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Sample GSM1219074 Query DataSets for GSM1219074
Status Public on Aug 24, 2014
Title Ethanol-treated A9
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_E
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 1806.229 0.00 77.25632 48
ILMN_2721178 772.2108 0.00 41.95873 44
ILMN_3033922 1248.554 0.00 58.53489 55
ILMN_3092673 3695.848 0.00 138.2315 47
ILMN_2816356 155.2157 0.4761905 8.971213 32
ILMN_2808939 750.464 0.00 44.06137 34
ILMN_2634564 611.9869 0.00 29.18711 44
ILMN_2737647 158.187 0.4035088 8.528743 39
ILMN_2734484 508.9841 0.00 32.14612 44
ILMN_2952292 188.8218 0.01879699 9.495085 44
ILMN_2699078 140.0836 0.906015 6.027804 36
ILMN_1213681 281.4545 0.00 13.67141 32
ILMN_2735413 156.368 0.4486215 8.953307 34
ILMN_2735415 135.8819 0.9573935 6.240248 33
ILMN_2891688 688.1633 0.00 37.78529 32
ILMN_2637698 892.0549 0.00 55.53724 32
ILMN_2674228 353.2091 0.00 20.4773 48
ILMN_2601546 175.3575 0.08646616 8.896307 34
ILMN_1230831 174.0604 0.09398496 11.48526 29
ILMN_2848071 205.7589 0.005012531 12.03534 35

Total number of rows: 25697

Table truncated, full table size 1058 Kbytes.




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

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