|
| Status |
Public on Apr 19, 2017 |
| Title |
ileum_Control_d51_m_3_878 |
| Sample type |
RNA |
| |
|
| Source name |
ileum, Control, d51, m
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: ileum
treatment: Control
age: d51
block: 3
pen: 4
gender: m
sow: 878
animal: 7767
|
| Treatment protocol |
From d 14 till 23 after weaning the experimental piglet diets were provided containing either a regular or a high zinc concentration (analysed zinc concentrations 100 and 2690 mg/kg, respectively). The contrast in Zn concentration was realised by supplementing ZnO to the control diet.
|
| Growth protocol |
The piglets were of the Tempo x Topigs 20 genotype. At the start of the study the piglets were divided per pen in a way that the mean body weight and its variation per pen were similar. The piglets were weaned at a mean age of 28 ± 1.5 d. The piglets received creep feed during the suckling period. The mean body weight of the piglets one day prior to the start of the study was 7.9 kg. The piglets were housed in floor pens (1.75 x 3.00 m) with 12 piglets per pen. Male (boars) and female piglets were equally distributed over pens and litter mates were divided equally over pens as far as possible. The piglets were fed ad libitum using a dry feed dispenser. The diets were provided as pellets. The animals had free access to water via an automatic drinking device. The ingredient and calculated nutrient composition of the weaning diet and the starter diet (control). The diets were formulated to be nutritionally adequate using data on the composition and nutritional value of feed ingredients according to CVB (2011). After weaning, the piglets were fed the same weaning diet during the period of d 0 till 14. From d 14 till 23 after weaning the experimental piglet diets were provided containing either a regular or a high zinc concentration (analysed zinc concentrations 100 and 2690 mg/kg, respectively). The contrast in Zn concentration was realised by supplementing ZnO to the control diet. From d 23 till 35 the piglets in both treatment groups received the same starter piglet diet with a regular Zn concentration (analysed 100 mg Zn per kg).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 50 to 100 mg tissue mucosal scrapings of jejunum and ileum. The jejunum and ileum samples were homogenised using the TisuPrep Homogenizer Omni TP TH220P) in TRizol reagent (Life Technologies) as recommended by the manufacturer with minor modifications. The homogenised tissue samples were dissolved in 5 ml of TRizol reagent. After centrifugation the supernatant was transferred to a fresh tube. Subsequently a phase separation with chloroform was performed as described by the manufacturer Life Technologies. The RNA was precipitated and dissolved and quantified by absorbance measurements at 260 nm.
|
| Label |
Cy3
|
| Label protocol |
Labelling of RNA was done as recommended by Agilent Technologies using the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling. The input was 10 ng of total RNA and 600 ng of labelled cRNA was used on the eight pack array. Hybridization was performed as described in the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling protocol from Agilent in the hybridization oven (G2545A hybridization Oven Agilent Technologies).
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| |
|
| Hybridization protocol |
The hybridization temperature was 65°C with rotation speed 10 rpm for 17 hours. After 17 hours the arrays were washed as described in the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling protocol from Agilent.
|
| Scan protocol |
The arrays were scanned using the DNA microarray scanner with Surescan high resolution Technology from Agilent Technologies. Agilent Scan Control with resolution of 5 µm, 16 bits and PMT of 100%. Feature extraction was performed using protocol 10.7.3.1 (v10.7) for one colour gene expression.
|
| Data processing |
The data were analysed by using R (v3.0.2) by executing different packages, including LIMMA and arrayQualityMetrics. The data were read in and background corrected (method=normexp and offset=1) with functions from the R package LIMMA [1] from Bioconductor [2]. Quantile normalisation of the data was performed between arrays. The duplicate probes mapping to the same gene were averaged (‘avereps’) and subsequently the lower percentile of probes was removed in a three-step procedure, 1) get the highest of the dark spots to get a base value, 2) multiply by 1.1 and 3) the gene/probe must be expressed in each of the samples in an experimental condition (e.g. in ileum d 14 control).
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| |
|
| Submission date |
Feb 01, 2017 |
| Last update date |
Apr 19, 2017 |
| Contact name |
Dirkjan Schokker |
| E-mail(s) |
dirkjan.schokker@wur.nl
|
| Organization name |
Wageningen UR
|
| Department |
Wageningen Livestock Research
|
| Street address |
Droevendaalsesteeg 1
|
| City |
Wageningen |
| ZIP/Postal code |
6708 PB |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL18045 |
| Series (1) |
| GSE94370 |
Effect of ZincOxide in Weaned Piglets |
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