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Sample GSM898999 Query DataSets for GSM898999
Status Public on Sep 10, 2012
Title KO4
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 3.
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 20.39071167 P
A_55_P2073489 783.1900833 P
A_52_P229709 3397.276667 P
A_55_P2092526 17355.68667 P
A_55_P2048358 5.122211 A
A_55_P2109122 10456.55167 P
A_55_P2032147 697.1093667 P
A_55_P1985351 2225.1005 P
A_55_P2145838 15.58140667 A
A_51_P163444 38541.85412 P
A_55_P2166688 6009.9925 P
A_55_P2230663 5.054337 A
A_55_P2195172 15.98276833 A
A_55_P1953663 5.146486167 A
A_55_P2135730 16.43315333 A
A_51_P174143 6.126216833 A
A_51_P419971 5602.940927 P
A_55_P1967880 28626.24333 P
A_55_P2364315 202.1184667 P
A_51_P154780 143.0574667 P

Total number of rows: 39429

Table truncated, full table size 1032 Kbytes.

Supplementary file Size Download File type/resource
GSM898999_252665512576_252665512576_S01_GE1_107_Sep09_1_4.txt.gz 9.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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