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Sample GSM830132 Query DataSets for GSM830132
Status Public on Nov 30, 2011
Title Liver wild type High Fat Diet, replicate 2
Sample type RNA
 
Source name Liver wild type 6 months High Fat Diet, replicate 2
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 10.7.3.1) in Atlas Biolabs (Berlin,Germany).
 
Submission date Nov 09, 2011
Last update date Nov 30, 2011
Contact name Dionysios Chartoumpekis
E-mail(s) dchart@upatras.gr
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
ID_REF
VALUE log2 quantile normalized signal

Data table
ID_REF VALUE
A_51_P411271 11.44539319
A_55_P2144686 5.50900053
A_55_P1982499 3.284722846
A_51_P493987 3.014142087
A_51_P456208 8.049326227
A_51_P329811 1.989732362
A_52_P562267 6.859980416
A_51_P450406 1.536464507
A_55_P2032946 12.12967809
A_52_P250400 0.896965706
A_51_P434758 0.85598611
A_55_P2075253 1.807624526
A_55_P2362635 1.452111205
A_52_P566840 4.114684974
A_55_P2114342 8.543000307
A_55_P2101792 1.087179621
A_55_P2048855 2.526980133
A_55_P2017116 5.141838461
A_55_P2163090 2.48183065
A_55_P2047163 1.188084845

Total number of rows: 39474

Table truncated, full table size 982 Kbytes.




Supplementary file Size Download File type/resource
GSM830132_252665510641_201010130827_S01_GE1_107_Sep09_1_3.txt.gz 8.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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