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Sample GSM1099596 Query DataSets for GSM1099596
Status Public on Jul 30, 2014
Title cHF+Phospholipids+Rosi, replicate 1
Sample type RNA
 
Channel 1
Source name cHF+Phospholipids+Rosi, replicate 1
Organism Mus musculus
Characteristics strain: C57BL/6N
gender: male
age: adult
tissue: liver
Treatment protocol Animals were fed a control corn oil-based high-fat diet (cHF), or one of the cHF supplementations: 1) ~7 % of dietary lipids was replaced by the EPA and DHA concentrate in the form of omega-3 phospholipids rich in phosphatidylcholine (PC); 2) low dose rosiglitazone (R); and 3) both PC and rosiglitazone (PC+R). All groups received the diet ad-libitum during 7 weeks intervention.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from liver tissue stored in RNAlater Solution using TRIZol Reagent (Sigma-Aldrich) according to the manufacturer’s instruction. 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 Experion automated electrophoresis system (BioRad).
Label Cy5
Label protocol 1,000 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously (Van Helden et al., Carcinogenesis 2010).
 
Channel 2
Source name reference pool
Organism Mus musculus
Characteristics strain: C57BL/6N
gender: male
age: adult
tissue: liver
Treatment protocol Animals were fed a control corn oil-based high-fat diet (cHF), or one of the cHF supplementations: 1) ~7 % of dietary lipids was replaced by the EPA and DHA concentrate in the form of omega-3 phospholipids rich in phosphatidylcholine (PC); 2) low dose rosiglitazone (R); and 3) both PC and rosiglitazone (PC+R). All groups received the diet ad-libitum during 7 weeks intervention.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from liver tissue stored in RNAlater Solution using TRIZol Reagent (Sigma-Aldrich) according to the manufacturer’s instruction. 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 Experion automated electrophoresis system (BioRad).
Label Cy3
Label protocol 1,000 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously (Van Helden et al., Carcinogenesis 2010).
 
 
Hybridization protocol Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using 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 sequential following Agilents' 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 Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.
Data processing Images were quantified using Agilent Feature Extraction Software (v 10.5.1.1) 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) based on the Cy3-reference pool, and log2 transformation.
 
Submission date Mar 18, 2013
Last update date Jul 30, 2014
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)
GSE45235 Marine omega-3 phospholipids suppress hepatic steatosis by a complex inhibition of biosynthetic pathways in dietary obese mice

Data table header descriptions
ID_REF
VALUE Normalized log2 value of sample over reference pool.

Data table
ID_REF VALUE
12 6.765295
14 7.429806
15 5.748027
16 9.681262
17 13.598287
20 7.009951
22 6.915233
23 15.824301
24 11.633942
25 8.839743
26 10.970055
27 10.84891
28 5.972476
30 7.702106
31 11.756685
35 14.025901
36 10.43154
38 6.144844
40 11.030262
41 12.178605

Total number of rows: 25806

Table truncated, full table size 379 Kbytes.




Supplementary file Size Download File type/resource
GSM1099596_US22502548_252665510688_S01_GE2-v4_95_Feb07_1_4.txt.gz 15.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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