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Sample GSM1219096 Query DataSets for GSM1219096
Status Public on Aug 24, 2014
Title Control C59
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_C
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 2386.569 0.00 81.07196 41
ILMN_2721178 688.6903 0.00 32.76211 37
ILMN_3033922 1281.209 0.00 34.42095 39
ILMN_3092673 4231.787 0.00 135.8111 46
ILMN_2816356 160.5305 0.3333333 5.279316 36
ILMN_2808939 740.1244 0.00 30.51517 38
ILMN_2634564 761.2928 0.00 52.68211 27
ILMN_2737647 151.4851 0.6403509 7.012099 35
ILMN_2734484 498.0407 0.00 22.49005 50
ILMN_2952292 181.4238 0.04260652 4.190197 38
ILMN_2699078 161.6667 0.3082707 8.000303 32
ILMN_1213681 340.3142 0.00 17.64121 40
ILMN_2735413 140.6141 0.9022557 4.691645 28
ILMN_2735415 165.7379 0.2030075 8.37317 36
ILMN_2891688 725.2296 0.00 46.20858 36
ILMN_2637698 837.7706 0.00 35.45826 37
ILMN_2674228 395.4503 0.00 19.74516 40
ILMN_2601546 171.6753 0.1177945 7.323002 33
ILMN_1230831 159.4608 0.3709273 5.0074 39
ILMN_2848071 191.2654 0.02130326 7.749093 43

Total number of rows: 25697

Table truncated, full table size 1056 Kbytes.




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

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