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Sample GSM144541 Query DataSets for GSM144541
Status Public on Jan 15, 2008
Title Mouse_Brain_HumanCafeDiet__Batch_2__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
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
Reanalyzed by GSE119085

Data table header descriptions
VALUE Normalized signal intensity (log2) calculated by the RMA method
ABS_CALL Label indicating whether the transcript was present (P; detection p-value < 0.05), absent (A; p >= 0.1), marginal (M; p < 0.1)
DETECTION P-VALUE Significance level of the detection call

Data table
1415670_at 8.21013281399234 P 0.00167287722066534
1415671_at 10.0582091564095 P 0.00167287722066534
1415672_at 9.16172897596454 P 0.00167287722066534
1415673_at 6.61316462466296 P 0.00382292568622067
1415674_a_at 7.75216146601951 P 0.00167287722066534
1415675_at 7.33434065306652 P 0.00167287722066534
1415676_a_at 10.0637905676987 P 0.00167287722066534
1415677_at 8.00434611350507 P 0.00167287722066534
1415678_at 9.0702123683329 P 0.00167287722066534
1415679_at 8.7460249100162 P 0.00167287722066534
1415680_at 6.39120632624743 P 0.00292359407424914
1415681_at 7.79578109366034 P 0.00167287722066534
1415682_at 6.28604458927303 P 0.00167287722066534
1415683_at 8.67924666180727 P 0.00167287722066534
1415684_at 5.73562735825208 P 0.00167287722066534
1415685_at 6.3866687509849 P 0.00167287722066534
1415686_at 8.11494189596315 P 0.00167287722066534
1415687_a_at 11.3104601937828 P 0.00167287722066534
1415688_at 8.78907968471707 P 0.00167287722066534
1415689_s_at 5.27339361071724 P 0.00167287722066534

Total number of rows: 45101

Table truncated, full table size 2165 Kbytes.

Supplementary file Size Download File type/resource
GSM144541.CEL.gz 5.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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