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Sample GSM2212896 Query DataSets for GSM2212896
Status Public on Jun 25, 2016
Title chow_liver_3
Sample type RNA
Source name liver, chow diet for 20 weeks
Organism Mus musculus
Characteristics strain/background: C57/BJ
tissue: liver
gender: male
age: 26 wks
treatment: control chow diet
Treatment protocol Male C57/BJ mice aged 6 weeks were randomly assigned to a high-fat diet (D12331; ResearchDiets, NJ, USA) or control chow diet (Provimi Kliba). All mice were sacrificed under anesthesia 20 weeks after food treatment and the livers were harvested.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared using Trizol (Invitrogen).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-026655 Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
Data processing The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Submission date Jun 24, 2016
Last update date Jun 25, 2016
Contact name Zhibo Gai
Phone +41 44 556 3143
Organization name University Hospital Zurich
Department Department of Clinical Pharmacology and Toxicology
Street address Wagistrasse 14
City Zurich
State/province Schweiz
ZIP/Postal code 8952
Country Switzerland
Platform ID GPL11202
Series (1)
GSE83700 Effect of High-Fat Diet on Mouse Liver Gene Expression

Data table header descriptions
VALUE Normalized signal intensity

Data table
A_55_P2015753 13.13
A_55_P2153517 13.77
A_55_P1959748 12.62
A_52_P566840 8.377
A_52_P251623 8.718
A_55_P2114110 9.18
A_55_P1999902 15.53
A_51_P209818 8.233
A_66_P111660 18.23
A_55_P2007249 7.359
A_55_P2082880 7.502
A_51_P153063 8.568
A_55_P2092219 8.057
A_55_P2064333 7.031
A_55_P2325038 6.071
A_55_P2065899 8.027
A_51_P456208 10.17
A_51_P354165 14.14
A_55_P2074406 4.276
A_55_P2019989 6.037

Total number of rows: 1615

Table truncated, full table size 30 Kbytes.

Supplementary file Size Download File type/resource
GSM2212896_chow_liver_3.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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