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Sample GSM1219098 Query DataSets for GSM1219098
Status Public on Aug 24, 2014
Title Control C60
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 5665159077_E
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 2320.434 0.00 103.6762 45
ILMN_2721178 743.4164 0.00 31.05318 44
ILMN_3033922 1353.74 0.00 60.5056 46
ILMN_3092673 4060.371 0.00 117.3872 46
ILMN_2816356 158.4082 0.3909774 8.800096 26
ILMN_2808939 801.8481 0.00 35.06629 42
ILMN_2634564 572.5973 0.00 24.79882 28
ILMN_2737647 162.8038 0.2606516 6.518095 42
ILMN_2734484 587.022 0.00 27.60975 36
ILMN_2952292 190.6045 0.01503759 7.308604 44
ILMN_2699078 139.8953 0.924812 4.571118 44
ILMN_1213681 348.736 0.00 12.62959 51
ILMN_2735413 142.8313 0.8621554 6.587039 35
ILMN_2735415 152.1868 0.6052632 5.938533 35
ILMN_2891688 689.2003 0.00 31.04218 37
ILMN_2637698 785.3898 0.00 25.30512 37
ILMN_2674228 394.8344 0.00 16.40195 45
ILMN_2601546 168.5808 0.1541353 6.643006 41
ILMN_1230831 162.7235 0.2619048 5.477094 36
ILMN_2848071 183.6351 0.03132832 8.386567 35

Total number of rows: 25697

Table truncated, full table size 1053 Kbytes.




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

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