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Sample GSM1219076 Query DataSets for GSM1219076
Status Public on Aug 24, 2014
Title Ethanol-treated A11
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_G
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 1835.239 0.00 91.07746 44
ILMN_2721178 605.1623 0.00 28.38905 41
ILMN_3033922 1199.345 0.00 42.78276 52
ILMN_3092673 4090.059 0.00 198.671 50
ILMN_2816356 156.7186 0.4035088 10.03936 35
ILMN_2808939 758.2363 0.00 51.71724 25
ILMN_2634564 601.1979 0.00 31.49985 27
ILMN_2737647 203.0399 0.003759399 15.90353 32
ILMN_2734484 532.0851 0.00 31.85192 46
ILMN_2952292 172.1226 0.08897243 7.620469 44
ILMN_2699078 146.999 0.7543859 6.390401 37
ILMN_1213681 325.9529 0.00 18.56782 38
ILMN_2735413 146.8101 0.7568922 8.201577 26
ILMN_2735415 177.8721 0.04511278 10.644 38
ILMN_2891688 652.4097 0.00 34.62646 44
ILMN_2637698 999.7638 0.00 55.93993 41
ILMN_2674228 328.3288 0.00 18.33906 46
ILMN_2601546 164.7035 0.197995 7.663229 41
ILMN_1230831 180.7551 0.03007519 11.39879 32
ILMN_2848071 193.9947 0.00877193 12.86969 32

Total number of rows: 25697

Table truncated, full table size 1058 Kbytes.




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

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