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Sample GSM453396 Query DataSets for GSM453396
Status Public on Sep 03, 2010
Title Mouse 157, gastrocnemius muscle, high fat diet, week 8
Sample type RNA
 
Source name mouse 157, gastrocnemius muscle, high fat diet, week 8
Organism Mus musculus
Characteristics subject: mouse 157
tissue: gastrocnemius muscle
diet: high fat diet
strain: C56BL/6J
gender: Male
age: 20 weeks
Treatment protocol After 8 weeks of diet intervention, mice were sacrificed, the gastrocnemius and quadriceps muscles were 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 randomly assigned to the LF or the HF group for 8 weeks
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 and FDR < 0.05
 
Submission date Sep 16, 2009
Last update date Sep 03, 2010
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)
GSE18127 Hoxd genes and fiber type-specific markers specify adult mouse muscle type in a diet-independent way

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

Data table
ID_REF VALUE
100009600_at 4.4
100012_at 4.4
100017_at 7.7
100019_at 11.1
100034251_at 8.6
100036521_at 190.1
100037258_at 144.1
100037278_at 5.3
100038570_at 8.4
100038635_at 4.6
100038680_at 1.9
100038887_at 2786.5
100038959_at 49.8
100039026_at 35.4
100039027_at 3.8
100039094_at 3.5
100039235_at 5.7
100039282_at 3.6
100039284_at 3.8
100039307_at 3.4

Total number of rows: 16539

Table truncated, full table size 228 Kbytes.




Supplementary file Size Download File type/resource
GSM453396_A103_47_157M3_HFW_56D.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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