|
| Status |
Public on Mar 24, 2016 |
| Title |
Sparrow_muscle_baseline |
| Sample type |
RNA |
| |
|
| Source name |
Horse before receiving low dose of clenbuterol
|
| Organism |
Equus caballus |
| Characteristics |
breed: Thoroughbred horse
treated with: none
time point: baseline before receiving low dose of clenbuterol drug
tissue: muscle
|
| Treatment protocol |
Five of the horses received 0.8 µg/kg clenbuterol PO BID for 30 days and an additional 4 horses received 0.8 µg/kg, BID x 3 days; 1.6 µg/kg, BID x 3 days; 2.4 µg/kg, BID x 3 days; 3.2 µg/kg, BID for 21 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Muscle biopsy samples were placed in 600 µl of lysis buffer, contaning 2-β- mercaptoethanol (Qiagen Inc, Valencia, CA). The tissue sample was then transferred to MagNa Green Beads tubes (Roche Diagnostics, Mannhein, Germany). Homogenization was performed using a MagNaLyse (Roche Diagnostics, Mannhein, Germany) at 6000 rpm for 30 sec followed by a 1.0 min cool down period. Homogenization intervals were continued until pieces of muscle were no longer visible (≤3 times). Total RNA was purified using an miRNeasy Mini kit (RNeasy Mini, Qiagen Inc, Valencia, CA) and following the manufacturer’s instructions. Total RNA integrity was assessed using the Experion Automated Electrophoresis System (Bio-rad, Hercules, CA). Only RNA samples with RIN ≥ 8 and 260/280 ratios between 1.7 and 2.1 were used (Denisov et al 2008) (Fleige et al 2006)
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according the standard Affymetrix protocol from 6ug total RNA (Expression Analysis Technical Manual 2001, Affymetrix)
|
| |
|
| Hybridization protocol |
Following fragmentation 10ug of cRNA were hypridized for 16 hr at 45C on Equus caballus Gene 1.0 ST Array [transcript (gene) version] represents the equine gene 1.ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400
|
| Scan protocol |
GeneChips were Scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
Gene expression data from horse muscle before administration of low dose of clenbuterol (0.8 µg/kg orally twice a day for 30 days); baseline1 time point
|
| Data processing |
Expression data was normalized, background corrected and summarized using the RMA algorithm implemented in the Affymetrix Expression Console. Data visualization and filtering was performed in Transcriptome Analysis console version 3.0
|
| |
|
| Submission date |
Mar 23, 2016 |
| Last update date |
Mar 24, 2016 |
| Contact name |
Heather Knych |
| E-mail(s) |
hkknych@ucdavis.edu
|
| Organization name |
University of California Davis
|
| Department |
CAHFS
|
| Lab |
EACL / Pharma
|
| Street address |
620 W. Health Sciencse Drive
|
| City |
Davis |
| State/province |
California |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL18123 |
| Series (1) |
| GSE79559 |
Differential Expression of Skeletal Muscle Genes Following Admnistration of Clenbuterol to Exercised Horses |
|
