|
| Status |
Public on Aug 27, 2019 |
| Title |
Liver, saturated fat, replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
background: C57BL/6J
diet: enriched in saturated fatty acids
|
| Treatment protocol |
Mice were randomly assigned to three groups (n = 8 mice per group). For 7 weeks, each group was fed a high-fat diet rich in trans-unsaturated (Trans), cis-unsaturated (Cis) or saturated (Saturated) fatty acids (modified TestDiet 58V8; TestDiet LTD, London). Fat sources were from partially hydrogenated soy oil for the Trans diet, canola and palm olein oil for the Cis diet, and cocoa butter for the Saturated diet. Total fat content in all three diets was 45% energy percent.
|
| Growth protocol |
Animal studies were performed using 4 to 6-month-old pure-bred male mice on a C57Bl/6 background.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from samples using the RNeasy kit (Qiagen) with a DNase digestion step according to the manufacturer’s protocol. RNA quality was verified on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands) using 6000 Nano Chips according to manufacturer’s instructions. RNA was considered suitable for array hybridization only if RNA integrity number exceeded 8.0.
|
| Label |
biotin
|
| Label protocol |
Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).
|
| |
|
| Hybridization protocol |
Hybridization and washing of the Affymetrix GeneChip Mouse Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).
|
| Scan protocol |
Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).
|
| Data processing |
Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.46.0).
|
| |
|
| Submission date |
Aug 23, 2019 |
| Last update date |
Aug 28, 2019 |
| Contact name |
Guido Hooiveld |
| E-mail(s) |
[email protected]
|
| Organization name |
Wageningen University
|
| Department |
Div. Human Nutrition & Health
|
| Lab |
Nutrition, Metabolism & Genomics Group
|
| Street address |
HELIX, Stippeneng 4
|
| City |
Wageningen |
| ZIP/Postal code |
NL-6708WE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL11533 |
| Series (2) |
| GSE136271 |
Industrial trans fatty acids stimulate SREBP2-mediated cholesterogenesis and promote non-alcoholic fatty liver disease [liver] |
| GSE136354 |
Industrial trans fatty acids stimulate SREBP2-mediated cholesterogenesis and promote non-alcoholic fatty liver disease |
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