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Sample GSM341881 Query DataSets for GSM341881
Status Public on Mar 02, 2009
Title Foxp2hum/hum_strKi_18d_m_run1_litter4
Sample type RNA
 
Source name Mus musculus striatum, genotype:Foxp2hum/hum, strain:Ki, age:18days
Organism Mus musculus
Characteristics genotype: Foxp2hum/hum
strain: Ki - a knock-in or wild-type mouse from crosses of Foxp2wt/hum animals (clone no. 5H11)
age: P18
sex: male
run (microarray batch): 1
litter: 4
biological replicate: 1
tissue: striatum (brain)
Treatment protocol Embryos (E16.5) were dissected and briefly washed in ice-cold dissection buffer (15mM HEPES (hemisodium salt, Research Organics, Cleveland, Ohio, USA), 30mM glucose (Sigma-Aldrich, Steinheim, Germany ), 1x Hanks balanced Salt solution (without Calcium, Magnesium, Phenol Red, Sodium Bicarbonate; Invitrogen, Carlsbad, California, USA) and 1.34 mM NaHCO3 (Sigma-Aldrich); sterile filtered). The brain of each embryo was then removed, dissected under a stereomicroscope in RNAlater (Ambion, Austin, Texas, USA) and stored in RNAlater until all brains of the litter had been prepared. For preparation of the striatum, the cerebellum was removed, the brain cut into the two hemispheres and the striatum (i.e. caudate nucleus, putamen and pallidum) was prepared from each hemisphere according to (Schambra et al., 1992). The striata of both hemispheres were combined and stored in RNAlater at -20° until further use. Tailbuds of the embryos were used for genotyping and sex determination. A second batch of embryos was prepared in a similar fashion. Striatal tissue from adult females was prepared in a similar fashion. All embryonic and adult samples were derived from crosses of Foxp2wt/hum animals (5C10 line). Striatal samples from young animals P15, P18 and P21) were prepared slightly different in that brains were cut in ice-cold PBS by a custom-build razorblade holder that allowed making 2 mm thick coronal sections. 2-3 slices were used to obtain striatal biopsy punches each 2 mm in diameter, which were then frozen in liquid nitrogen. We picked individuals so that genotypes were balanced as much as possible for sex, litter and run in the two different “strains” (“Ki” for pups from crosses of Foxp2wt/hum animals (5H11 line with the Neomycin cassette removed(Foxp2hum?neo)) and “Ko” for pups from crosses of Foxp2wt/ko and C57BL/6J animals).
Growth protocol The two nucleotide substitutions that occurred during human evolution are both located in exon seven of the FOXP2 gene. We introduced these two substitutions into the orthologous exon of the mouse Foxp2 gene by homologous recombination in embryonic stem (ES) cells derived from C57BL/6 mice, thus generating mice carrying the Foxp2hum allele. Mice carrying the Foxp2hum allele were generated by Ozgene (Bentley, Australia) from two C57BL/6 ES cell clones that had integrated the vector via homologous recombination. Whereas the first line (clone 5H10) was used for initial analyses, the second one (clone 5H11) was used for testing the reproducibility of the results from the first line. To this end, some mice were generated that carried a Foxp2hum allele in which the Neomycin resistance cassette had been removed by crossings with a FLPe deleter strain (Jackson Laboratory, Stock Number 003800; C57BL/6J) followed by removal of the FLPe transgene by crossings. Mice carrying the Foxp2ko allele were generated by crossing chimeric mice (clone 5H11) to a B6 Cre deleter strain (Ozgene, Bentley, Australia) and subsequent crosses to remove the Cre transgene. Mice were bred at the MPI-EVA facility under standard conditions. We picked individuals so that genotypes were balanced as much as possible for sex, litter and run in the three different “strains.”
Extracted molecule total RNA
Extraction protocol For RNA isolation, the tissue was transferred to 1ml of TRIZol reagent (Invitrogen) and immediately homogenized using a teflon pestle (cylindrical) in a 2ml glass homogenizer on a Schütt homgenplus homogenizer (Schütt Labortechnik, Göttingen, Germany). RNA and genomic DNA were isolated according to the TRIZol protocol with addition of 250µg Glycogen (Roche Diagnostics, Mannheim, Germany) to 1ml of homogenate. DNA was used to confirm genotypes and RNA was further purified using the MiniElute kit (Qiagen, Valencia, California, USA). High and equal quality RNA was ensured on an Agilent 2100 Bioanalyzer system (Foster City, California, USA).
Label biotin
Label protocol Biotinylated cRNA were prepared from 3.5 micrograms (embryonic striatum), 3.3 micrograms (adult striatum) and 1microgram (young animals) of total RNA following standard Affymetrix protocols.
 
Hybridization protocol Embryonic samples were processed in two batches, adult samples in one batch, and the young animals in three batches. For the young animals, all probes were labelled together but hybridised in three different runs. 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 striatum of a 18 days old mouse homozygous for the human Foxp2 allele (Foxp2hum/hum), belonging to strain Ki
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 (CDF) based on Ensembl gene annotation rather than the standard Affymetrix annotation (customCDF v. 10; see Dai et al., PMID: 16284200). We used the R Bioconductor 'affy' software package for further data analysis (Gautier et al., PMID: 14960456). 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.
 
Submission date Nov 13, 2008
Last update date Mar 04, 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 GPL7635
Series (1)
GSE13588 Gene expression in striatums of Foxp2-hum, Foxp2-ko and wild-type mice

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 8.701906453 P 0.000175805
ENSMUSG00000000003_at 3.83164076 A 0.500000024
ENSMUSG00000000028_at 5.382193633 A 0.187129631
ENSMUSG00000000031_at 4.019401225 A 0.429431532
ENSMUSG00000000037_at 4.637829722 M 0.099852447
ENSMUSG00000000049_at 4.636376722 A 0.306044945
ENSMUSG00000000056_at 7.786985874 P 3.79E-05
ENSMUSG00000000058_at 8.333858351 P 0.001672877
ENSMUSG00000000078_at 6.626634282 P 6.63E-09
ENSMUSG00000000085_at 9.452305112 P 0.003455264
ENSMUSG00000000088_at 12.47929534 P 6.15E-06
ENSMUSG00000000094_at 4.269705138 A 0.827276243
ENSMUSG00000000103_at 5.643701081 P 0.00032753
ENSMUSG00000000120_at 5.653016462 A 0.604215908
ENSMUSG00000000125_at 4.003872032 A 0.605162372
ENSMUSG00000000126_at 4.328364012 M 0.05706417
ENSMUSG00000000127_at 5.993467308 P 0.003181444
ENSMUSG00000000134_at 8.788352893 P 0.013115575
ENSMUSG00000000142_at 7.853859699 P 0.000774413
ENSMUSG00000000148_at 7.078795337 P 0.00109085

Total number of rows: 15768

Table truncated, full table size 728 Kbytes.




Supplementary file Size Download File type/resource
GSM341881.CEL.gz 6.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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