|
| Status |
Public on Oct 04, 2006 |
| Title |
LDmuscle_NNgenotype_T0_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Longissimus dorsi (LD) muscle sample, Callipyge genotype (NN) at birth (T=0), technical rep1
|
| Organism |
Ovis aries |
| Characteristics |
Genotype: NN
Age: T=0 birth
|
| Treatment protocol |
Skeletal muscle samples were obtained from a flock of Dorset/Suffolk/Rambouillet cross-bred sheep raised at Utah State University. Matings were conducted to produce the genotypes for transcript profiling comparisons, particularly the genotypes NN and NCpat , where NN is the wild type and NCpat is the paternal heterozygote. The genotypes of all animals were confirmed using a genotyping test (Freking et al. 2002; Smit et al. 2003). Longissimus dorsi (LD) skeletal muscle samples were obtained from 8 male lambs representing four of each genotype, at birth (T0) and 11-12 weeks of age (T12). In addition, samples were also taken of semimembranosis (SM) and semitendonosis (ST) skeletal muscles from wild type lambs at 12 weeks of age. All muscles were carefully dissected out and weighed. Samples were then collected from each muscle at pre-determined sites. The samples were dissected from the animal within 15 minutes of euthanasia and immediately frozen under liquid nitrogen and stored at –80oC.
|
| Growth protocol |
Animals were reared and euthanased in accordance with the animal ethics guidelines of Utah State University (Utah, USA)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Bovine Genomer Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
|
| Description |
Gene expression data from the Callipyge genotype (NN) at birth (T=0) from muscle type (LD)
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.
|
| |
|
| Submission date |
Oct 03, 2006 |
| Last update date |
Oct 03, 2006 |
| Contact name |
Ross L Tellam |
| E-mail(s) |
Ross.Tellam@csiro.au
|
| Phone |
07 3214 2476
|
| Organization name |
CSIRO Animal, Food and Health Sciences
|
| Department |
Level 6 Queensland Biosciences Precinct
|
| Lab |
University of Qld.
|
| Street address |
306 Carmody Road St.Lucia
|
| City |
Brisbane |
| State/province |
QLD |
| ZIP/Postal code |
4067 |
| Country |
Australia |
| |
|
| Platform ID |
GPL2112 |
| Series (1) |
| GSE5955 |
Expression data from Callipyge muscle types (ST, LD, SS, SM) at birth (T=0) and 12 weeks (T=12) |
|
