|
| Status |
Public on Apr 11, 2014 |
| Title |
muscle_rfi_pr2 |
| Sample type |
RNA |
| |
|
| Source name |
Longissimus cervicis, excised ~45 min post-exsanguination
|
| Organism |
Bos indicus x Bos taurus |
| Characteristics |
gender: steer
age: approx. 18 months
efficiency: Low
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1. RNA was extracted once with TRI Reagent and bromochloropropane (Molecular Research Center) according to the manufacturer's protocol, once with TRI Reagent and BCP in a 2:1 ratio, and once with BCP alone (again according to the manufacturer's protocol). RNA was precipitated with isopropanol, washed with ethanol, dried, and resuspended in nuclease-free water.
2. RNA was quantified on a NanoDrop ND-1000 spectrophotometer. RNA quality was assayed on an Agilent 2100 Bioanalyzer.
3. RNA was purified on Qiagen RNeasy columns using their RNA cleanup protocol, and Dnase-treated with Ambion's DNA-free kit.
|
| Label |
Cy3
|
| Label protocol |
1. Samples from steers with high residual feed efficiency were paired randomly with samples from steers with low residual feed efficiency. Four samples were randomly chosen to be labeled with Cy3 and four with Cy5; the other member of each pair was labeled with the opposite dye.
2. RNA (2.5 μg/sample) was labeled with the Agilent two-color QuickAmp Labeling Kit, according to the manufacturer's protocol.
|
| |
|
| Hybridization protocol |
RNA was hybridized to Agilent bovine 4x44K slides according to the hybridization procedures in the QuickAmp Labeling kit manual. Hybridized slides were also washed and dried according to that protocol.
|
| Scan protocol |
Slides were scanned on an Axon GenePix Personal 4100A scanner. Data were quantified in GenePix Pro v.6.0.
|
| Description |
Biological replicate 2 of 16: high vs. low rfi
|
| Data processing |
Agilent GeneSpring software (v 10.0.02) was used for background subtraction and LOWESS normalization.
|
| |
|
| Submission date |
Apr 10, 2014 |
| Last update date |
Apr 11, 2014 |
| Contact name |
Robert Neil Vaughn |
| E-mail(s) |
bobv527@gmail.com
|
| Phone |
9794502765
|
| Organization name |
Texas A&M University
|
| Department |
Soil and Crop Sciences
|
| Lab |
New Beasley Lab
|
| Street address |
0965 Agronomy
|
| City |
College Station |
| State/province |
TX |
| ZIP/Postal code |
77845 |
| Country |
USA |
| |
|
| Platform ID |
GPL9712 |
| Series (1) |
| GSE56705 |
Muscle in beef steers with low vs. high residual feed efficiency |
|
