|
| Status |
Public on Dec 31, 2019 |
| Title |
252364710456___2 |
| Sample type |
RNA |
| |
|
| Source name |
Longissimus_Dorsi_Muscle___ANGUS___Pasture_Feeding___Replicate_2
|
| Organism |
Bos taurus |
| Characteristics |
fat depot: Longissimus_Dorsi_Muscle
breed: ANGUS
feeding protocol: Pasture_Feeding
replicate number: Replicate_2
age: 259 days
|
| Treatment protocol |
post-slaughter tissue samples were dissected in an abattoir and snap frozen prior to RNA extraction
|
| Growth protocol |
259 d in a feedlot
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the phenol chloroform extraction methodology with Trizol reagent
|
| Label |
Cy3
|
| Label protocol |
We used the Agilent one colour microarray based gene expression analysis low input Quick Amp labeling. We used an input of 50 ng of total RNA
|
| |
|
| Hybridization protocol |
1.65 ug of fragmented, labeled cRNA was prepared for hybridisation. Samples were hybridised to arrays for 17 hours at 45 degree C rotating at 10 rpm in the Agilent hybridisation oven. Arrays were washed using Gene Expression Wash buffer kit in a slide staining dish with slide rack.
|
| Scan protocol |
Arrays were scanned in the Agilent C scanner using the AgilentHD_GX_1 color protocol
|
| Description |
LDM_ANG_PAST_2
gene expresson after 259 d in a feedlot
|
| Data processing |
We applied the base-2 log-transformation followed by a normalization using a previously described mixed model approach (Reverter et al. 2004. Bioinformatics 21:1112-1120. https://doi.org/10.1093/bioinformatics/bti124). In brief, the mixed model contained the fixed effect of library sample with 96 levels and the random effects of gene, gene by breed interaction, gene by tissue interaction and residual.
|
| |
|
| Submission date |
Sep 05, 2019 |
| Last update date |
Jan 01, 2020 |
| Contact name |
Sean McWilliam |
| E-mail(s) |
[email protected]
|
| Organization name |
CSIRO
|
| Department |
Agriculture and Food
|
| Street address |
306 Carmody Road
|
| City |
St Lucia |
| State/province |
Queensland |
| ZIP/Postal code |
4067 |
| Country |
Australia |
| |
|
| Platform ID |
GPL11649 |
| Series (1) |
| GSE136981 |
Gene expression identifies metabolic and functional differences between intramuscular and subcutaneous adipocytes in cattle |
|
