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Sample GSM1254247 Query DataSets for GSM1254247
Status Public on Oct 30, 2013
Title M18 FAT
Sample type RNA
 
Source name Male MKR mice, Biological replicate 3
Organism Mus musculus
Characteristics tissue: Adipose
genotype: MKR Mice - Mutation in skeletal muscle IGF1 Receptor
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 MKR mice's adipose - 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 2.45767
10338069 1.90978
10338070 2.18342
10338071 2.24247
10338072 2.1973
10338073 2.49293
10338074 3.04315
10338075 2.91712
10338076 2.97729
10338077 2.93023
10338078 2.99044
10338079 2.26919
10338080 2.3457
10338081 2.43582
10338082 2.80577
10338083 2.22809
10338084 2.50703
10338085 3.33202
10338086 3.02561
10338087 2.97731

Total number of rows: 241419

Table truncated, full table size 3982 Kbytes.




Supplementary file Size Download File type/resource
GSM1254247_05-09-12_Y_Shiloach_M18_Fat.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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