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Sample GSM1219075 Query DataSets for GSM1219075
Status Public on Aug 24, 2014
Title Ethanol-treated A20
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_F
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 2061.076 0.00 118.3974 44
ILMN_2721178 646.2921 0.00 32.10645 40
ILMN_3033922 1366.528 0.00 105.2391 36
ILMN_3092673 4705.576 0.00 313.1661 40
ILMN_2816356 171.0361 0.08270676 13.31693 23
ILMN_2808939 746.153 0.00 42.83376 38
ILMN_2634564 479.8622 0.00 37.68782 27
ILMN_2737647 163.0764 0.2218045 10.10084 39
ILMN_2734484 437.2148 0.00 27.41407 46
ILMN_2952292 180.1635 0.03634085 10.24554 48
ILMN_2699078 134.5379 0.9548872 6.353752 41
ILMN_1213681 346.8368 0.00 18.95273 40
ILMN_2735413 154.6238 0.4761905 8.59936 37
ILMN_2735415 153.2804 0.5225564 10.37502 31
ILMN_2891688 655.7464 0.00 35.60457 39
ILMN_2637698 1011.111 0.00 69.22977 45
ILMN_2674228 411.4224 0.00 24.62896 45
ILMN_2601546 158.9412 0.339599 8.265654 39
ILMN_1230831 191.9112 0.006265664 10.51195 33
ILMN_2848071 188.2084 0.0112782 13.78408 29

Total number of rows: 25697

Table truncated, full table size 1060 Kbytes.




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

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