|
| Status |
Public on Mar 18, 2011 |
| Title |
APP_R6_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
APP_R6
|
| Organism |
Mus musculus |
| Characteristics |
tissue: prefrontal cortex from adult APP knock-out mouse
genetic background: back-crossed to C57BL/6 for 6 generations
gender: male
|
| Treatment protocol |
Animals were sacrificed by cervical dislocation. Dissected brains were stored at -20°C in RNAlater (Qiagen). Subsequently, prefrontal cortices were dissected.
|
| Growth protocol |
Animals were kept under specific pathogen free housing conditions (SPF unit) according to the guidelines of the German Council on Animal Care.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using the RNAeasy kit from Qiagen and following the manufacturer's recommendations. RNA quality was assessed with the Bioanalyzer 2100 (Agilent) to ensure high sample quality across all samples.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1µg total RNA (Expression Analysis Technical Manual, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 15µg cRNA were hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.
|
| Data processing |
The data was processed in R using the RMA algorithm including RMA background correction, quantile normalization, and median polish as summarization method implemented in the affy package and provided by Bioconductor.
|
| |
|
| Submission date |
Dec 08, 2010 |
| Last update date |
Mar 18, 2011 |
| Contact name |
Ulrike Müller |
| E-mail(s) |
u.mueller@urz.uni-hd.de
|
| Organization name |
Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg
|
| Department |
Bioinformatics and Functional Genomics
|
| Street address |
Im Neuenheimer Feld 364
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE25926 |
Comparative transcriptome profiling of Amyloid Precursor Protein APP family members in the adult cortex |
|
