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Sample GSM1049936 Query DataSets for GSM1049936
Status Public on Apr 01, 2013
Title PFC_Chronic-treated_1
Sample type RNA
 
Source name mouse prefrontal cortex
Organism Mus musculus
Characteristics strain: C57BL/6J
age: 2.5 months
tissue: prefrontal cortex
paradigm: continuous chronic two bottle choice
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using mirVana™ miRNA Isolation kit, followed by DNase treatment with Turbo DNA-free™ according to the protocol supplied by the manufacturer (Ambion, Austin, TX). Quality control was performed with the Agilent Bioanalyzer.
Label biotin
Label protocol Biotinylated cRNAs were prepared with the Illumina® TotalPrep™ RNA Amplification kit from Ambion.
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description Replicate 1
Data processing The R package Lumi was used to transform and normalize the data using variance stabilization transformation and quantile normalization. Only genes with a detection p value ≤ 0.05 and present on ≥ 80% of arrays are included in the normalized data.
Expression value outliers were identified with Grubbs' test and removed.
 
Submission date Dec 06, 2012
Last update date Apr 01, 2013
Contact name Elizabeth Osterndorff-Kahanek
Organization name University of Texas at Austin
Street address 2500 Speedway
City Austin
State/province TX
ZIP/Postal code 78712
Country USA
 
Platform ID GPL6885
Series (1)
GSE42789 Gene expression in brain and liver produced by three different regimens of alcohol consumption in mice: Comparison with immune activation

Data table header descriptions
ID_REF
VALUE Lumi-computed normalized data after selection by detection p value and presence on arrays; expression value outliers are removed.

Data table
ID_REF VALUE
ILMN_1212612 11.02636506
ILMN_1212619 8.368080176
ILMN_1212632 8.29134679
ILMN_1212636 11.10275867
ILMN_1212637 9.25428594
ILMN_1212645 9.020948022
ILMN_1212648 9.052011199
ILMN_1212653 9.842320482
ILMN_1212672 8.65426156
ILMN_1212693 8.427930093
ILMN_1212702 12.98553684
ILMN_1212703 8.482340014
ILMN_1212720 9.820484689
ILMN_1212759 9.495042265
ILMN_1212791 8.309810861
ILMN_1212794 9.008852171
ILMN_1212875 8.839051173
ILMN_1212894 10.3718036
ILMN_1212902 10.13134179
ILMN_1212907 13.33514932

Total number of rows: 12125

Table truncated, full table size 294 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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