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Sample GSM1219087 Query DataSets for GSM1219087
Status Public on Aug 24, 2014
Title Control C52
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_B
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 2326.19 0.00 143.8892 42
ILMN_2721178 797.0867 0.00 40.15878 49
ILMN_3033922 1280.616 0.00 61.25119 41
ILMN_3092673 4028.909 0.00 181.2041 44
ILMN_2816356 177.1248 0.04385965 10.1307 31
ILMN_2808939 753.2988 0.00 42.09517 46
ILMN_2634564 535.8727 0.00 32.68908 38
ILMN_2737647 164.6462 0.2180451 9.134034 29
ILMN_2734484 550.0513 0.00 33.37157 48
ILMN_2952292 176.6472 0.04636591 6.510918 33
ILMN_2699078 140.365 0.9172933 6.573977 46
ILMN_1213681 361.5365 0.00 15.03716 52
ILMN_2735413 150.2276 0.6365915 7.818397 36
ILMN_2735415 175.3575 0.05513784 8.947701 38
ILMN_2891688 646.8071 0.00 42.65104 41
ILMN_2637698 1020.6 0.00 56.05203 53
ILMN_2674228 331.1458 0.00 21.48802 44
ILMN_2601546 169.043 0.1290727 7.507154 37
ILMN_1230831 210.3535 0.001253133 11.73014 32
ILMN_2848071 178.6331 0.03634085 7.010083 34

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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