|
| Status |
Public on May 10, 2011 |
| Title |
APPsa-DM_hippocampus_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Hippocampus from adult APPsα-DM knock-out mouse
|
| Organism |
Mus musculus |
| Characteristics |
tissue: hippocampus
background strain: C57BL/6
gender: female
genotype/variation: APPsα-DM (APPα/αAPLP2-/-)
age: adult (38 - 40 weeks)
|
| Treatment protocol |
Animals were sacrificed by cervical dislocation. Dissected brains were stored at -20°C in RNAlater (Qiagen). Subsequently, prefrontal cortices and hippocampi were dissected.
|
| Growth protocol |
Animals were kept under specific pathogen free housing conditions (SPF unit) and in compliance with the regulations of the German animal protection law.
|
| 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.
|
| Description |
back-crossed to C57BL/6 for 6 generations
|
| 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 |
Mar 10, 2011 |
| Last update date |
May 10, 2011 |
| Contact name |
Ulrike Müller |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE27888 |
Comparative transcriptome analysis of APPsα-DM and APLP2-KO brains |
|
