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Sample GSM1219082 Query DataSets for GSM1219082
Status Public on Aug 24, 2014
Title Ethanol-treated A32
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 5665159054_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 1914.121 0.00 99.13329 34
ILMN_2721178 637.6359 0.00 42.53666 40
ILMN_3033922 1104.972 0.00 56.77811 42
ILMN_3092673 4236.431 0.00 249.638 43
ILMN_2816356 186.5246 0.03258145 9.609998 39
ILMN_2808939 800.8215 0.00 46.98164 41
ILMN_2634564 492.256 0.00 26.04732 29
ILMN_2737647 144.3008 0.8345864 7.695456 34
ILMN_2734484 481.9686 0.00 38.10035 41
ILMN_2952292 166.3864 0.2017544 6.15367 53
ILMN_2699078 175.1236 0.07393484 9.36478 33
ILMN_1213681 291.8622 0.00 11.68047 46
ILMN_2735413 144.4916 0.8320802 6.583746 37
ILMN_2735415 184.5542 0.03759398 10.47713 24
ILMN_2891688 547.3705 0.00 28.32592 33
ILMN_2637698 1114.79 0.00 98.52721 34
ILMN_2674228 372.343 0.00 18.8724 52
ILMN_2601546 176.2757 0.06641604 9.511713 49
ILMN_1230831 177.0685 0.06015038 8.792471 41
ILMN_2848071 170.3281 0.1290727 10.2284 32

Total number of rows: 25697

Table truncated, full table size 1056 Kbytes.




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

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