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Sample GSM1254257 Query DataSets for GSM1254257
Status Public on Oct 30, 2013
Title W20 LIVER
Sample type RNA
 
Source name Male wild type (WT) mice, Biological replicate 3
Organism Mus musculus
Characteristics tissue: Liver
genotype: Wild Type
age: 10 weeks
genetic background: FVB/N
Treatment protocol Death of the mice was caused by subjecting them to CO2. Liver, Skeletal muscle, and adipose tissues were flash frozen in liquid nitrogen, stored at -80 oC, shipped on dry ice overnight, and kept at -80 oC prior to processing
Growth protocol Mice were kept on a 12-h light/dark cycle, they were allowed free access to diet (Picolab rodent diet #5053) and fresh water.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's (Qiagen) instructions.
Label biotin
Label protocol 100 ng of RNA from each sample was amplified to generate cDNA using NUGEN Applause WT – Amp ST system (NuGEN Technologies, CA), according to the manufacturer’s instructions. 2.5 µg of cDNA was fragmented and biotinylated using Encore Biotin module (NUGEN Technologies, CA).
 
Hybridization protocol Following labeling, samples were mixed with hybridization reagents (Affymetrix Inc. CA) and injected into affymetrix Mouse Gene 1.0 ST arrays and incubated for 18 + 2hours in hybridization oven rotating at 60 rpm at 45oC (Affymetrix Inc, CA) .
Scan protocol GeneChips were scanned using Affymetrix GeneChip scanner 3000 operated by Gene Chip Operating Software, version 1. 4 (GCOS 1.4)
Description Gene expression data from male wild type mice's liver - Biological replicate 3
Data processing The microarray raw data was analyzed using Partek software, version 6.3 Copyright 2008 Partek Inc., St. Louis, MO, USA. Raw data were subjected to Robust Multichip Average (RMA) quantile normalization to remove biases introduced by technical and experimental effects. All expression data were log base 2 -transformed to get near normal distribution for accurate statistical inference.
 
Submission date Oct 29, 2013
Last update date Oct 30, 2013
Contact name Amit Kumar
E-mail(s) amit.kumar3@nih.gov
Phone 443-850-6787
Organization name National Institutes of Health
Department NIDDK
Lab NIDDK Biotechnology Core Lab
Street address 14A Service Rd West., Room 176
City Bethesda
State/province MD
ZIP/Postal code 20814
Country USA
 
Platform ID GPL10740
Series (1)
GSE51866 Gene expression data for liver, adipose, and skeletal muscle tissues of MKR and Healthy mice.

Data table header descriptions
ID_REF
VALUE Log2 RMA normalized signal intensities

Data table
ID_REF VALUE
10338068 2.25791
10338069 1.88142
10338070 2.1549
10338071 2.11039
10338072 2.19655
10338073 2.29769
10338074 3.2142
10338075 2.63632
10338076 2.8602
10338077 3.06768
10338078 3.06923
10338079 2.14332
10338080 2.19594
10338081 2.26742
10338082 2.21361
10338083 2.17915
10338084 2.60743
10338085 3.15415
10338086 3.10867
10338087 2.93568

Total number of rows: 241419

Table truncated, full table size 3982 Kbytes.




Supplementary file Size Download File type/resource
GSM1254257_05-09-12_Y_Shiloach_W20_Liver.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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