|
| Status |
Public on Nov 15, 2008 |
| Title |
HFD, WT, eWAT n=10 (virtual pool) vs. Mouse143_Pro/Pro_HFD_Male_eWAT |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
epididymal fat pad
|
| Organism |
Mus musculus |
| Characteristics |
Mouse143_Pro/Pro_HFD_Male_eWAT
|
| Treatment protocol |
Diet as specified
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol Lysis + RNeasy Column
|
| Label |
Cy3
|
| Label protocol |
One round of RT-IVT to cRNA
|
| |
|
| Channel 2 |
| Source name |
epididymal fat pad
|
| Organism |
Mus musculus |
| Characteristics |
HFD, WT, eWAT n=10 (virtual pool)
|
| Treatment protocol |
Diet as specified
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol Lysis + RNeasy Column
|
| Label |
Cy5
|
| Label protocol |
One round of RT-IVT to cRNA
|
| |
|
| |
| Hybridization protocol |
Labeled cRNAs were fragmented to an average size of approximately 50 to 100 nucleotides in the presence of 10 mM zinc chloride and adding a hybridization buffer containing 1 M sodium chloride, 0.5 percent sodium sarcosine, 50 mM morpholino-ethane sulfonic acid (pH 6.5), and formamide (final concentration, 30 percent at 40°C); After hybridization, the slides were washed
|
| Scan protocol |
slides were scanned using a confocal laser scanner (Agilent Technologies, Palo Alto, CA). Fluorescence intensities of the scanned images were quantified, normalized, and balanced
|
| Description |
Samples from liver, adipose (epididymal fat pads) and muscle (gastrocnemius) were acquired from 10 male wildtype mice and 10 male pro12ala knock-in mice. All mice were fed a chow diet for eight weeks then half were switched to high fat (R&D, D12907B, 41% milk fat, 43% carbohydrate) diet for an additional 12 weeks while the remaining mice stayed on chow. Individuals from each strain were compared to a common pool created from equal portions of RNA from 10 wildtype samples
|
| Data processing |
Rosetta Resolver Ratio Experiment using Rosetta Resolver Agilent Error Model
|
| |
|
| Submission date |
Oct 09, 2008 |
| Last update date |
Nov 14, 2008 |
| Contact name |
eric e schadt |
| E-mail(s) |
eric_schadt@merck.com
|
| Organization name |
Merck
|
| Department |
Genetics
|
| Street address |
401 Terry Ave N
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL7368 |
| Series (1) |
| GSE13305 |
Molecular mechanisms underlying the metabolic changes induced by the Pro12Ala PPARγ2 variant in mice |
|
