|
| Status |
Public on Oct 14, 2008 |
| Title |
brain_Insm1_wildtype_rep4 |
| Sample type |
RNA |
| |
|
| Source name |
dorsal telencephanlon, wildtype
|
| 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, wildtype
|
| 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 |
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