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Sample GSM1219071 Query DataSets for GSM1219071
Status Public on Aug 24, 2014
Title Ethanol-treated A13
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_B
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 2240.132 0.00 90.54263 50
ILMN_2721178 733.5289 0.00 50.34407 31
ILMN_3033922 1199.345 0.00 61.80473 51
ILMN_3092673 4411.98 0.00 182.9709 57
ILMN_2816356 164.1443 0.2255639 10.27339 23
ILMN_2808939 760.425 0.00 54.15615 28
ILMN_2634564 530.3721 0.00 30.33193 40
ILMN_2737647 174.1072 0.07393484 11.56098 34
ILMN_2734484 481.5287 0.00 32.37073 37
ILMN_2952292 166.1624 0.1942356 7.540548 44
ILMN_2699078 138.7408 0.9160401 6.588439 38
ILMN_1213681 326.6026 0.00 20.19232 33
ILMN_2735413 129.4456 0.9874687 5.958452 31
ILMN_2735415 161.8507 0.2756892 7.957929 31
ILMN_2891688 599.4409 0.00 32.20162 45
ILMN_2637698 876.5858 0.00 46.90592 38
ILMN_2674228 346.4744 0.00 21.27493 40
ILMN_2601546 154.6261 0.5025063 6.358232 43
ILMN_1230831 187.0939 0.01378446 8.141476 33
ILMN_2848071 160.9636 0.302005 9.038324 30

Total number of rows: 25697

Table truncated, full table size 1052 Kbytes.




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

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