|
| Status |
Public on Dec 31, 2011 |
| Title |
Male control diet heart, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
32-week male mouse cardiac tissue
|
| Organism |
Mus musculus |
| Characteristics |
diet: control diet
biological replicate: 2
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).
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| |
|
| 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.
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| |
|
| 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 |
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