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Sample GSM1219090 Query DataSets for GSM1219090
Status Public on Aug 24, 2014
Title Control C54
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 5665159057_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 2482.634 0.00 113.6919 50
ILMN_2721178 681.4382 0.00 30.32007 49
ILMN_3033922 1265.041 0.00 54.46155 34
ILMN_3092673 4139.07 0.00 168.8857 44
ILMN_2816356 166.1369 0.1779449 8.316897 38
ILMN_2808939 791.9831 0.00 34.56953 41
ILMN_2634564 533.0184 0.00 32.3784 30
ILMN_2737647 164.9466 0.1967418 7.755353 39
ILMN_2734484 450.1796 0.00 25.42645 45
ILMN_2952292 170.565 0.1140351 5.387231 55
ILMN_2699078 142.1197 0.877193 5.383518 56
ILMN_1213681 369.9662 0.00 20.04425 34
ILMN_2735413 152.5906 0.5739349 5.899475 40
ILMN_2735415 158.3547 0.3859649 6.139514 40
ILMN_2891688 583.2867 0.00 23.36403 48
ILMN_2637698 897.8333 0.00 38.54975 46
ILMN_2674228 366.3363 0.00 20.31451 40
ILMN_2601546 177.1248 0.05513784 12.01548 31
ILMN_1230831 217.0559 0.001253133 12.19115 38
ILMN_2848071 180.5585 0.03258145 9.41421 41

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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