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Sample GSM830133 Query DataSets for GSM830133
Status Public on Nov 30, 2011
Title Liver wild type High Fat Diet, replicate 3
Sample type RNA
Source name Liver wild type 6 months High Fat Diet, replicate 3
Organism Mus musculus
Characteristics treatment: high fat diet
tissue: liver
genotype: wild type
gender: male
genetic background: C57BL/6J
Treatment protocol Liver from wild type and Nrf2-KO mice was excised after perfusion with ice-cold saline and then it was immersed in RNA later solution (Ambion,Foster City, CA).
Growth protocol Mice were housed in the animal facility in the University of Patras Medical School in temperature-, light- and humidity-controlled rooms with a 12-h light/dark cycle.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using a guanidinium thiocyanate based method using the Trizol reagent (Invitrogen, Carlsbad,CA) and was further purified using the Rneasy minikit (Qiagen,Hilden,Germany) following the manufacturer's instructions.
Label Cy3
Label protocol Labelling of total RNA was performed in Atlas Biolabs (Berlin, Germany) using the following kit: Low Input Quick Amp Labeling Kit, One Color (#5190-2305), Agilent Technologies, using 100 ng of total RNA as starting material, according to the manufacturer´s instructions (Manual One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, Version 6.5, Mai 2010, Agilent Technologies). cRNA synthesis was regarded successful provided that =1.65 μg of cRNA with a Cy3-incorporation rate =8.0 pmol/μg cRNA were synthesized.
Hybridization protocol Hybridization was performed in Atlas Biolabs (Berlin,Germany) as follows;1.65 μg of Cy3-labelled cRNA were fragmented according to the manufacturer´s instructions, and 1.425 μg of fragmented cRNA were hybridized (conc: 15 ng/μl). Hybridization conditions: 65°C, 10 rpm, 17 h; in an Agilent hybridization oven
Scan protocol Scanning was performed using an Agilent DNA Microarray Scanner (Model G2505C) and Agilent´s Scan Control Software (version A.8.3.1) in Atlas Biolabs (Berlin,Germany).
Description Gene expression after 6 months on high-fat diet
Data processing Primary data analysis was performed using Agilent´s Feature Extraction Software (version in Atlas Biolabs (Berlin,Germany).
Submission date Nov 09, 2011
Last update date Nov 30, 2011
Contact name Dionysios Chartoumpekis
Organization name Lausanne University Hospital CHUV
Department Service of Endocrinology Diabetes and Metabolism
Street address Ave de la Sallaz 8
City Lausanne
ZIP/Postal code 1011
Country Switzerland
Platform ID GPL11202
Series (1)
GSE33575 Hepatic gene expression profiles after long-term high-fat diet feeding in wild type and Nrf2 knock-out mice.

Data table header descriptions
VALUE log2 quantile normalized signal

Data table
A_51_P411271 11.44090134
A_55_P2144686 5.055258517
A_55_P1982499 1.721498111
A_51_P493987 1.895137536
A_51_P456208 8.220019726
A_51_P329811 2.068892743
A_52_P562267 6.555718385
A_51_P450406 1.313351655
A_55_P2032946 12.23489765
A_52_P250400 0.888167907
A_51_P434758 1.544600248
A_55_P2075253 2.297014995
A_55_P2362635 1.351143416
A_52_P566840 3.758754349
A_55_P2114342 8.32142622
A_55_P2101792 1.042325123
A_55_P2048855 3.522831752
A_55_P2017116 7.567319077
A_55_P2163090 3.640259631
A_55_P2047163 1.279943994

Total number of rows: 39474

Table truncated, full table size 982 Kbytes.

Supplementary file Size Download File type/resource
GSM830133_252665510734_201010130835_S01_GE1_107_Sep09_1_1.txt.gz 9.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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