NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1219084 Query DataSets for GSM1219084
Status Public on Aug 24, 2014
Title Ethanol-treated A34
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_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 2065.332 0.00 110.3991 50
ILMN_2721178 683.7386 0.00 46.36287 42
ILMN_3033922 1302.245 0.00 71.60376 36
ILMN_3092673 4011.945 0.00 176.5242 39
ILMN_2816356 150.5638 0.6340852 6.541032 26
ILMN_2808939 744.508 0.00 58.25699 42
ILMN_2634564 500.9012 0.00 30.67385 34
ILMN_2737647 160.2861 0.3145363 8.243451 42
ILMN_2734484 416.4106 0.00 30.54693 44
ILMN_2952292 174.1427 0.08270676 8.613916 45
ILMN_2699078 153.8517 0.5062656 6.608093 50
ILMN_1213681 305.2945 0.00 17.2909 44
ILMN_2735413 146.3649 0.7756892 6.928955 30
ILMN_2735415 150.8617 0.6240602 5.004992 44
ILMN_2891688 693.6188 0.00 56.38291 32
ILMN_2637698 846.6041 0.00 53.32153 38
ILMN_2674228 338.5983 0.00 19.53458 48
ILMN_2601546 174.6717 0.0802005 8.603663 38
ILMN_1230831 208.4715 0.002506266 10.10175 48
ILMN_2848071 172.6664 0.0952381 9.070996 34

Total number of rows: 25697

Table truncated, full table size 1054 Kbytes.




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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap