2891688 2781.173 0
ILMN_2637698 6217.596 0
ILMN_2674228 1657.318 0
ILMN_2601546 314.6934 0.0764411
ILMN_1230831 281.6997 0.1290727
ILMN_2848071 359.2185 0.04010025

Total number of rows: 25697

Table truncated, full table size 727 Kbytes.




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

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