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Sample GSM1219097 Query DataSets for GSM1219097
Status Public on Aug 24, 2014
Title Control C64
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_D
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 2250.049 0.00 74.63105 42
ILMN_2721178 790.1078 0.00 32.38501 45
ILMN_3033922 1213.64 0.00 43.19606 54
ILMN_3092673 4225.902 0.00 152.7488 49
ILMN_2816356 140.2114 0.8934837 6.248531 26
ILMN_2808939 779.1571 0.00 34.95534 35
ILMN_2634564 560.2651 0.00 26.9405 31
ILMN_2737647 169.823 0.1265664 5.506759 31
ILMN_2734484 604.0025 0.00 34.80161 40
ILMN_2952292 178.7939 0.05137845 7.984513 38
ILMN_2699078 156.9743 0.4097744 5.241881 46
ILMN_1213681 310.0216 0.00 12.38021 44
ILMN_2735413 146.7315 0.7593985 5.326288 45
ILMN_2735415 163.4267 0.2368421 6.676105 36
ILMN_2891688 705.6511 0.00 34.23941 45
ILMN_2637698 818.1287 0.00 40.0684 38
ILMN_2674228 322.5897 0.00 16.78594 38
ILMN_2601546 159.019 0.3483709 6.557167 37
ILMN_1230831 176.9185 0.06390978 6.691692 25
ILMN_2848071 177.444 0.06140351 8.556438 31

Total number of rows: 25697

Table truncated, full table size 1051 Kbytes.




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

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