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Sample GSM1219083 Query DataSets for GSM1219083
Status Public on Aug 24, 2014
Title Ethanol-treated A44
Sample type RNA
 
Source name treated mouse
Organism Mus musculus
Characteristics strain: C57BL/6J x FVB/NJ F1
tissue: frontal cortex
stress: ethanol
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 5665159054_F
treated 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 2100.224 0.00 94.3925 43
ILMN_2721178 799.2938 0.00 35.17367 44
ILMN_3033922 1168.833 0.00 57.41912 53
ILMN_3092673 4404.976 0.00 285.8571 31
ILMN_2816356 156.9234 0.4197995 7.496729 36
ILMN_2808939 697.4619 0.00 49.20801 26
ILMN_2634564 468.9529 0.00 27.38358 37
ILMN_2737647 174.2616 0.07518797 9.743902 38
ILMN_2734484 549.2759 0.00 28.78316 44
ILMN_2952292 169.9063 0.1265664 7.523396 36
ILMN_2699078 150.8313 0.6265664 6.007699 59
ILMN_1213681 357.2473 0.00 19.6266 57
ILMN_2735413 165.0229 0.1954887 12.25233 32
ILMN_2735415 159.0571 0.358396 8.299631 31
ILMN_2891688 559.1818 0.00 27.18891 51
ILMN_2637698 949.077 0.00 64.19157 35
ILMN_2674228 388.1425 0.00 24.69001 46
ILMN_2601546 161.2423 0.3045113 7.546547 43
ILMN_1230831 216.4272 0.001253133 11.97952 38
ILMN_2848071 171.8844 0.1065163 10.96194 25

Total number of rows: 25697

Table truncated, full table size 1059 Kbytes.




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

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