|
| Status |
Public on Nov 04, 2014 |
| Title |
5458 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Brain_neocortex_mouse_APPPS1_transgenic_rep2
|
| Organism |
Mus musculus |
| Characteristics |
model: APPPS1 (Radde et al EMBO Rep 2006)
mutations: APP-K670N/M671L & PSEN1-L166P
strain: C57BL/6
gender: female
age: 3 months
condition: transgenic
tissue: brain neocortex
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RiboPure kit (Ambion, Huntingdon, Cambridgeshire, UK) followed by DNase treatment (DNA-free™, Ambion).
|
| Label |
Cy3
|
| Label protocol |
~1µg of sample was spiked with 10 viral polyA transcript controls (Agilent), converted to double stranded cDNA in a reverse transcription reaction, converted to antisense cRNA, amplified and labeled with Cy3 in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).
|
| |
|
| Channel 2 |
| Source name |
Brain_neocortex_mouse_APPPS1_non-transgenic_rep2
|
| Organism |
Mus musculus |
| Characteristics |
model: APPPS1 (Radde et al EMBO Rep 2006)
mutations: APP-K670N/M671L & PSEN1-L166P
strain: C57BL/6
gender: female
age: 3 months
condition: non-transgenic
tissue: brain neocortex
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RiboPure kit (Ambion, Huntingdon, Cambridgeshire, UK) followed by DNase treatment (DNA-free™, Ambion).
|
| Label |
Cy5
|
| Label protocol |
~1µg of sample was spiked with 10 viral polyA transcript controls (Agilent), converted to double stranded cDNA in a reverse transcription reaction, converted to antisense cRNA, amplified and labeled with Cy5 in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).
|
| |
|
| |
| Hybridization protocol |
For Cy3 14 pmol and for Cy5 14 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 frontal neocortical brain tissue of APPPS1 mice compared to their littermate controls.
|
| Data processing |
Log-ratios of the Agilent processed signal values (i.e., feature gProcessedSignal for the Cy3 signal and rProcessedSignal for the Cy5 signal from Agilent Feature Extraction v9.5.3.1) were used for the data analysis. 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) |
| GSE15058 |
Expression profiling of laser-microdissected tissue from APPPS1 plaque-depositing mouse model of Alzheimer's disease |
| GSE15128 |
Laser-microdissected tissue from Tg2576 and APPPS1 plaque-depositing mouse model of Alzheimer's disease |
|
