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Sample GSM591482 Query DataSets for GSM591482
Status Public on Sep 09, 2010
Title liver_WT_LFH_rep6
Sample type RNA
 
Source name liver from C57Bl/6 mouse fed LFD for 21 weeks, high gainer, replicate 6
Organism Mus musculus
Characteristics tissue: liver
strain: C57Bl/6
diet: LFD for 21 weeks
phenotype: high gainer
Treatment protocol Livers were dissected from 18 mice after 21 weeks of diet intervention. Based in liver histology, mice were divided in 4 groups. Liver RNA samples from all mice were used for microarray analysis.
Growth protocol Eight week old male wildtype C57Bl/6 mice were fed LFD (D12450B, Research Diets Inc.) for 3 weeks. Thereafter, mice were either kept on LFD for 21 weeks or put on HFD (D12451, research Diets Inc.) for 21 weeks. Lard in the HFD was replaced by palm oil. Mice were divided into 4 groups based on liver histology. LF-low (LFL) responders displaying normal liver morphology, LF-high (LFH) responders showing benign hepatic steatosis, HF-low (HFL) responders displaying pre-NASH with macrovesicular lipid droplets, and HF-high (HFH) responders exhibiting overt NASH characterized by ballooning of hepatocytes, presence of Mallory bodies, and activated inflammatory cells.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from mouse livers 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 Sep 08, 2010
Last update date Sep 09, 2010
Contact name Guido Hooiveld
E-mail(s) [email protected]
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 (1)
GSE24031 Adipose tissue dysfunction signals progression of hepatic steatosis towards nonalcoholic steatohepatitis in C57Bl/6 mice

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

Data table
ID_REF VALUE
1415670_at 8.596144055
1415671_at 9.169311902
1415672_at 9.670437605
1415673_at 6.517632535
1415674_a_at 8.51178514
1415675_at 6.560254263
1415676_a_at 10.05611212
1415677_at 10.50589279
1415678_at 9.523882243
1415679_at 10.24543291
1415680_at 7.879457961
1415681_at 8.828344531
1415682_at 7.187061644
1415683_at 8.997969572
1415684_at 9.006336961
1415685_at 7.978844934
1415686_at 8.823576111
1415687_a_at 11.07412646
1415688_at 8.814786106
1415689_s_at 5.594697375

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.




Supplementary file Size Download File type/resource
GSM591482.CEL.gz 3.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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