|
| Status |
Public on Mar 31, 2016 |
| Title |
20133403 Liver Low gain-low intake |
| Sample type |
RNA |
| |
|
| Source name |
Liver of steer
|
| Organism |
Bos taurus |
| Characteristics |
Sex: Male
tissue: Liver
phenotype: Low gain-low intake
|
| Treatment protocol |
Animals most divergent from the bivariate mean from in each of the four phenotypic Cartesian quadrants for gain x intake were selected and liver tissue samples were collected. The transcriptomes of the samples from the 16 animals selected were evaluated by microarray.
|
| Growth protocol |
Steers were fed a high-concentrate diet with WDGS for 78 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TriPure Reagent was used to extract total RNA according to manufacturer's instructions, except that a 20 minute centrifugation (rather than 15 min) was used following the addition of chloroform and the pellets were washed twice with 1 ml of 75% ethanol. RNA pellets were centrifuged through RNeasy Plus Mini Kit columns (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions to remove genomic DNA.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, cRNA was hybridized for 20 hr at 45C on Bovine 1.1ST Array. GeneChips were washed and stained in the Affymetrix GeneAtlas Fluidics Station.
|
| Scan protocol |
GeneChips were scanned with the Affymetrix GeneAtlas Imager.
|
| Data processing |
The data were transformed by Affymetrix and analyzed with Affymetrix Expression Console and Affymetrix Transcriptome Analysis Console using the one-way between-Subject ANOVA (Unpaired) algorithm was (Linear Fold Change cutoff of 2 and ANOVA p-value (Condition pair) <0.05).
|
| |
|
| Submission date |
Dec 04, 2015 |
| Last update date |
Mar 31, 2016 |
| Contact name |
Amanda K Lindholm-Perrry |
| E-mail(s) |
amanda.lindholm@ars.usda.gov
|
| Phone |
402-762-4189
|
| Organization name |
USMARC
|
| Department |
NEMRU
|
| Street address |
State Spur 18D
|
| City |
Clay Center |
| State/province |
NE |
| ZIP/Postal code |
68933 |
| Country |
USA |
| |
|
| Platform ID |
GPL20768 |
| Series (1) |
| GSE75700 |
Differential gene expression in the liver among crossbred beef steers with divergent gain and feed intake phenotypes |
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