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Sample GSM940307 Query DataSets for GSM940307
Status Public on Aug 27, 2013
Title HFD, 12weeks, replicate 3
Sample type RNA
 
Channel 1
Source name epididymal white adipose tissue, HFD, 12 weeks
Organism Mus musculus
Characteristics strain: C57BL/6J
genotype: wildtype
gender: male
developmental stage: adult
tissue: epididymal white adipose
treatment: high-fat diet
treatment duration: 12 weeks
Treatment protocol Animals were fed a purified high-fat diet (HDF) or low-fat diet (LFD); diets are published elsewhere (Hoevenaars et al., Genes Nutrition 2012 (PMID 22228221)). All groups received the diet ad-libitum during 5 days or 12 weeks intervention. Animals were fasted for 2 hr prior to anaesthetization and sacrification.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from epididymal white adipose tissue using TRIZol Reagent (Sigma-Aldrich) according to the manufacturer's instructions. After extraction, RNA was purified by using RNeasy columns (Qiagen). RNA concentration and purity were measured using the NanoDrop spectrophotometer (IsoGen Life Science). The integrity of RNA was checked with the Experion automated electrophoresis system (BioRad).
Label Cy5
Label protocol 1,000 ng of purified individual total RNA was used for cDNA synthesis. The cDNA was split into two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent Low RNA Input Fluorescent Linear Amplification protocol, as described previously (Van Helden et al., Carcinogenesis 2010 (PMID 20472610)).
 
Channel 2
Source name Reference pool of all samples
Organism Mus musculus
Characteristics strain: C57BL/6J
genotype: wildtype
gender: male
developmental stage: adult
tissue: epididymal white adipose
sample type: reference
Treatment protocol Animals were fed a purified high-fat diet (HDF) or low-fat diet (LFD); diets are published elsewhere (Hoevenaars et al., Genes Nutrition 2012 (PMID 22228221)). All groups received the diet ad-libitum during 5 days or 12 weeks intervention. Animals were fasted for 2 hr prior to anaesthetization and sacrification.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from epididymal white adipose tissue using TRIZol Reagent (Sigma-Aldrich) according to the manufacturer's instructions. After extraction, RNA was purified by using RNeasy columns (Qiagen). RNA concentration and purity were measured using the NanoDrop spectrophotometer (IsoGen Life Science). The integrity of RNA was checked with the Experion automated electrophoresis system (BioRad).
Label Cy3
Label protocol 1,000 ng of purified individual total RNA was used for cDNA synthesis. The cDNA was split into two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent Low RNA Input Fluorescent Linear Amplification protocol, as described previously (Van Helden et al., Carcinogenesis 2010 (PMID 20472610)).
 
 
Hybridization protocol Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturer's procedure using the Agilent In Situ Hybridization Kit Plus and GEx Hybridization Buffer HI-RPM. Samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequentially following Agilent's recommendations and finally covered with Ozone-barrier slides.
Scan protocol Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.
Description HFD_12wk 3
Cy3 samples were pooled on an equimolar basis and served as the reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.
Data processing Images were quantified using Agilent Feature Extraction Software (v 10.5.5.1) to obtain raw median signal and background values for both Cy5 and Cy3. Spots with a mean signal higher than twice the background value over all arrays were considered to be expressed. Data was normalized according to Pellis et al., (Physiol Genomics 2003; 16:99-106 (PMID 14570982)) based on the Cy3-reference pool, and log2 transformed.
 
Submission date May 30, 2012
Last update date Aug 27, 2013
Contact name Evert M. van Schothorst
E-mail(s) evert.vanschothorst@wur.nl
Organization name Wageningen University
Lab Human and Animal Physiology
Street address De Elst 1
City Wageningen
ZIP/Postal code 6708 WD
Country Netherlands
 
Platform ID GPL10333
Series (1)
GSE38337 Short-term, high fat-feeding-induced changes in white adipose tissue gene expression are highly predictive for long-term changes

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio of sample over reference pool (Cy5/Cy3)

Data table
ID_REF VALUE
12 8.557023
14 12.163065
15 6.177385
16 8.879604
17 12.489222
20 9.685541
21 7.741753
22 6.079686
23 14.678045
24 7.811109
25 7.858315
26 4.965819
27 9.773174
28 7.132092
30 10.209469
31 11.143018
32 5.534068
33 5.997792
35 12.792115
36 10.888615

Total number of rows: 25150

Table truncated, full table size 366 Kbytes.




Supplementary file Size Download File type/resource
GSM940307_US22502548_252665510660_S01_GE2-v5_95_Feb07_1_1.txt.gz 15.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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