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Sample GSM785108 Query DataSets for GSM785108
Status Public on Sep 23, 2011
Title SAM/P-8 + CCH_3
Sample type RNA
 
Source name hippocampus, SAM/P-8, CCH, reprecate3
Organism Mus musculus
Characteristics background strain: AKR/J
tissue: hippocampus
age: 8-week-old
gender: male
genotype/variation: SAM/P-8
diet: CCH
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the tissues by using the RNeasy Lipid Tissue Mini Kit (Qiagen, Valencia, CA). RNA was treated with DNase 1 (Qiagen) and cleaned using the RNeasy Mini Kit (Qiagen). The purity and integrity of the isolated total RNA were analyzed by ultraviolet spectrophotometry and an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA). All RNA samples exhibited a 260/280 ratio between 2.0 and 2.2, and a 28S:18S ratio of >1.6; the RNA integrity number (RIN) was >9.0.
Label Cy3
Label protocol Five hundred ng of the RNA sample was transcribed using oligo(dT)-based T7 promoter primer and MMLV-RT in the first- and second-strand cDNA synthesis reactions. The double-stranded cDNAs were used as templates in the preparation of fluorescent complementary RNAs (cRNAs) in the presence of T7 RNA polymerase and cyanine 3-CTP dye in an in vitro transcription reaction.
 
Hybridization protocol The labeled cRNAs were purified, fragmented, and hybridized to microarrays in a rotating hybridization oven at 10 rpm for 17 h at 65 °C.
Scan protocol After hybridization, the microarrays were washed according to the manufacturer’s protocol and scanned on an Agilent DNA Microarray Scanner with the Scan Control software (Agilent Technologies).
Description The mouse model we used in our experiment (the senescence-accelerated mouse (SAM)) was established through phenotypic selection from a common genetic pool of AKR/J strain of mice.
Gene expression of SAM/P-8 with CCH feeding
Data processing The resulting images were processed, and raw data were collected using Agilent’s Feature Extraction software. The gene expression data were analyzed using GeneSpring GX 10 (Agilent). The signal intensity for each probe was normalized by a percentile shift, in which each measurement was divided by the 75th percentile of all measurements in its array.
 
Submission date Aug 23, 2011
Last update date Sep 24, 2011
Contact name Toshio Kojima
Organization name Toyohashi University of Technology
Department Health Care Center
Street address 1-1 Hibarigaoka Tenpaku-cho
City Toyohashi
ZIP/Postal code 441-8580
Country Japan
 
Platform ID GPL7202
Series (1)
GSE31606 Hippocampal gene network analysis to determine the effects of coral calcium hydride in an experimental model of accelerated senescence

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
GE_BrightCorner -0.25561857
DarkCorner -0.02366972
A_52_P616356 -0.004347801
A_52_P580582 0.095517635
A_52_P403405 -0.003896713
A_52_P819156 -0.16186213
A_51_P331831 0.09093022
A_51_P430630 -0.004055977
A_52_P502357 2.8190422
A_52_P299964 0.21696329
A_51_P356389 0.22758484
A_52_P684402 0.026145458
A_51_P414208 -0.021440506
A_51_P280918 -0.044322014
A_52_P613688 0.027679443
A_52_P258194 0.07520294
A_52_P229271 0.06534338
A_52_P214630 -0.30919743
A_52_P579519 0.104409695
A_52_P979997 0.80263996

Total number of rows: 41252

Table truncated, full table size 991 Kbytes.




Supplementary file Size Download File type/resource
GSM785108.txt.gz 1.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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