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Sample GSM1219073 Query DataSets for GSM1219073
Status Public on Aug 24, 2014
Title Ethanol-treated A19
Sample type RNA
 
Source name treated mouse
Organism Mus musculus
Characteristics strain: C57BL/6J x FVB/NJ F1
tissue: frontal cortex
stress: ethanol
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Ambion's mirVana™ miRNA Isolation Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Label biotin
Label protocol Biotinylated cRNA were prepared with the Illumina® TotalPrep RNA Amplification Kit
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description 5665159043_D
treated mouse
Data processing The data were normalized using quantile normalization with lumi package in R
The quality of the Illumina bead summary data was assessed using the Bioconductor packages Lumi and arrayQualityMetrics. Data preprocessing included variance stabilization and quantile normalization using the Lumi package. Statistical analysis comparing ethanol-treated and control groups was performed using the Bioconductor package limma, which implements an empirical Bayes approach in R (Smyth 2005). False discovery rate (FDR) was assessed using the Benjamini-Hochberg method.
 
Submission date Aug 29, 2013
Last update date Aug 24, 2014
Contact name Yury O. Nunez
E-mail(s) nunezyo@gmail.com
Phone 210-567-8094
Organization name University of Texas at Austin
Department Pharmacy
Lab Pharmacogenomics
Street address 7703 Floyd Curl Drive MC6220
City San Antonio
State/province TX
ZIP/Postal code 78229
Country USA
 
Platform ID GPL6885
Series (1)
GSE50427 Gene (mRNA) expression profiling in frontal cortex of ethanol-treated mice

Data table header descriptions
ID_REF
VALUE Quantile normalized signal (AVG_Signal)
Detection Pval
BEAD_STDERR
Avg_NBEADS

Data table
ID_REF VALUE Detection Pval BEAD_STDERR Avg_NBEADS
ILMN_2896528 2175.113 0.00 94.08575 43
ILMN_2721178 822.8325 0.00 43.22862 40
ILMN_3033922 1133.525 0.00 72.70849 36
ILMN_3092673 4236.431 0.00 215.8088 52
ILMN_2816356 152.145 0.5651629 8.315577 32
ILMN_2808939 759.0598 0.00 42.74099 47
ILMN_2634564 540.1534 0.00 36.62329 30
ILMN_2737647 180.6888 0.03258145 9.506711 43
ILMN_2734484 455.7132 0.00 27.68025 35
ILMN_2952292 178.6331 0.03884712 9.439466 45
ILMN_2699078 163.4655 0.20802 8.870127 37
ILMN_1213681 331.274 0.00 18.624 43
ILMN_2735413 148.4138 0.7067669 6.571627 39
ILMN_2735415 174.5506 0.05889724 10.25276 34
ILMN_2891688 550.0513 0.00 23.9626 33
ILMN_2637698 955.4709 0.00 43.10806 42
ILMN_2674228 343.169 0.00 24.34736 32
ILMN_2601546 159.5502 0.3107769 8.475146 35
ILMN_1230831 185.866 0.01879699 11.75794 29
ILMN_2848071 188.4452 0.01629073 13.95351 27

Total number of rows: 25697

Table truncated, full table size 1055 Kbytes.




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

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