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Sample GSM785116 Query DataSets for GSM785116
Status Public on Sep 23, 2011
Title SAM/R-1 + CCH_3
Sample type RNA
Source name hippocampus, SAM/R-1, CCH, reprecate3
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
VALUE Normalized signal intensity

Data table
GE_BrightCorner 0.39511442
DarkCorner -0.44876623
A_52_P616356 -0.40707302
A_52_P580582 0.21359777
A_52_P403405 -0.40071106
A_52_P819156 0.12212014
A_51_P331831 -0.10658431
A_51_P430630 -0.39252663
A_52_P502357 -2.2787666
A_52_P299964 -0.1359067
A_51_P356389 -0.01293993
A_52_P684402 -0.06039667
A_51_P414208 -0.40489388
A_51_P280918 -0.0966568
A_52_P613688 0.17112827
A_52_P258194 -0.07925987
A_52_P229271 0.27914
A_52_P214630 0.060237885
A_52_P579519 -8.74E-04
A_52_P979997 1.2622175

Total number of rows: 41252

Table truncated, full table size 986 Kbytes.

Supplementary file Size Download File type/resource
GSM785116.txt.gz 1.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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