|
| Status |
Public on Nov 04, 2014 |
| Title |
5289 |
| Sample type |
RNA |
| |
|
| Source name |
Brain_hippocampus_mouse_Tg2576_nontransgenic_rep1
|
| Organism |
Mus musculus |
| Characteristics |
model: Tg2576 (Hsiao et al, Science, 1995)
mutation: huAPP-K670N/M671L
strain: C57BL/6-CBA
gender: female
age: 17 months
condition: non-transgenic
tissue: Brain hippocampus
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy micro kit with an on-column DNase-treatment as recommended (Qiagen, Venlo, The Netherlands)
|
| Label |
Cy3
|
| Label protocol |
2-cycle amplification (Baugh et al, Nucl Acids Res, 2001) with labeling (2.4µl dye in stead of 4.8µl) in the second in vitro transcription according to Agilent’s protocol.
|
| |
|
| Hybridization protocol |
For Cy3 28 pmol incorporated dye was fragmented and resuspended in 55ul hybridization buffer HI-RPM (Agilent). The arrays were hybridized in microarray hybridization chambers (Agilent) overnight at 65ºC, rpm=10 for 17 hours.
|
| Scan protocol |
After washing the slides were scanned with a DNA microarray scanner (Agilent) using the `extended dynamic range' and images were processed with the Feature Extraction Software version 9.5 (Agilent).
|
| Description |
Amyloid-ß (Aß) plaques are pathological hallmarks of Alzheimer disease. However, the precise neuropathological changes that occur in brain in response to amyloid deposition are largely unknown. To study the molecular mechanism(s) responsible for Aß-mediated neuropathology, we performed a gene expression analysis on laser-microdissected brain tissue of Tg2576 mice compared to their littermate controls.
|
| Data processing |
The Agilent processed signal values (i.e., feature gProcessedSignal from Agilent Feature Extraction v9.5.3.1) were used for the data analysis. Intensities were base 2 log-transformed and in case of multiple probes for the same Agilent ID, log-intensities were averaged. Control probes were remove prior to analysis.
|
| |
|
| Submission date |
Mar 02, 2009 |
| Last update date |
Nov 04, 2014 |
| Contact name |
Rekin's Janky |
| E-mail(s) |
Nucleomics.Bioinformatics@vib.be
|
| Organization name |
VIB
|
| Department |
Nucleomics Core
|
| Street address |
Herestraat 49 Box 816
|
| City |
Leuven |
| ZIP/Postal code |
B-3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL7202 |
| Series (2) |
| GSE15056 |
Expression profiling of laser-microdissected tissue from Tg2576 plaque-depositing mouse model of Alzheimer's disease |
| GSE15128 |
Laser-microdissected tissue from Tg2576 and APPPS1 plaque-depositing mouse model of Alzheimer's disease |
|
