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Sample GSM376021 Query DataSets for GSM376021
Status Public on Nov 04, 2014
Title 5455
Sample type RNA
 
Channel 1
Source name Brain_neocortex_mouse_APPPS1_transgenic_rep1
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_rep1
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

Data table header descriptions
ID_REF
VALUE normalized log2 ratios (Cy3/Cy5)
INV_VALUE normalized log2 ratios (Cy5/Cy3)

Data table
ID_REF VALUE INV_VALUE
A_51_P100021 -1.17904 1.17904217249773
A_51_P100034 0.133477 -0.133477057690284
A_51_P100052 -0.202481 0.202481423815707
A_51_P100063 -0.333508 0.333507588166305
A_51_P100084 -0.166016 0.16601579567437
A_51_P100099 -0.101111 0.101111140287274
A_51_P100155 0.156643 -0.156642560138332
A_51_P100174 0.177249 -0.177249047979917
A_51_P100181 -0.0454376 0.0454376010094215
A_51_P100218 0.0440386 -0.0440385753849652
A_51_P100227 0.0380944 -0.0380944390788926
A_51_P100238 0.0161346 -0.016134633232665
A_51_P100246 0.160546 -0.16054568186666
A_51_P100289 -0.0341035 0.034103496203008
A_51_P100298 0.905885 -0.90588474574514
A_51_P100309 0.0411226 -0.0411225928290985
A_51_P100327 1.48727 -1.48726822910974
A_51_P100347 0.0640722 -0.0640722293946058
A_51_P100379 -0.0987623 0.0987622626925754
A_51_P100428 0.0507277 -0.0507277247524004

Total number of rows: 41174

Table truncated, full table size 1679 Kbytes.




Supplementary file Size Download File type/resource
GSM376021.txt.gz 14.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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