GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM898995 Query DataSets for GSM898995
Status Public on Sep 10, 2012
Title W3
Sample type RNA
Source name Wild type
Organism Mus musculus
Characteristics background/strain: C57BL/6J
genotype/variation: wild type
tissue: ovary
gender: female
age: 20 weeks
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy kit (QIAGEN).
Label Cy3
Label protocol Cyanine-3 (Cy3)-labeled cRNA was prepared from 0.5 μg RNA using a One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by purification with an RNeasy column (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked by NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol Cy3-labeled cRNA (1.5 µg) was fragmented at 60°C for 30 min in a reaction mixture (250 µl) containing 1x fragmentation buffer and 2x blocking agent obtained from Agilent. On completion of the fragmentation reaction, 250 µl 2x Agilent hybridization buffer was added to the mixture, and this mixture was then hybridized to Agilent Whole Mouse Genome Oligo Microarrays for 17 hours at 65°C in a rotating oven. After hybridization, the microarray slides were washed with GE Wash Buffer 1 (Agilent) for 1 min at room temperature, and with GE Wash buffer 2 (Agilent) for 1 min at 37°C. Immediately after the washing, the slides were dried by centrifugal evaporator.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area, 61x21.6 mm; Scan resolution, 10 um; and Dye channel setting for Green and Green PMT; 100%).
Description Replicate 2.
Data processing The scanned images were analyzed by Feature Extraction Software (Agilent) using default parameters to subtract background and to obtain processed signal intensities by the algorithm of Spatially Detrend in the software.
Submission date Mar 21, 2012
Last update date Sep 10, 2012
Contact name Tomoki Takeda
Phone +81-92-642-6587
Fax +81-92-642-6588
Organization name Kyushu University
Department Pharmaceutical sciences
Lab Molecular life sciences
Street address 3-1-1 Maidashi, Higashi-ku
City Fukuoka
ZIP/Postal code 812-8582
Country Japan
Platform ID GPL11202
Series (1)
GSE36697 Effect of deletion of the selenium-binding protein 1 gene on gene expression in the ovary of C57BL/6J mouse

Data table header descriptions
VALUE Quantile-normalized signal (non-log scaled)

Data table
A_55_P2116608 19.46814667 A
A_55_P2073489 578.2546167 P
A_52_P229709 4017.210579 P
A_55_P2092526 17558.75667 P
A_55_P2048358 8.290367667 A
A_55_P2109122 10894.34817 P
A_55_P2032147 465.9838833 P
A_55_P1985351 2892.067322 P
A_55_P2145838 13.99710083 A
A_51_P163444 37236.25853 P
A_55_P2166688 6313.9305 P
A_55_P2230663 6.756418 A
A_55_P2195172 6.464552667 A
A_55_P1953663 4.965733167 A
A_55_P2135730 29.71230667 P
A_51_P174143 6.802678167 A
A_51_P419971 7178.321667 P
A_55_P1967880 28679.365 P
A_55_P2364315 204.3251572 P
A_51_P154780 176.0779667 P

Total number of rows: 39429

Table truncated, full table size 1032 Kbytes.

Supplementary file Size Download File type/resource
GSM898995_252665511638_252665511638_S01_GE1_107_Sep09_1_4.txt.gz 9.1 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap