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Sample GSM376013 Query DataSets for GSM376013
Status Public on Nov 04, 2014
Title 5288
Sample type RNA
 
Source name Brain_hippocampus_mouse_Tg2576_transgenic_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: 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

Data table header descriptions
ID_REF
VALUE 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.

Data table
ID_REF VALUE
A_51_P100021 6.32730975687294
A_51_P100034 11.5458525659474
A_51_P100052 3.76375786470585
A_51_P100063 10.0048019223977
A_51_P100084 8.73474179264384
A_51_P100099 12.6207151513115
A_51_P100155 12.9968538849587
A_51_P100174 10.0988071916558
A_51_P100181 7.9063891719544
A_51_P100218 3.52349295594852
A_51_P100227 13.3195902755969
A_51_P100238 3.62616926323513
A_51_P100246 9.09082009314268
A_51_P100289 14.6484940922547
A_51_P100298 3.98792565226266
A_51_P100309 3.86093301031645
A_51_P100327 3.89654020969354
A_51_P100347 3.8500792958058
A_51_P100379 8.40105997528192
A_51_P100428 3.98711345223755

Total number of rows: 41174

Table truncated, full table size 1199 Kbytes.




Supplementary file Size Download File type/resource
GSM376013.txt.gz 8.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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