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Sample GSM1139087 Query DataSets for GSM1139087
Status Public on Jan 13, 2014
Title WT-HF-rep2
Sample type RNA
 
Source name Wild type, high fat
Organism Mus musculus
Characteristics strain/background: C57BL/6J
genotype/variation: WT
gender: female
tissue: colon epithelium
treatment: high fat diet
processing batch: 2
Treatment protocol Female h-NAG-1 transgenic mice and wild type C57BL/6J mice at 5 weeks of age were placed on either 10% fat diet (D12450B) or 60% fat diet (D12492, Research Diets, New Brunswick, NJ) for 20 weeks.
Extracted molecule total RNA
Extraction protocol Total RNA in colon epithelium was prepared using AllPrep DNA/RNA Mini Kit (Qiagen).
Label Cy3
Label protocol Starting with 500ng of total RNA, Cy3-labeled cRNA was produced according to Agilent's protocol.
 
Hybridization protocol For each sample, 1.65ug of Cy3-labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.
Scan protocol Slides were washed and then scanned with an Agilent Scanner.
Data processing The feature extractor processed signal intensity values were log2 transformed, quantile normalized, the multiple values for same probe were summarized using median polish. The resulting value was batch corrected using Emprical Bayes method from Johnson et al. 2006 (Johnson EW, Rabinovic A, Li C . Adjusting batch effects in microarray expression data using Empirical Bayes methods. Biostatistics Advance Access published on April 21, 2006, DOI 10.1093/biostatistics/kxj037).
 
Submission date May 10, 2013
Last update date Jan 14, 2014
Contact name Deepak Mav
Organization name Sciome LLC
Street address 2 Davis Drive
City Research Triangle Park
State/province NC
ZIP/Postal code 27709
Country USA
 
Platform ID GPL7202
Series (1)
GSE46843 Obesity primes the enhancer landscape of colon epithelium for cancer

Data table header descriptions
ID_REF
VALUE Normalized, batch corrected log2 signal intensity

Data table
ID_REF VALUE
A_51_P100021 2.345956975
A_51_P100034 14.60710447
A_51_P100052 2.3738396
A_51_P100063 11.70592991
A_51_P100084 4.783618888
A_51_P100099 8.666925159
A_51_P100155 12.91024488
A_51_P100174 9.109143181
A_51_P100181 9.136513992
A_51_P100218 2.135843218
A_51_P100227 11.0699334
A_51_P100238 3.702750362
A_51_P100246 12.22646867
A_51_P100289 12.06078712
A_51_P100298 10.81098143
A_51_P100309 2.369686417
A_51_P100327 9.156663874
A_51_P100347 2.416512399
A_51_P100379 7.157194248
A_51_P100428 2.62550218

Total number of rows: 41174

Table truncated, full table size 999 Kbytes.




Supplementary file Size Download File type/resource
GSM1139087_US23502387_251486836122_S01_GE1-v5_95_Feb07_1_3.txt.gz 9.1 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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