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Sample GSM211642 Query DataSets for GSM211642
Status Public on Nov 30, 2007
Title muscle_HF_ d3_biorep3
Sample type RNA
 
Source name mouse 1769, quadriceps muscle, high fat diet, day 3
Organism Mus musculus
Characteristics Strain: C56BL/6J, Gender: Male, Age: 12 weeks
Treatment protocol After 3 or 28 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 2 weeks prior to switching to the LF run-in diet for 3 weeks. Following the run-in period mice were randomly assigned to the LF or the HF group for 3 or 28 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 and raw p value < 0.05
 
Submission date Jul 19, 2007
Last update date Aug 14, 2011
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 GPL5766
Series (1)
GSE8524 Short-term high fat-feeding results in morphological and metabolic adaptations in the skeletal muscle of C57BL/6J mice

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

Data table
ID_REF VALUE
100012_at 3.003900152
100017_at 4.314741159
100019_at 5.689788656
100061_at 4.343948653
100066_at 3.675950496
100072_at 12.56198637
100087_at 218.5582434
100088_at 9.952083139
100090_at 4.174267463
100102_at 4.939349138
100121_at 56.02179844
100129_at 7.612062138
100163_at 14.30704562
100169_at 14.4910144
100177_at 17.94612324
100198_at 99.53786337
100201_at 501.2108502
100206_at 7.730835501
100210_at 10.20548543
100213_at 16.80082174

Total number of rows: 16361

Table truncated, full table size 339 Kbytes.




Supplementary file Size Download File type/resource
GSM211642.CEL.gz 3.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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