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Sample GSM1219085 Query DataSets for GSM1219085
Status Public on Aug 24, 2014
Title Ethanol-treated A45
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_H
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 2104.65 0.00 93.89597 39
ILMN_2721178 758.7379 0.00 34.45698 40
ILMN_3033922 1247.919 0.00 52.85088 59
ILMN_3092673 3940.43 0.00 172.797 42
ILMN_2816356 181.3252 0.03634085 9.643886 29
ILMN_2808939 788.1144 0.00 38.40094 40
ILMN_2634564 450.0732 0.00 26.54037 27
ILMN_2737647 157.8623 0.4010025 7.811305 39
ILMN_2734484 546.5703 0.00 34.40154 40
ILMN_2952292 180.4973 0.04010025 7.356326 48
ILMN_2699078 140.6588 0.9223058 6.156343 34
ILMN_1213681 362.6686 0.00 20.3974 53
ILMN_2735413 142.0528 0.9022557 7.077269 43
ILMN_2735415 157.8215 0.4047619 6.81483 37
ILMN_2891688 499.6078 0.00 30.99102 32
ILMN_2637698 986.7849 0.00 64.79781 28
ILMN_2674228 349.0109 0.00 22.34766 39
ILMN_2601546 174.6133 0.07017544 7.974298 43
ILMN_1230831 204.5722 0.003759399 12.85329 33
ILMN_2848071 153.6362 0.556391 7.108407 30

Total number of rows: 25697

Table truncated, full table size 1052 Kbytes.




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

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