|
| Status |
Public on Jun 25, 2016 |
| Title |
HFD_liver_1 |
| Sample type |
RNA |
| |
|
| Source name |
liver, HFD for 20 weeks
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57/BJ
tissue: liver
gender: male
age: 26 wks
treatment: high-fat diet (HFD)
|
| Treatment protocol |
Male C57/BJ mice aged 6 weeks were randomly assigned to a high-fat diet (D12331; ResearchDiets, NJ, USA) or control chow diet (Provimi Kliba). All mice were sacrificed under anesthesia 20 weeks after food treatment and the livers were harvested.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using Trizol (Invitrogen).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-026655 Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Jun 24, 2016 |
| Last update date |
Jun 25, 2016 |
| Contact name |
Zhibo Gai |
| E-mail(s) |
[email protected]
|
| Phone |
+41 44 556 3143
|
| Organization name |
University Hospital Zurich
|
| Department |
Department of Clinical Pharmacology and Toxicology
|
| Street address |
Wagistrasse 14
|
| City |
Zurich |
| State/province |
Schweiz |
| ZIP/Postal code |
8952 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL11202 |
| Series (1) |
| GSE83700 |
Effect of High-Fat Diet on Mouse Liver Gene Expression |
|
