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Sample GSM438009 Query DataSets for GSM438009
Status Public on Aug 10, 2010
Title muscle_HF_ d56_biorep6
Sample type RNA
 
Source name mouse 149, quadriceps muscle, high fat diet, day 56
Organism Mus musculus
Characteristics protocol: high fat diet
time: day 56
tissue: quadriceps muscle
strain: C56BL/6J
gender: Male
age: 20 weeks
Treatment protocol After 0 days or 56 days of diet intervention, mice were sacrificed, the quadriceps muscle was dissected and snap-frozen in liquid nitrogen
Growth protocol Mice were fed a standard growth diet for 3 weeks prior to switching to the LF run-in diet for 3 weeks. Following the run-in period mice were sacrificed or randomly assigned to the LF or the HF group for 56 days
Extracted molecule total RNA
Extraction protocol According the manufactures instruction, total RNA was extracted from the quadriceps muscle with Trizol reagent (Invitrogen, Breda, the Netherlands) and purified with the Rneasy Mini Kit
(Qiagen, Venlo, the Netherlands). Contaminating genomic DNA was removed with the RNase-free DNase set (Qiagen, Venlo, the Netherlands) according the manufactures instructions.
Label biotin
Label protocol Labeling was performed according to the manufactures instructions as described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual (Affymetrix, 2004)
 
Hybridization protocol Hybridization was performed according to the manufactures instructions as described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual (Affymetrix, 2004)
Scan protocol Scanning was performed according to the manufactures instructions as described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual (Affymetrix, 2004)
Description Before the diet intervention mice (age: 9 weeks) were switched to the LF run-in diet for 3 weeks
Data processing Expression levels of probe sets were normalized using GC-RMA(slow) (unlogged scale). Probe sets were redefined according to Dai et al (Nucleic Acids Research, 2005). In this method probes are annotated
using up to date databases and assigned to unique gene identifiers, in this case Entrez ID's, instead of the classic GeneChip probe sets. As selection criteria we used: fold change > 1.3 a p value < 0.05 and FDR < 0.05
 
Submission date Aug 10, 2009
Last update date Aug 10, 2009
Contact name Janneke de Wilde
E-mail(s) j.dewilde@HB.unimaas.nl
Phone +31 433 881 509
Fax +31 43 367 09 76
Organization name Maastricht University
Department Human Biology
Street address Universiteitssingel 50
City Maastricht
ZIP/Postal code 6229 ER
Country Netherlands
 
Platform ID GPL7546
Series (1)
GSE17576 A high fat diet causes obesity and insulin resistance in mice, but induces small changes in the muscle transcriptome

Data table header descriptions
ID_REF
VALUE slow GC-RMA normalized signal intensity data

Data table
ID_REF VALUE
100009600_at 4.5
100012_at 3.7
100017_at 10
100019_at 8.8
100034251_at 8
100036521_at 160.1
100037258_at 122.6
100037278_at 5.6
100038570_at 6.7
100038635_at 6
100038680_at 2.8
100038887_at 2587.6
100038959_at 40.6
100039026_at 27.9
100039027_at 4.9
100039094_at 4.4
100039235_at 8
100039282_at 3.9
100039284_at 5.2
100039307_at 3.6

Total number of rows: 16539

Table truncated, full table size 225 Kbytes.




Supplementary file Size Download File type/resource
GSM438009_A103_19_149M1_HFW_56D.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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