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Sample GSM756426 Query DataSets for GSM756426
Status Public on Feb 21, 2012
Title WT_Control_rep1
Sample type RNA
 
Source name heart
Organism Mus musculus
Characteristics strain: Sv129
gender: male
age: 9-12weeks
genotype: 129S1/SvImJ
treatment: none
Treatment protocol Starting at 5AM the animals were fasted for 4 hours followed by an intragastric gavage of 400 µL synthetic triolein, trilinolein, trilinolenin, or tridocosahexaenoin. Wy14643 was given as 400 µL of a 10 mg/mL suspension in 0.5% carboxylmethyl cellulose (CMC). CMC only served as control treatment (400uL). Six hours after the oral gavage, mice were anaesthetized with a mixture of isofluorane (1.5%), nitrous oxide (70%) and oxygen (30%). Blood was collected by orbital puncture, followed by sacrifice of the mice by cervical dislocation. Hearts were removed, snap-frozen in liquid nitrogen and stored at -80ºC.
Growth protocol Pure-bred wild type (129S1/SvImJ) and PPARα-/- (129S4/SvJae) mice, aged 2-6 months, were used. Animals were put on a run-in diet consisting of a modified AIN76A diet (corn oil was replaced with olive oil) two weeks before the start of the experiment.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from mouse hearts using TRIzol reagent, followed by purification of total RNA 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 The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).
 
Hybridization protocol Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).
Scan protocol Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
Data processing Expression estimates were calculated using GCRMA (v2.2.0) in Bioconductor, applying the emperical Bayes (EB) model for background estimation.
 
Submission date Jul 07, 2011
Last update date Feb 24, 2012
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 GPL1261
Series (2)
GSE30495 Detailed transcriptomics analysis of the effect of dietary fatty acids on gene regulation in the murine heart.
GSE30649 Detailed transcriptomics analysis of the effect of dietary fatty acids on gene regulation in the murine heart [superseries]

Data table header descriptions
ID_REF
VALUE GCRMA signal (as log2).

Data table
ID_REF VALUE
1415670_at 7.949108444
1415671_at 8.489470808
1415672_at 9.214968836
1415673_at 5.148956619
1415674_a_at 6.947813126
1415675_at 5.250709291
1415676_a_at 10.43073365
1415677_at 7.760856828
1415678_at 9.361644077
1415679_at 9.195906157
1415680_at 7.371314374
1415681_at 8.461366019
1415682_at 6.71384192
1415683_at 9.347825421
1415684_at 6.778662092
1415685_at 8.287699366
1415686_at 8.65084271
1415687_a_at 11.54737561
1415688_at 9.728030425
1415689_s_at 4.646487833

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.




Supplementary file Size Download File type/resource
GSM756426.CEL.gz 3.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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