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Sample GSM1219072 Query DataSets for GSM1219072
Status Public on Aug 24, 2014
Title Ethanol-treated A7
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 5665159043_C
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 2028.221 0.00 107.3296 45
ILMN_2721178 621.0489 0.00 28.84309 39
ILMN_3033922 1361.284 0.00 75.53976 39
ILMN_3092673 4060.371 0.00 190.5586 40
ILMN_2816356 179.4857 0.05263158 12.15649 29
ILMN_2808939 765.375 0.00 49.60345 28
ILMN_2634564 653.128 0.00 40.86113 28
ILMN_2737647 165.0949 0.2280702 8.984809 38
ILMN_2734484 467.8572 0.00 38.80259 38
ILMN_2952292 178.9185 0.05388471 8.050823 43
ILMN_2699078 154.9146 0.4937343 5.74793 45
ILMN_1213681 307.3112 0.00 13.75307 36
ILMN_2735413 150.0223 0.6616541 6.967994 35
ILMN_2735415 156.7953 0.4360902 6.889312 45
ILMN_2891688 736.538 0.00 55.25372 34
ILMN_2637698 1090.778 0.00 54.3768 41
ILMN_2674228 386.7805 0.00 32.76374 26
ILMN_2601546 163.0462 0.2719298 9.53224 28
ILMN_1230831 165.6516 0.2180451 10.12983 33
ILMN_2848071 172.1755 0.1140351 8.625834 39

Total number of rows: 25697

Table truncated, full table size 1057 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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