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Sample GSM1219077 Query DataSets for GSM1219077
Status Public on Aug 24, 2014
Title Ethanol-treated A21
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_H
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 2196.414 0.00 101.695 49
ILMN_2721178 859.4932 0.00 54.04202 35
ILMN_3033922 1124.55 0.00 59.19064 48
ILMN_3092673 4248.969 0.00 201.5308 49
ILMN_2816356 143.2058 0.8408521 9.109056 27
ILMN_2808939 741.6778 0.00 38.28674 54
ILMN_2634564 523.9226 0.00 30.60328 32
ILMN_2737647 159.8318 0.3621554 11.20459 29
ILMN_2734484 512.0544 0.00 45.93729 35
ILMN_2952292 207.4128 0.002506266 11.8413 51
ILMN_2699078 136.3774 0.952381 5.421749 37
ILMN_1213681 317.3076 0.00 17.81177 48
ILMN_2735413 153.4746 0.5463659 8.141139 27
ILMN_2735415 173.9958 0.0914787 12.8109 39
ILMN_2891688 677.5238 0.00 44.8833 41
ILMN_2637698 882.4514 0.00 46.55098 39
ILMN_2674228 338.2628 0.00 15.28956 59
ILMN_2601546 175.0834 0.08521304 10.47462 46
ILMN_1230831 223.3859 0.001253133 18.32009 30
ILMN_2848071 170.997 0.1240602 11.06966 28

Total number of rows: 25697

Table truncated, full table size 1057 Kbytes.




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

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