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Sample GSM1184539 Query DataSets for GSM1184539
Status Public on Jul 12, 2013
Title BNST/POA XXY male 3
Sample type RNA
 
Source name BNST/POA XXY male
Organism Mus musculus
Characteristics strain: MF1
age: 152 days
tissue: BNST/POA
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 3, Batch 1
B_XXY.Sry_3
Data processing Microarray data were processed using the statistical software program R (http://www.r-project.org/). Data were first background corrected using the nec function in the limma package (W. Shi, Oshlack, & Smyth, 2010). Probes with low-quality data (detection p-value of >0.05 in more than a third of the samples) were then removed from the dataset. Next, batch effects were corrected using the ComBat R script and the data underwent quantile normalization and log2 transformation using the limma package (Johnson, Li, & Rabinovic, 2007).
 
Submission date Jul 11, 2013
Last update date Jul 12, 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)
GSE48783 Feminized behavior and gene expression in the BNST/POA in a novel mouse model of Klinefelter Syndrome

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

Data table
ID_REF VALUE Detection Pval
ILMN_2939579 5.763485253 0.01879699
ILMN_2721452 5.853231572 0.02506266
ILMN_2625035 6.340742462 0.002506266
ILMN_1229430 5.273488389 0.0952381
ILMN_2594066 6.118934386 0.005012531
ILMN_1256927 6.385697971 0
ILMN_2775300 5.445219515 0.0952381
ILMN_2676716 5.976890119 0.02130326
ILMN_1238733 9.062065466 0
ILMN_2647427 5.620070523 0.0914787
ILMN_2928498 5.533496236 0.0689223
ILMN_1220874 5.187833519 0.160401
ILMN_1219743 5.832433421 0.02130326
ILMN_2752597 5.730708156 0.02506266
ILMN_2744129 6.089053763 0.01879699
ILMN_2602125 6.443350663 0.005012531
ILMN_2593338 6.263604622 0.01879699
ILMN_3112856 5.756791151 0.02756892
ILMN_1226259 5.561306303 0.1240602
ILMN_2987599 5.644934878 0.04761905

Total number of rows: 12980

Table truncated, full table size 356 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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