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Sample GSM908495 Query DataSets for GSM908495
Status Public on May 01, 2012
Title Methyl deficient diet mouse colon 1 sample 2
Sample type RNA
 
Source name MDD
Organism Mus musculus
Characteristics strain: ApcMin
tissue: colon
Treatment protocol ApcMin mice were fed methyl deficient diets (MDD) or methyl sufficient diet MSD (CONTROL) for 11 weeks and normal colons were harvested for expression profiling, duplicate samples were taken from each animal
2 control animals and 4 methyl deficient animals were used for expression profiling
Extracted molecule total RNA
Extraction protocol Colon RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini 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 Ambion MessageAmp kit for Illumina arrays
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description Methyl deficient diet mouse colon 1 sample 2
Data processing The data were normalised using 75th percentile shift in Genespring GX
 
Submission date Apr 03, 2012
Last update date May 01, 2012
Contact name Petr Protiva
E-mail(s) petr.protiva@yale.edu
Phone 230-932-5711
Organization name Yale University and VA CT Healthcare System
Street address 950 Campbell Avenue
City West Haven
ZIP/Postal code 06516
Country USA
 
Platform ID GPL6885
Series (1)
GSE37010 Effect of dietary methyl donor depletion on gene expression in normal colons of ApcMin mice

Data table header descriptions
ID_REF
VALUE 75 percentile shift normalized
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1212607 -0.48591542 0.09022556
ILMN_1212612 -2.0405269 0.3095238
ILMN_1212619 0.60434985 0.007518797
ILMN_1212628 2.1736674 0.2568922
ILMN_1212632 0.004962921 0.1817043
ILMN_1212636 -0.02695918 0
ILMN_1212637 0.11426902 0
ILMN_1212645 -0.17352581 0.6553885
ILMN_1212648 0.39495468 0
ILMN_1212653 0.68241143 0
ILMN_1212672 -0.07391834 0
ILMN_1212682 0.046108484 0.03634085
ILMN_1212683 -0.17352581 0.9172933
ILMN_1212685 -0.17352581 0.8734336
ILMN_1212692 0.042818546 0
ILMN_1212693 0.37524748 0
ILMN_1212695 -0.17682981 0.6015037
ILMN_1212698 -0.17352581 0.9774436
ILMN_1212702 -0.24907064 0
ILMN_1212703 -0.023465633 0.001253133

Total number of rows: 25697

Table truncated, full table size 804 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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