|
| Status |
Public on Jan 15, 2008 |
| Title |
Mouse_Brain_HumanCafeDiet__Batch_1__replicate_1 |
| Sample type |
RNA |
| |
|
| Source name |
Dissected Mouse Brain
|
| Organism |
Mus musculus |
| Characteristics |
Strain: NMR-1.
Gender: Female.
Age: 8 weeks at the experiment start.
|
| Treatment protocol |
Mice were euthanized by cervical dislocation and brain (right cerebral hemisphere) tissue was dissected. RNA was extracted from the 24 samples as per established lab protocols (Franz et al, 2005, PMID: 16420671) and processed in two batches (containing equal numbers of individuals from all treatment groups).
|
| Growth protocol |
Laboratory mice were fed a HumanCafe diet for two weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared from 5 microg. total RNA following standard Affymetrix® protocols
|
| |
|
| Hybridization protocol |
Hybridization to Affymetrix® GeneChip® Mouse Genome 430 2.0 arrays was carried out following standard Affymetrix® protocols.
|
| Scan protocol |
GeneChips® were scanned using GeneChip Scanner 3000
|
| Description |
Gene expression data from Brain of a laboratory mouse fed a HumanCafe diet for two weeks.
|
| Data processing |
Affymetrix® microarray image data were collected with Affymetrix® GeneChip® Operating Software version 1.1 using default parameters. We used the Bioconductor 'affy' software package for further data analysis. Signal intensities were calculated with the 'rma' function using default parameters, including quantile normalization and log2 transformation. Detection p-values were calculated with the 'mas5calls' function using default parameters.
|
| |
|
| Submission date |
Nov 15, 2006 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Mehmet Somel |
| E-mail(s) |
[email protected]
|
| Phone |
+49-(0)341-3550-530
|
| Fax |
+49-(0)341-3550-555
|
| Organization name |
Max Planck Institute for Evolutionary Anthropology
|
| Department |
Evolutionary Genetics
|
| Street address |
Deutscher Platz 6
|
| City |
Leipzig |
| ZIP/Postal code |
D-04103 |
| Country |
Germany |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE6285 |
Expression data from brains of mice fed four different diets |
|
| Relations |
| Reanalyzed by |
GSE119085 |
