|
| Status |
Public on Jun 01, 2013 |
| Title |
S-1 |
| Sample type |
RNA |
| |
|
| Source name |
Longissimus Dorsi muscle tissue of Chinese Red Steppe, stored, -80°C
|
| Organism |
Bos taurus |
| Characteristics |
gender: male
age: 1-month old
tissue: Longissimus Dorsi muscle
breed: Chinese Red Steppe
|
| Treatment protocol |
The bulls were humanely killed at the slaughter house of the academy, and fresh longissimus dorsi muscle tissues were obtained during slaughter, immediately frozen in liquid nitrogen and stored at -80°C for microarray analysis.
|
| Growth protocol |
A total of 18 bulls (9 were 1month old while another 9 were 24 months old) of the same breed (Chinese Red Steppe) were maintained in standard conditions and fed with standard diet.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from muscle samples was extracted using Trizol reagent (Invitrogen, USA) and purified using QIAGEN RNeasy Total RNA Isolation kit (QIAGEN, USA) following manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Amplified and labeled according to Affymetrix GeneChip experiment operation process.
|
| |
|
| Hybridization protocol |
according to AFFX Eukaryotic expression profile of single-round PCR chip experiment Protocol.
|
| Scan protocol |
according to Affymetrix GeneChip data analysis.
|
| Description |
18 bulls in our study included 9 bulls of 1 month old (3 samples: S-1; S-2; S-3) and 9 bulls of 24 month old (3 samples: P-2; P-3; P-4); each sample was the pool mixed by total RNA from 3 individuals to enlarge the samples for gene expression difference elimination between the individuals and show the really differential expression genes between different development stages in LM tissue.
|
| Data processing |
The chips rectified were made by normalization processing using dChip (Affymetrix) software. False discovery rates for the genes were calculated by using t test and P values. Fold changes were calculated based on the unadjusted data’s means. Genes were annotated with NetAffx, and differentially expressed genes were identified using Significance Analysis of Microarrays (SAM). Using the criterion of cutoff
limitation as a fold change≧2 or ≦0.5 and q-value≦5%, differential expression genes were screened and clustered with the Cluster 3.0 software. The selected genes were further analyzed in the context of gene ontology (GO) biological process and KEGG biological pathway using the molecule annotation system 2.0 (MAS 2.0, http://bioinfo.capitalbio.com/mas/) software (CapitalBio, Beijing, China).
|
| |
|
| Submission date |
May 11, 2010 |
| Last update date |
Jun 01, 2013 |
| Contact name |
qin li hong |
| E-mail(s) |
qlhqlh2005@yahoo.com.cn
|
| Phone |
+86-431-87836156
|
| Fax |
+86-431-87836156
|
| Organization name |
Jilin University
|
| Department |
College of Animal Science and Veterinary Medicine
|
| Lab |
Keylab of animal embryo engineering
|
| Street address |
5333,xi'an road
|
| City |
Changchun |
| State/province |
jilin |
| ZIP/Postal code |
130062 |
| Country |
China |
| |
|
| Platform ID |
GPL2112 |
| Series (1) |
| GSE21782 |
Microarray Analysis on the Differences of Gene Expression in Longissimus Dorsi Muscle Tissue between 1-month and 24-month Chinese Red Steppes |
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