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Sample GSM898998 Query DataSets for GSM898998
Status Public on Sep 10, 2012
Title KO2
Sample type RNA
 
Source name SeBP1 knockout
Organism Mus musculus
Characteristics background/strain: C57BL/6J
genotype/variation: SeBP1 knockout
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
E-mail(s) takeda@phar.kyushu-u.ac.jp
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
ID_REF
VALUE Quantile-normalized signal (non-log scaled)
ABS_CALL

Data table
ID_REF VALUE ABS_CALL
A_55_P2116608 13.862016 A
A_55_P2073489 724.0627833 P
A_52_P229709 3403.8 P
A_55_P2092526 20967.62833 P
A_55_P2048358 5.098422 A
A_55_P2109122 7396.722 P
A_55_P2032147 658.4785833 P
A_55_P1985351 2893.659833 P
A_55_P2145838 5.465661167 A
A_51_P163444 42923.10396 P
A_55_P2166688 5967.438167 P
A_55_P2230663 5.1869825 A
A_55_P2195172 8.3357095 A
A_55_P1953663 12.82310183 A
A_55_P2135730 17.4272 A
A_51_P174143 5.084806333 A
A_51_P419971 5970.770333 P
A_55_P1967880 31575.00333 P
A_55_P2364315 261.7436167 P
A_51_P154780 74.74312833 P

Total number of rows: 39429

Table truncated, full table size 1032 Kbytes.




Supplementary file Size Download File type/resource
GSM898998_252665512576_252665512576_S01_GE1_107_Sep09_1_3.txt.gz 9.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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