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Sample GSM1049999 Query DataSets for GSM1049999
Status Public on Apr 01, 2013
Title Liver_CI-treated_4
Sample type RNA
 
Source name mouse liver
Organism Mus musculus
Characteristics strain: C57BL/6J
age: 2.5 months
tissue: liver
paradigm: Chronic Intermittent with two bottles choice every other day
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 4
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_2707227 13.18745972
ILMN_2896528 11.21182299
ILMN_2721178 9.320406348
ILMN_1227723 8.648965364
ILMN_3033922 9.951958495
ILMN_3092673 12.20379625
ILMN_2730714 12.13683389
ILMN_3162224 9.686833855
ILMN_2808939 10.82269207
ILMN_2634564 8.914366982
ILMN_1216623 8.94304267
ILMN_1215157 9.140014068
ILMN_2734484 9.287660056
ILMN_2952292 8.020577989
ILMN_2660815 11.09289744
ILMN_1243593 9.0684459
ILMN_1219797 8.92487711
ILMN_1231132 9.979985677
ILMN_2718462 8.055441353
ILMN_2653881 9.271004507

Total number of rows: 9561

Table truncated, full table size 231 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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