|
| Status |
Public on Sep 28, 2016 |
| Title |
Liver_control_5 |
| Sample type |
RNA |
| |
|
| Source name |
Liver control
|
| Organism |
Bos taurus |
| Characteristics |
breed: Holstein
gender: female
condition: control
tissue: liver
Stage: week 5 of lactation
|
| Treatment protocol |
Cows were milked twice daily and milk yields of each cow were recorded automatically. Data on milk yield and milk composition have been reported in (Schlegel et al., J Dairy Sci. 2012;95:3905-18). At wk 1, 5 and 14 of lactation, blood samples and liver biopsies were taken. The liver biopsy procedure has been described in detail in (Schlegel et al., J Dairy Sci. 2012;95:3905-18). The liver biopsy samples were immediately snap-frozen in liquid nitrogen and stored at -80°C until analysis. In the present study, transcript profiling was carried out in the liver samples from wk 5 of lactation in order to identify genes and pathways regulated by rumen-protected CLA during early lactation. The first wks after parturition represent a critical phase in the productive cycle of high-yielding dairy cows because the liver experiences pronounced metabolic and inflammatory stress which increases the risk to develop liver-associated diseases, such as fatty liver and ketosis.
|
| Growth protocol |
A total of 40 primi- and multiparous Holstein cows with an average parity number of 2.6 were used for this study. The study was carried out at the Agricultural Experimental Station Hirschau of the Technical University of Munich (Germany) and was approved by the Bavarian state animal care and use committee. The experimental period lasted from wk 3 prepartum to wk 14 postpartum. Details on feeding regimen and husbandry conditions can be found in a recent publication (Schlegel et al., J Dairy Sci. 2012;95:3905-18). In brief, the cows were allotted to two groups of 20 cows each: control group and CLA group. Cows of both groups received an identical partial mixed ration (PMR) ad libitum, which was calculated to meet the energy and protein demand of a cow weighing 650 kg and producing 21 kg milk/d. In addition, cows of both groups were individually offered a limited amount of concentrate via transponder-access feeding stations in order to cover the individual extra requirements for milk production. Calculations for energy and protein supply followed the recommendations of the German Society of Nutrition Physiology (2001). The composition and the nutrient and energy concentrations of both, PMR and concentrate, and the amount of concentrate offered are shown in (Schlegel et al., J Dairy Sci. 2012;95:3905-18). The rumen-protected fat supplements, either control fat or CLA fat, were fed via an extra portion of concentrate (supplemental concentrate) containing 27.3 % fat supplement (either control fat or CLA fat) for both groups. The supplemental concentrate was fed during the experimental period at a constant amount of 630 g of DM/d and cow by hand once daily. The composition and the nutrient and energy concentrations of the supplemental concentrate and the contents of major fatty acids in the fat supplements are also given in (Schlegel et al., J Dairy Sci. 2012;95:3905-18).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from liver samples using Trizol® according to the manufacturer’s protocol and stored at -80 °C. Concentration and purity of the RNA were estimated from the optical density at 260 and 280 nm, respectively, using a NanoQuant plateTM (Infinite® 200, Tecan).
|
| Label |
Biotin
|
| Label protocol |
The cRNA was labeled with biotin using the Affymetrix GeneChip labeling kit.
|
| |
|
| Hybridization protocol |
After checking the quality and quantity of the labeled cRNA, cRNA was fractionated and hybridized with the Affymetrix GeneChips. GeneChips were washed and stained with the Affymetrix GeneChip Fluidics station 450. The GeneChips were then scanned with an Affymetrix GeneChip scanner 3000. All procedures were performed according to Affymetrix protocols (GeneChip expression analysis, Technical manual from Affymetrix). The quality of hybridization was assessed in all samples following the manufacturer´s recommendations.
|
| Scan protocol |
After scanning the gene chips, cell intensity (CEL) files containing a single intensity value for each probe cell were generated from the raw image data with GeneChip Operating Software v1.2 (Affymetrix).
|
| Data processing |
CEL files were imported into Expression Console v1.1 (Affymetrix) and subjected to global normalization using the Robust Multiarray Average (RMA) algorithm.
|
| |
|
| Submission date |
Sep 27, 2016 |
| Last update date |
Sep 28, 2016 |
| Contact name |
Robert Ringseis |
| E-mail(s) |
robert.ringseis@ernaehrung.uni-giessen.de
|
| Organization name |
JLU Gießen
|
| Department |
Institute of Animal Nutrition and Nutrition Physiology
|
| Street address |
Heinrich-Buff-Ring 26-32
|
| City |
Gießen |
| ZIP/Postal code |
35390 |
| Country |
Germany |
| |
|
| Platform ID |
GPL2112 |
| Series (1) |
| GSE87391 |
Transcript profiling in the liver of early-lactating dairy cows fed conjugated linoleic acid |
|
