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Sample GSM785114 Query DataSets for GSM785114
Status Public on Sep 23, 2011
Title SAM/R-1 + CCH_1
Sample type RNA
 
Source name hippocampus, SAM/R-1, CCH, reprecate1
Organism Mus musculus
Characteristics background strain: AKR/J
tissue: hippocampus
age: 8-week-old
gender: male
genotype/variation: SAM/R-1
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/R-1 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 -0.08057833
DarkCorner -0.8036771
A_52_P616356 -0.820344
A_52_P580582 -0.05651331
A_52_P403405 -0.8200636
A_52_P819156 0.013092279
A_51_P331831 -0.17770076
A_51_P430630 -0.82012177
A_52_P502357 -2.4895382
A_52_P299964 0.07709837
A_51_P356389 -0.11664915
A_52_P684402 -0.090370655
A_51_P414208 -0.83709717
A_51_P280918 0.09486675
A_52_P613688 -0.14684582
A_52_P258194 -0.015471458
A_52_P229271 0.47023964
A_52_P214630 0.19064236
A_52_P579519 8.74E-04
A_52_P979997 0.7400098

Total number of rows: 41252

Table truncated, full table size 987 Kbytes.




Supplementary file Size Download File type/resource
GSM785114.txt.gz 1.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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