NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM290526 Query DataSets for GSM290526
Status Public on Mar 10, 2009
Title Mus musculus whole brain 56 days old, rep2
Sample type RNA
 
Source name Dissected Mus musculus whole brain
Organism Mus musculus
Characteristics age: 56 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 56 days old Mus musculus 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

Data table header descriptions
ID_REF
VALUE Quantile normalized log2-transformed signal intensities
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
ENSMUSG00000000001_at 8.60251848532038 P 0.00382292568622067
ENSMUSG00000000028_at 4.88487019253777 M 0.0865355230931175
ENSMUSG00000000037_at 4.34031636688656 A 0.645547273374325
ENSMUSG00000000056_at 7.53450068928861 P 0.00420942662344048
ENSMUSG00000000058_at 5.67246204289635 P 0.00542187338760336
ENSMUSG00000000078_at 7.32050937291545 P 1.21567983457638e-08
ENSMUSG00000000085_at 8.10836606215364 P 0.00382292568622067
ENSMUSG00000000088_at 12.021889259537 P 6.59400644765773e-05
ENSMUSG00000000093_at 4.06449243260448 A 0.123873163210698
ENSMUSG00000000094_at 3.8218154360672 A 0.319453264512412
ENSMUSG00000000120_at 5.62214858343166 A 0.401105968737734
ENSMUSG00000000125_at 3.62106539180448 A 0.813027629406118
ENSMUSG00000000126_at 5.11487349716302 P 0.00499822391608662
ENSMUSG00000000127_at 7.29367701342168 P 0.000642415987287426
ENSMUSG00000000131_at 8.96098704366206 P 0.00253107676274655
ENSMUSG00000000134_at 8.34851768663915 P 0.0331579576283270
ENSMUSG00000000142_at 6.89386285226209 P 0.0078534285830174
ENSMUSG00000000148_at 6.52750397799468 P 0.0237891855253296
ENSMUSG00000000154_at 5.6999147812894 A 0.621815485272688
ENSMUSG00000000157_at 5.17247576989694 A 0.253812114760311

Total number of rows: 12346

Table truncated, full table size 725 Kbytes.




Supplementary file Size Download File type/resource
GSM290526.CEL.gz 6.2 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap