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| Status |
Public on Jun 03, 2015 |
| Title |
male TFA diet liver, biological replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
male TFA diet liver
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57Bl/6J
gender: male
tissue: liver
age: 20 wks
diet group: TFA (Trans Fatty Acids)
|
| Treatment protocol |
The four dietary regimens used in this study were:[1] TFA diet: consisting of 20% (w/w) Partially Hydrogenated Vegetable Shortening (Test Diet #5C4M containing 8.68% w/w Trans fatty acids; Test Diet Purina, USA), with ad lib drinking water. [2] MSG+TFA diet: TFA diet with ad lib drinking water containing 0.75 g/L of L -Glutamic acid monosodium salt hydrate (MSG catalog G1626 Sigma Aldrich). [3] ASP+TFA diet: (TFA diet with ad lib drinking water containing 0.25 g/L Asp-Phe methyl ester (aspartame, ASP, catalog A5139 Sigma Aldrich). [4] ASP+MSG+TFA diet: TFA diet with ad lib drinking water containing 0.25 g/L aspartame and 0.75 g/L monosodium glutamate. After the 3-week period of adjustment to the respective diets, 15 male offspring were bred, weaned and maintained on these diets for the duration of the study. Offspring were weaned at 4 weeks of age.
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| 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 liver tissue using QIAGEN RNeasy® Kit 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 (Affymetrix GeneChip WT Terminal Labeling and Hybridization user manual, 2010, in conjunction with the Ambion WT Expression Kit protocol, 2009).
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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 20-week male TFA diet liver tissue
Liver 3_(MoGene-1_0-st-v1).CEL.pimg
|
| Data processing |
Microarray analysis was performed using the Partek genomic suite software version 6.3 (Partek, MO, USA). Probe set data were summarized, background adjusted, and quantile normalized using the GC-Robust Multi-Array (GCRMA) algorithm.
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| |
|
| Submission date |
Jun 04, 2012 |
| Last update date |
Jun 03, 2015 |
| 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 |
GPL10740 |
| Series (2) |
| GSE38444 |
Expression data from murine liver tissue |
| GSE38446 |
Expression data from murine liver and adipose tissue |
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