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Sample GSM1219091 Query DataSets for GSM1219091
Status Public on Aug 24, 2014
Title Control C55
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_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 2065.332 0.00 117.3886 44
ILMN_2721178 819.1784 0.00 57.65498 29
ILMN_3033922 1242.055 0.00 49.48877 40
ILMN_3092673 4527.824 0.00 165.4429 35
ILMN_2816356 152.2096 0.5726817 4.952487 41
ILMN_2808939 738.2131 0.00 34.4361 43
ILMN_2634564 566.3793 0.00 36.80616 31
ILMN_2737647 142.071 0.8696742 4.885796 29
ILMN_2734484 475.5518 0.00 30.51504 44
ILMN_2952292 190.5368 0.0112782 10.20841 50
ILMN_2699078 153.0826 0.5488722 6.810312 51
ILMN_1213681 372.7979 0.00 18.2739 40
ILMN_2735413 156.3004 0.443609 6.574547 43
ILMN_2735415 149.8186 0.6641604 5.826644 46
ILMN_2891688 607.4807 0.00 34.78703 32
ILMN_2637698 905.0245 0.00 47.03543 36
ILMN_2674228 426.6765 0.00 26.72713 43
ILMN_2601546 172.77 0.09022556 7.618211 52
ILMN_1230831 185.6736 0.01879699 9.676713 35
ILMN_2848071 175.195 0.0651629 8.431832 24

Total number of rows: 25697

Table truncated, full table size 1053 Kbytes.




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

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