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| Status |
Public on Apr 20, 2017 |
| Title |
hippocampus_F1_methyldiet_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
hippocampus of F1 offspring of methyl diet supplemented fathers
|
| Organism |
Mus musculus |
| Characteristics |
strain: congenic C57BL/6J x 129S6/SvEv hybrids
diet (for fathers or grandfathers): experimental methyl donor diet (3MS ZM)
generation: F1 offspring
age: 4w
tissue: hippocampus
|
| Treatment protocol |
F1 and F2 mice fed a control diet were derived from fathers or grandfathers, respectively fed a control diet (T.2918.12, Envigo) or an experimental methyl donor diet (3MS ZM) supplemented with 7.5 g l-methionine, 15 g choline, 15 g betaine, 15 mg folic acid, 1.5 mg vitamin B12 and 150 mg zinc for 6 weeks prior to mating.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using Qiagen RNeasy kits
|
| Label |
Cy3
|
| Label protocol |
Cy3 labeled cRNA was prepared from 0.6 ug RNA using the Low RNA Input linear Amplification Kit Plus, One Color protocol (Agilent 5188-5339) and the Agilent One color RNA Spike-In Kit (Agilent 5188-5252) following the manufacturer's standard protocols.
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| |
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| Hybridization protocol |
The hybridizations were performed for 17 hours at 10 rpm and 65°C in a hybridization oven (Agilent) using the Mouse GE 4x44K v2 Microarray Kit (Cat. No. G4846A). Washing and staining of the arrays were performed according to the manufacturer’s recommendation.
|
| Scan protocol |
Cy3 intensities were detected by one-color scanning using an Agilent DNA microarray scanner (G2505B) at 5 μm resolution. Scanned image files were inspected for artifacts and then analyzed.
|
| Description |
M1
|
| Data processing |
ntensity data were extracted using Agilent’s Feature Extraction (FE) software (version 9.5.3.1) including a quality control based on internal controls using Agilent’s protocol GE1_107_Sep09. All chips passed the quality control and were analyzed using the Limma package of Bioconductor. The microarray data analysis consists of the following steps: 1. between-array normalization, 2. global clustering and PCA-analysis, 3. fitting the data to a linear model, 4. detection of differential gene expression and 5. over-representation analysis of differentially expressed genes. We applied quantile-normalization to the log2-transformed intensity values as a method for between-array normalization.
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| |
|
| Submission date |
Nov 22, 2016 |
| Last update date |
Apr 20, 2017 |
| Contact name |
Dan ehninger |
| E-mail(s) |
dan.ehninger@dzne.de
|
| Phone |
+49 0228 43302-530
|
| Organization name |
German Center for Neurodegenerative Diseases
|
| Street address |
Sigmund-Freud-Straße 27
|
| City |
Bonn |
| ZIP/Postal code |
53127 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11202 |
| Series (2) |
| GSE90158 |
A paternal methyl donor-rich diet altered cognitive and neural functions in offspring mice [expression profiling] |
| GSE90504 |
A paternal methyl donor-rich diet altered cognitive and neural functions in offspring mice |
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