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Sample GSM994216 Query DataSets for GSM994216
Status Public on Jan 08, 2013
Title Muscle_NCoR1-MKO_rep2
Sample type RNA
 
Source name Gastrocnemius muscle from NCoR1 MKO mouse
Organism Mus musculus
Characteristics strain: C57BL/6
gender: Male
genotype/variation: NCoR1-MKO
Extracted molecule total RNA
Extraction protocol RNA from gastrocnemius was isolated with miRNeasy Mini Kit (QIAGEN)
Label Biotin
Label protocol Target synthesis was prepared starting from 250ng total RNA using the WT Expression kit (Ambion). Fragmentation and labeling of amplified cDNA were performed using the WT Terminal Labeling Kit (Affymetrix).
 
Hybridization protocol 85µl cocktail (containing 2µg labeled DNA) was loaded on Mouse Gene 1.0 ST Array (Affymetrix) and hybridized for 17 hours (45°C, 60rpm) in Hybridization oven 645 (Affymetrix). The arrays were washed and stained on Fluidics Stations 450 (Affymetrix) by using the Hybridization Wash and Stain Kit (Affymetrix) under FS450_0007 protocol.
Scan protocol GeneChips were scanned with an Affymetrix GeneChip Scanner 3000 7G.
Description Gene expression data from gastrocnemius muscle of adult male mice.
Data processing DAT images and CEL files of the microarrays were generated using Affymetrix GeneChip Command Control 3.0.0.1214.
Affymetrix CEL files were normalized according to RMA method (Irizarry, 2003) and data were log 2.0 transformed. To select differently expressed genes a 1-way ANOVA model by using Method of Moments (Eisenhart, 1947) was applied using Partek Genomic Suite (version 6.6).
 
Submission date Aug 28, 2012
Last update date Jan 08, 2013
Contact name Joaquín Pérez-Schindler
E-mail(s) j.perezschindler@unibas.ch
Organization name University of Basel
Department Biozentrum
Street address Klingelbergstrasse 50 / 70
City Basel
ZIP/Postal code 4056
Country Switzerland
 
Platform ID GPL6246
Series (1)
GSE40439 Gene expression analysis of Ncor1 muscle-specific knockout and PGC-1alpha muscle-specific transgenic skeletal muscle

Data table header descriptions
ID_REF
VALUE RMA normalized and log2 transformed

Data table
ID_REF VALUE
10338001 12.0996
10338002 6.66686
10338003 10.3953
10338004 9.18589
10338005 3.20305
10338006 3.46462
10338007 3.67356
10338008 4.14507
10338009 8.7427
10338010 3.25983
10338011 5.99759
10338012 3.38044
10338013 3.04728
10338014 3.15321
10338015 3.07412
10338016 7.87652
10338017 13.0805
10338018 7.17216
10338019 5.31046
10338020 8.56917

Total number of rows: 35556

Table truncated, full table size 586 Kbytes.




Supplementary file Size Download File type/resource
GSM994216_NCoR1_MKO_2.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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