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Sample GSM1219099 Query DataSets for GSM1219099
Status Public on Aug 24, 2014
Title Control C65
Sample type RNA
 
Source name control mouse
Organism Mus musculus
Characteristics strain: C57BL/6J x FVB/NJ F1
tissue: frontal cortex
stress: control
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 5665159077_F
control 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 2528.89 0.00 95.06301 41
ILMN_2721178 932.11 0.00 24.39612 42
ILMN_3033922 1302.245 0.00 58.72256 36
ILMN_3092673 4517.324 0.00 156.0441 58
ILMN_2816356 174.1626 0.09022556 9.176657 35
ILMN_2808939 867.5485 0.00 36.40932 33
ILMN_2634564 627.386 0.00 41.26987 31
ILMN_2737647 152.3816 0.5889724 6.12473 22
ILMN_2734484 497.6257 0.00 26.96142 45
ILMN_2952292 190.8021 0.01629073 8.189805 45
ILMN_2699078 147.1887 0.7443609 4.89263 56
ILMN_1213681 308.6243 0.00 14.35333 38
ILMN_2735413 159.1488 0.3809524 5.839246 35
ILMN_2735415 163.6893 0.2807018 6.172808 44
ILMN_2891688 549.3965 0.00 23.31908 32
ILMN_2637698 833.1613 0.00 34.87626 41
ILMN_2674228 329.1532 0.00 10.56643 42
ILMN_2601546 180.715 0.03759398 9.213428 33
ILMN_1230831 162.6433 0.302005 6.275466 37
ILMN_2848071 200.1512 0.006265664 8.627636 37

Total number of rows: 25697

Table truncated, full table size 1058 Kbytes.




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

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