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Sample GSM309063 Query DataSets for GSM309063
Status Public on Oct 14, 2008
Title brain_heterozygous_Insm1_knockout_rep2
Sample type RNA
 
Source name dorsal telencephanlon, heterozygous_Insm1_knockout
Organism Mus musculus
Characteristics E13.5
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from mice brain tissues using TRIZOL (GibcoBRL) reagent following the protocol according to the manufacturers instructions. Quality was assessed by running nano assays on a Bioanalyzer (Agilent). Ribosomal RNA was reduced following the GeneChip Whole Transcript (WT) sense Target labeling Assay Manual Version 4 (Affymetrix) which is optimized for the use of 1µg total RNA.
Label biotin
Label protocol The RNA samples were processed following the GeneChip Whole Transcript (WT) sense Target labeling Assay Manual Version 4 (Affymetrix) which is optimized for the use of 1µg total RNA as input.
 
Hybridization protocol Hybridisation (16 hours), washing and staining were done by following the GeneChip Whole Transcript (WT) sense Target labeling Assay Manual Version 4 (Affymetrix).
Scan protocol The chips were scanned with a GeneChip scanner 3000 7G system. Image analysis was done with the GeneChip® Command Console™ Software Version 1.0 (Affymetrix).
Description dorsal telencephanlon, heterozygous_Insm1_knockout
Data processing Low level data analysis, such as the calculation of expression values (RMA) and the calculation of detection P-values for the genes that are annotated in the core set of probes (23238 transcript clusters) on the Mouse Exon 1.0 ST Array was carried out with the Expression Console Software version 1.1 (Affymetrix). A gene was considered as expressed if at least 60% of the exons of a gene were significantly (P<=0.05) higher expressed than the background signals in 80% of the samples. High level data analysis was done in R. Gene by gene t-tests were carried between the control and the Insm1 over expressed samples and between wt and Insm1 KO mice. To adjust P-values for multiple hypothesis testing, we chose to control the false discovery rate (FDR), which is less conservative and more powerful than other adjustments. FDR adjustments were performed to reduce the number of false significant genes to fewer than 5%.
 
Submission date Jul 30, 2008
Last update date Oct 14, 2008
Contact name Thomas Giger
E-mail(s) giger@eva.mpg.de
Organization name Max-Planck-Institute of Evolutionary Anthropology
Department Evolutionary Genetics
Street address Deutscher Platz 6
City Leipzig
ZIP/Postal code 04106
Country Germany
 
Platform ID GPL6096
Series (1)
GSE12294 The role of Insulinoma associated 1 protein in the development of the mammalian neocortex

Data table header descriptions
ID_REF
VALUE RMA values were determined by Expression Console Software version 1.1 (Affymetrix).

Data table
ID_REF VALUE
6848511 5.624955
6864895 1.666069
6766590 0.2740394
6914045 0.3821039
6963197 0.6617835
6766588 0.3491736
6995964 3.439592
6766587 0.1722996
6815739 1.47691
6766586 3.909061
7012346 0.2162766
6766585 0.8059734
6848505 0.7379109
6766584 0.7020139
6848504 1.34673
6979576 0.7805995
6995960 7.870495
6766583 0.4966855
6963191 1.04545
6979575 0.767216

Total number of rows: 23238

Table truncated, full table size 392 Kbytes.




Supplementary file Size Download File type/resource
GSM309063.CEL.gz 17.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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