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Sample GSM1219086 Query DataSets for GSM1219086
Status Public on Aug 24, 2014
Title Ethanol-treated A46
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_A
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 2004.45 0.00 114.5785 42
ILMN_2721178 737.3405 0.00 41.18711 46
ILMN_3033922 1117.525 0.00 55.19762 62
ILMN_3092673 4139.07 0.00 187.1953 50
ILMN_2816356 152.1977 0.6203008 6.727952 33
ILMN_2808939 740.7313 0.00 45.49153 38
ILMN_2634564 551.4567 0.00 49.252 21
ILMN_2737647 162.0751 0.2882206 8.139801 39
ILMN_2734484 540.7953 0.00 37.37566 41
ILMN_2952292 181.4363 0.03884712 9.826954 43
ILMN_2699078 140.095 0.9122807 3.887886 55
ILMN_1213681 305.9276 0.00 14.7308 44
ILMN_2735413 163.7353 0.2418546 10.47672 30
ILMN_2735415 162.6894 0.2756892 8.490187 42
ILMN_2891688 536.1421 0.00 26.91671 41
ILMN_2637698 848.9786 0.00 46.18343 33
ILMN_2674228 347.1653 0.00 18.81865 50
ILMN_2601546 184.8625 0.02756892 11.07657 41
ILMN_1230831 196.338 0.005012531 16.1844 26
ILMN_2848071 154.8837 0.5325814 5.97285 39

Total number of rows: 25697

Table truncated, full table size 1053 Kbytes.




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

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