|
| Status |
Public on Apr 19, 2010 |
| Title |
Liver_OSe_animal#23 |
| Sample type |
RNA |
| |
|
| Source name |
Liver tissue from organic Se supplmented heifers
|
| Organism |
Bos taurus |
| Characteristics |
tissue: Biopsied liver (right lobe) tissue
agent: organic selenium
|
| Treatment protocol |
The treatment protocol (i.e., dietary Se supplementation) has been described in the “overall design” and “growth protocol” sections above.
|
| Growth protocol |
Thirty Angus heifers (Age 261 ± 6 d) obtained from and raised at the University of Kentucky Agricultural Research and Education Center (Princeton, KY) were fed a corn silage-based diet without Se supplementation for 75 d. Then the heifers (BW 393 ± 9 kg) were randomly assigned to 3 dietary treatment groups (Ctrl, ISe, OSe; n = 10) as described in the “overall design” section above. To achieve a growth rate of 0.5 kg/d, heifers were individually fed a basal cracked corn and cottonseed hull-based diet (7.8 kg/d for the first 80 d and 8.2 kg/d for the last 25 to 26 d) using a Calan gate system. A commercial mineral-vitamin premix (Kentucky Nutrition Service, Lawrenceburg, KY) with or without Se supplementation was administered daily by manually mixing into each individual animal’s basal diet. The basal diet plus the mineral-vitamin premix totally provide intrinsic Se to the animals at 0.48 mg/animal daily.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol extraction of total RNA was performed according to the manufacturer's instructions (Invitrogen Corporation, Carlsbad, CA).
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA was prepared from 4 μg of total RNA as per the standard labeling protocol described in the Affymetrix GeneChip Technical Analysis Manual (2005; Affymetrix, Santa Clara, CA). Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA) and oligo(dT)24 primers. Biotin-labeled cRNA was prepared by cDNA in vitro transcription using the GeneChip IVT Labeling kit (Affymetrix, Santa Clara, CA) incorporating biotinylated UTP.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 μg of labeled cRNA was hybridized to Affymetrix Bovine Genome Array for 16 hr at 45°C using the GeneChip Hybridization Oven 640 (Affymetrix Technical Analysis Manual). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
GeneChips were stained with R-Phycoerythrin Streptavidin, followed by an antibody solution and a second R-Phycoerythrin Streptavidin solution, with all liquid handling performed by a GeneChip Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner (GCS) 3000 7G.
|
| Description |
Liver tissue was obtained with aspiration biopsy technique
|
| Data processing |
The raw data were collected with the GeneChip Operating Software (GCOS, version 1.2). The expression intensity values from the software (i.e., the “.cel” files) were imported into Partek Genomics Suite software (version 6.4; Partek Inc., St. Louis, MO). The algorithm of Robust Multichip Averaging adjusted with GC oligo content was implemented for background correction. The background-corrected data were further converted into expression values via the algorithms of Quantile normalization of different chips and then Median Polish summarization of multiple probes.
|
| |
|
| Submission date |
Dec 29, 2009 |
| Last update date |
Apr 19, 2010 |
| Contact name |
Shengfa F Liao |
| E-mail(s) |
sfliao2@uky.edu
|
| Organization name |
University of Kentucky
|
| Department |
Dept of Animal & Food Sciences
|
| Street address |
214 WP Garrigus Bldg
|
| City |
Lexington |
| State/province |
KY |
| ZIP/Postal code |
40546-0215 |
| Country |
USA |
| |
|
| Platform ID |
GPL2112 |
| Series (1) |
| GSE19696 |
Effect of Dietary Supplementation of Selenium (Organic vs. Inorganic) on Liver Gene Expression Profile in Beef Heifers |
|
