|
| Status |
Public on Mar 10, 2009 |
| Title |
Mus spretus whole brain 0 days old, rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Dissected Mus spretus whole brain
|
| Organism |
Mus spretus |
| Characteristics |
age: 0 days after birth
sex: Male
tissue: whole brain
|
| Treatment protocol |
We dissected whole brains (excluding the ofactory bulb) of mice at three age stages: neonates within the first postnatal day, pups at 14 days of age, and adults at 56 days of age.
|
| Growth protocol |
WSB/EiJ (Mus musculus) and SPRET/EiJ (Mus spretus) strain mice were purchased from the Jackson Laboratory (Bar Harbor, Maine, USA) and bred in at the MPI-EVA facility under standard conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA from the whole tissue sample was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared from 5 micrograms of total RNA following standard Affymetrix protocols.
|
| |
|
| Hybridization protocol |
Hybridization to Affymetrix MG-430 2.0 GeneChip arrays was carried out following standard Affymetrix protocols.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000.
|
| Description |
Gene expression data from the whole brain of a 0 days old Mus spretus individual
|
| Data processing |
Affymetrix microarray image data were collected with Affymetrix GeneChip Operating Software version 1.1 using default parameters. For summarizing the expression data, we used Custom Chip Definition Files (Custom CDF, version 11) based on Ensembl gene annotation rather than Affymetrix annotation (Dai et al., PMID: 16284200). Further, we masked out probes that which were estimated to show genotype differences between M.musculus and M.spretus, by employing a method which utilizes the discrepancy between the expression levels of pairs of probes within a probe set (e.g. see Khaitovich et al., PMID: 15289471). 19% of all probes are thus masked. Further, we did not include probesets with less than 8 probes in our analysis. The list of exluded probes is supplied as supplement to the CDF file. We used the R 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. Note that, for analyses of gene expression changes during postnatal development within a single species, it is advisable to use non-masked CDF files. This is because masking out probes decreases statistical power.
|
| |
|
| Submission date |
May 21, 2008 |
| Last update date |
Mar 09, 2009 |
| Contact name |
Mehmet Somel |
| E-mail(s) |
somel@eva.mpg.de
|
| 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 |
GPL6886 |
| Series (1) |
| GSE11528 |
Gene expression data from mouse postnatal brain development |
|
