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Sample GSM1425078 Query DataSets for GSM1425078
Status Public on Feb 09, 2017
Title si2_chow_replicate3
Sample type RNA
 
Source name small intestine segment 2, epithelial cell scraping, chow diet
Organism Mus musculus
Characteristics strain: C57BL/6J
Sex: male
tissue: small intestine, epithelial cell scraping
peg plate: G014
labeling batch: 2
individual scraped: researcher1
Treatment protocol After 3 weeks, at the age of seven weeks, a subset of mice (n=8) were fed a low fat diet (LFD) for 2 weeks. The remaining mice (n=4) remained on the standard laboratory chow (RMH-B) diet. Subsequently, after these 2 weeks, at the age of nine weeks, half of the mice fed the LFD were put on a high fat diet (HFD; n=4), whereas the remaining mice were kept on the LFD (n=4). The chow fed mice remained on the RHM-B diet. After 2 additional weeks, at the age of 11 weeks, all mice were killed, after which the small intestine was removed, cut into 10 equal parts [1=duodenum, 10=terminal ileum], epithelial cells scraped off, snap-frozen in liquid nitrogen, and stored at -80° until analysis. The standard laboratory chow, RMH-B (cat. no. 2181), containing 5% of energy derived from fat, was obtained from ABDiets, Woerden, the Netherlands. The LFD and HFD contained 10% respectively 45% of energy derived from fat (diet formulations based on formulation D12450B resp. D12451; OpenResearch Diets, Research Diets, Inc). Exact diet formulations are available in the supplemental data. Throughout the whole experiment mice had free access to feed and water.
Growth protocol Four-week old male C57BL/6J mice (N=12) were purchased from Harlan (Horst, The Netherlands) and were housed in pairs in the light- and temperature-controlled animal facility of Wageningen University. Mice had free access to feed and water and prior to the start of the diet intervention they received standard laboratory chow (RMH-B). All animal procedures were conducted under protocols approved by the Local Committee for Care and Use of Laboratory Animals of Wageningen University, the Netherlands.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from scrapings using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).
Label biotin
Label protocol One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).
 
Hybridization protocol Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.
Scan protocol Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).
Data processing Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.28.2).
 
Submission date Jul 03, 2014
Last update date Feb 09, 2017
Contact name Guido Hooiveld
E-mail(s) guido.hooiveld@wur.nl
Organization name Wageningen University
Department Div. Human Nutrition & Health
Lab Nutrition, Metabolism & Genomics Group
Street address HELIX, Stippeneng 4
City Wageningen
ZIP/Postal code NL-6708WE
Country Netherlands
 
Platform ID GPL11533
Series (1)
GSE59054 Detailed localisation of diet-induced changes in gene expression in the murine small intestine.

Data table header descriptions
ID_REF
VALUE RMA signal (as log2)

Data table
ID_REF VALUE
10338001 11.45156786
10338002 4.687929788
10338003 9.42157641
10338004 8.803923164
10338005 2.334381837
10338006 2.578615073
10338007 2.801142244
10338008 3.176782188
10338009 7.02702703
10338010 2.347855104
10338011 4.387608486
10338012 2.442226776
10338013 2.179553854
10338014 2.241050436
10338015 2.200995782
10338016 5.844927459
10338017 12.44955049
10338018 5.225914864
10338019 3.798287235
10338020 6.668590683

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.




Supplementary file Size Download File type/resource
GSM1425078_G014_G07_15_803_I2_chow.CEL.gz 4.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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