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Sample GSM1211164 Query DataSets for GSM1211164
Status Public on Aug 29, 2013
Title Striatum Day 4 Female 1
Sample type RNA
 
Source name Striatum Day 4 Female 1
Organism Mus musculus
Characteristics strain: C57BL/6J
age: 4 days
tissue: Striatum
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from the BNST/POA using Qiagen AllPrep DNA/RNA Mini Kit (catalog no. 80204).
Label biotin
Label protocol Biotinylated cRNA were prepared by the UCLA Neuroscience Genomics Core.
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description Biological Replicate 1
Data processing Microarray data were processed using the statistical software program R (http://www.r-project.org/) and Bioconductor packages. The raw intensity data were first log2 transformed and then the outlier samples were detected based on the average inter-sample correlations. Three samples with average inter-sample correlations larger than two standard deviations (SDs) from the mean across all samples were removed from follow-up analysis. Then the samples were normalized by quantile normalization. Probes were considered robustly expressed if the detection p value was <0.05 in at least 20 samples (the total number of samples for every genetic/treatment group) in the data set. 57 samples with 13776 probes were retained for differential expression analysis.
 
Submission date Aug 19, 2013
Last update date Aug 29, 2013
Contact name Tuck Cheong Ngun
E-mail(s) tuckngun@g.ucla.edu
Phone 310-267-2456
Organization name UCLA
Department Human Genetics
Lab Vilain Lab
Street address 695 Charles E Young Dr S Gonda 5524
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platform ID GPL6885
Series (1)
GSE49986 The organizational effects of testosterone on brain DNA methylome

Data table header descriptions
ID_REF
VALUE log2 quantile normalized signal intensity
Detection.Pval

Data table
ID_REF VALUE Detection.Pval
ILMN_2707227 7.158383279 0.1390978
ILMN_2896528 13.31288402 0
ILMN_2721178 11.37991978 0
ILMN_1227723 8.28665193 0
ILMN_3033922 10.9656835 0
ILMN_3092673 13.19442878 0
ILMN_2730714 11.98905533 0
ILMN_3162224 11.71002103 0
ILMN_2816356 7.485588411 0.006265664
ILMN_2808939 11.10696175 0
ILMN_2634564 9.576559676 0
ILMN_1216623 9.608388962 0
ILMN_1215157 10.06668627 0
ILMN_2737647 7.021542729 0.3471178
ILMN_2734484 8.818248974 0
ILMN_2952292 7.73530986 0
ILMN_2660815 11.56443793 0
ILMN_1243593 8.748522954 0
ILMN_1219797 7.710296632 0
ILMN_1231132 9.846714274 0

Total number of rows: 13776

Table truncated, full table size 393 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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