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Sample GSM1219093 Query DataSets for GSM1219093
Status Public on Aug 24, 2014
Title Control C56
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_H
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 2171.045 0.00 100.6489 51
ILMN_2721178 648.4648 0.00 26.85902 48
ILMN_3033922 1262.19 0.00 77.07275 41
ILMN_3092673 4143.923 0.00 182.6104 50
ILMN_2816356 140.5081 0.9097744 5.279304 25
ILMN_2808939 733.0979 0.00 38.55552 38
ILMN_2634564 541.2228 0.00 40.47989 30
ILMN_2737647 162.3595 0.2556391 7.949551 34
ILMN_2734484 513.5721 0.00 38.3116 44
ILMN_2952292 173.8748 0.07518797 7.413872 39
ILMN_2699078 152.6694 0.556391 6.798261 49
ILMN_1213681 371.6219 0.00 12.95348 41
ILMN_2735413 156.0543 0.4536341 7.343953 42
ILMN_2735415 150.7229 0.6253133 7.516028 32
ILMN_2891688 592.1826 0.00 27.29591 40
ILMN_2637698 934.8414 0.00 46.22361 47
ILMN_2674228 357.4242 0.00 19.58084 40
ILMN_2601546 201.5989 0.002506266 12.3034 32
ILMN_1230831 211.2861 0.001253133 13.69046 36
ILMN_2848071 176.209 0.05513784 7.707311 29

Total number of rows: 25697

Table truncated, full table size 1062 Kbytes.




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

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