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Sample GSM830138 Query DataSets for GSM830138
Status Public on Nov 30, 2011
Title Liver Nrf2 knock-out High Fat Diet, replicate 4
Sample type RNA
 
Source name Liver Nrf2 knock-out 6 months High Fat Diet, replicate 4
Organism Mus musculus
Characteristics treatment: high fat diet
tissue: liver
genotype: Nrf2 KO
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 1.450692308
A_55_P2144686 12.28238968
A_55_P1982499 8.967691673
A_51_P493987 8.335518706
A_51_P456208 14.48014787
A_51_P329811 8.205129408
A_52_P562267 1.414649682
A_51_P450406 6.081026577
A_55_P2032946 7.970791332
A_52_P250400 5.116970963
A_51_P434758 5.421238745
A_55_P2075253 5.725317514
A_55_P2362635 4.974554263
A_52_P566840 7.350962158
A_55_P2114342 4.687142734
A_55_P2101792 1.036443198
A_55_P2048855 7.223284129
A_55_P2017116 3.051515298
A_55_P2163090 3.634405354
A_55_P2047163 4.603000473

Total number of rows: 39474

Table truncated, full table size 982 Kbytes.




Supplementary file Size Download File type/resource
GSM830138_252665510734_201010130835_S01_GE1_107_Sep09_1_4.txt.gz 9.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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