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Sample GSM1219078 Query DataSets for GSM1219078
Status Public on Aug 24, 2014
Title Ethanol-treated A28
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_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 2115.118 0.00 125.017 39
ILMN_2721178 699.1412 0.00 38.7546 36
ILMN_3033922 1366.528 0.00 81.2795 53
ILMN_3092673 4084.291 0.00 221.9905 41
ILMN_2816356 154.0685 0.5162907 8.796693 33
ILMN_2808939 681.8187 0.00 37.53566 43
ILMN_2634564 605.4938 0.00 57.32517 25
ILMN_2737647 167.722 0.1754386 11.68991 30
ILMN_2734484 538.4313 0.00 45.45264 48
ILMN_2952292 173.0557 0.09398496 8.414359 50
ILMN_2699078 149.9024 0.6616541 8.212016 42
ILMN_1213681 286.5628 0.00 11.37055 34
ILMN_2735413 151.6035 0.6090226 9.123241 43
ILMN_2735415 178.3307 0.05764411 11.58751 38
ILMN_2891688 647.9518 0.00 41.97309 41
ILMN_2637698 1060.672 0.00 92.10023 31
ILMN_2674228 325.9529 0.00 19.52242 48
ILMN_2601546 164.9466 0.2155388 9.71951 31
ILMN_1230831 167.3306 0.1842105 10.15467 25
ILMN_2848071 152.761 0.5614035 9.133169 33

Total number of rows: 25697

Table truncated, full table size 1057 Kbytes.




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

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