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Sample GSM1049950 Query DataSets for GSM1049950
Status Public on Apr 01, 2013
Title Liver_Chronic-control_5
Sample type RNA
 
Source name mouse liver
Organism Mus musculus
Characteristics strain: C57BL/6J
age: 2.5 months
tissue: liver
paradigm: water
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 5
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 14.15342498
ILMN_2896528 11.43979305
ILMN_2721178 9.534938375
ILMN_1227723 9.422028916
ILMN_3033922 9.580459795
ILMN_3092673 13.1473358
ILMN_2730714 12.56712677
ILMN_3162224 9.686936467
ILMN_2808939 11.45898209
ILMN_2634564 9.949678195
ILMN_1216623 10.1413372
ILMN_1215157 10.2548712
ILMN_2734484 9.436882675
ILMN_2952292 8.46707301
ILMN_2660815 11.57946058
ILMN_1243593 9.385751787
ILMN_1219797 8.440236459
ILMN_1231132 10.85762939
ILMN_2718462 8.621459107
ILMN_2653881 10.20723679

Total number of rows: 10068

Table truncated, full table size 244 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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