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Sample GSM1050076 Query DataSets for GSM1050076
Status Public on Apr 01, 2013
Title Liver_LPS-treated_1
Sample type RNA
 
Source name mouse liver
Organism Mus musculus
Characteristics strain: C57BL/6J
age: 2.5 months
tissue: liver
paradigm: 2 lipopolysaccharide injections (1 mg/kg i.p.) spaced one week apart
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using mirVana™ miRNA Isolation kit, followed by DNase treatment with Turbo DNA-free™ according to the protocol supplied by the manufacturer (Ambion, Austin, TX). Quality control was performed with the Agilent Bioanalyzer.
Label biotin
Label protocol Biotinylated cRNAs were prepared with the Illumina® TotalPrep™ RNA Amplification kit from Ambion.
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description Replicate 1
Data processing The R package Lumi was used to transform and normalize the data using variance stabilization transformation and quantile normalization. Only genes with a detection p value ≤ 0.05 and present on ≥ 80% of arrays are included in the normalized data.
Expression value outliers were identified with Grubbs' test and removed.
 
Submission date Dec 06, 2012
Last update date Apr 01, 2013
Contact name Elizabeth Osterndorff-Kahanek
Organization name University of Texas at Austin
Street address 2500 Speedway
City Austin
State/province TX
ZIP/Postal code 78712
Country USA
 
Platform ID GPL6885
Series (1)
GSE42789 Gene expression in brain and liver produced by three different regimens of alcohol consumption in mice: Comparison with immune activation

Data table header descriptions
ID_REF
VALUE Lumi-computed normalized data after selection by detection p value and presence on arrays; expression value outliers are removed.

Data table
ID_REF VALUE
ILMN_2896528 11.49981188
ILMN_2721178 9.614250904
ILMN_3033922 10.20855335
ILMN_3092673 12.78864037
ILMN_2808939 11.39549289
ILMN_2634564 9.426796162
ILMN_2734484 9.090837684
ILMN_2952292 8.196120873
ILMN_1213681 8.730247709
ILMN_2735413 10.1600681
ILMN_2735415 10.13901192
ILMN_2891688 9.338884063
ILMN_2637698 9.725212387
ILMN_2674228 8.735971047
ILMN_2848071 10.89289496
ILMN_1248518 11.71085848
ILMN_2658619 11.20831739
ILMN_2972403 10.11662976
ILMN_2727437 8.440870143
ILMN_2628021 10.21732719

Total number of rows: 9550

Table truncated, full table size 230 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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