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Sample GSM1219089 Query DataSets for GSM1219089
Status Public on Aug 24, 2014
Title Ethanol-treated A49
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 5665159057_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 2207.8 0.00 101.9734 36
ILMN_2721178 732.1097 0.00 37.62734 37
ILMN_3033922 1237.069 0.00 51.641 49
ILMN_3092673 3979.843 0.00 173.4524 47
ILMN_2816356 172.5523 0.0802005 9.325627 43
ILMN_2808939 706.7186 0.00 31.3271 40
ILMN_2634564 654.898 0.00 50.18325 32
ILMN_2737647 161.9704 0.264411 7.40921 34
ILMN_2734484 424.858 0.00 21.22059 44
ILMN_2952292 181.1148 0.02631579 6.264316 49
ILMN_2699078 150.5689 0.650376 5.985011 44
ILMN_1213681 334.8479 0.00 23.27158 33
ILMN_2735413 159.5975 0.3483709 8.421296 32
ILMN_2735415 178.0548 0.03508772 8.433663 41
ILMN_2891688 621.2399 0.00 44.26338 30
ILMN_2637698 1040.982 0.00 55.2324 42
ILMN_2674228 404.496 0.00 28.3326 31
ILMN_2601546 171.0397 0.1027569 7.456242 36
ILMN_1230831 196.0958 0.007518797 10.52307 32
ILMN_2848071 188.874 0.01503759 12.67645 26

Total number of rows: 25697

Table truncated, full table size 1054 Kbytes.




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

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