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Sample GSM565225 Query DataSets for GSM565225
Status Public on Dec 31, 2011
Title Male control diet heart, biological rep1
Sample type RNA
 
Source name 32-week male mouse cardiac tissue
Organism Mus musculus
Characteristics diet: control diet
biological replicate: 1
gender: Male
age: 32-week
tissue: heart
Treatment protocol The four dietary regimens used in this study were: [1] Standard Chow (Control diet) with ad lib drinking water. [2] Standard Chow, with ad lib drinking water containing 0.64 g/L Monosodium Glutamate (MSG diet). [3] Trans fat diet of 20% (w/w) Partially Hydrogenated Vegetable Shortening containing 8.68% w/w Trans fatty acids(TFA diet). [4] Trans fat Diet #5C4M together with ad lib drinking water containing 0.64 g/L Monosodium Glutamate (TFA+MSG diet). Following mating, the 4 groups of dams were maintained on their respective diets throughout the gestation and nursing period. Male and female offspring used in the following experiments were weighed, weaned onto the same diets and maintained on their respective dietary regimens until they reached 32 weeks of age.
Growth protocol Our study animals were bred from female C57Bl/6J mice fed a standard chow diet until 6 weeks of age whereupon they were placed on one of 4 different dietary regimens for a period of 3 weeks prior to mating.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from snap-frozen cardiac tissue using QIAGEN RNeasy® Kit Fibrous Tissue according to manufacturers' instructions. The integrity of the RNA was measured using a 2100 Bioanalyzer instrument and an RNA 6000 Nano LabChip assay (Agilent Technologies).
Label biotin
Label protocol Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 250ng total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Technical Manual, 2009, Affymetrix).
 
Hybridization protocol Following fragmentation, 5.5 ug of ssDNA was hybridized for 17 hr at 45°C on GeneChip Mouse Gene 1.0ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix 3000 7G Scanner and GeneChip Operating Software version 1.4 to produce .CEL files
Description Gene expression data from 32-week Male control diet heart.
Data processing Microarray analysis was performed using the Partek genomic suite software version 6.3 (Partek, MO, USA). We imported the interrogating probes using the file MoGene-1_0-st-v1.na30.1.mm9.probeset.csv.zip downloaded from http://www.affymetrix.com/support/technical/byproduct.affx?product=mogene-1_0-st-v1 for the annotation purpose. Probe set data were summarized, background adjusted, and quantile normalized using the GC-Robust Multi-Array (GCRMA) algorithm, no log, a pre-background adjustment for probe sequence was also applied.
 
Submission date Jul 12, 2010
Last update date Dec 31, 2011
Contact name Kate S Collison
Organization name King Faisal Specialist Hospital & Research Centre
Street address Department Biological & Medical Research
City Riyadh
ZIP/Postal code POB3354
Country Saudi Arabia
 
Platform ID GPL10655
Series (1)
GSE22881 Expression data from murine cardiac tissue

Data table header descriptions
ID_REF
VALUE Probe set data were summarized, background adjusted, and quantile normalized using the GC-Robust Multi-Array (GCRMA) algorithm, no log, a pre-background adjustment for probe sequence was also applied.

Data table
ID_REF VALUE
10344615 20.930
10344617 45.491
10344621 25.196
10344623 421.309
10344625 156.648
10344626 641.345
10344627 260.650
10344628 761.292
10344629 346.507
10344630 358.714
10344631 670.858
10344632 203.925
10344634 25.470
10344635 358.999
10344636 158.908
10344638 27.978
10344639 514.065
10344640 842.319
10344641 277.567
10344642 202.114

Total number of rows: 241293

Table truncated, full table size 3793 Kbytes.




Supplementary file Size Download File type/resource
GSM565225.CEL.gz 3.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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