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Sample GSM898997 Query DataSets for GSM898997
Status Public on Sep 10, 2012
Title KO1
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 1.
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 5.127687333 A
A_55_P2073489 813.6485 P
A_52_P229709 3789.435667 P
A_55_P2092526 14846.29171 P
A_55_P2048358 5.127825833 A
A_55_P2109122 12093.675 P
A_55_P2032147 382.28995 P
A_55_P1985351 2649.5595 P
A_55_P2145838 16.90894167 A
A_51_P163444 38090.82108 P
A_55_P2166688 6118.2825 P
A_55_P2230663 5.102632667 A
A_55_P2195172 6.890495667 A
A_55_P1953663 5.192999833 A
A_55_P2135730 15.42494333 A
A_51_P174143 12.07288683 A
A_51_P419971 5185.397333 P
A_55_P1967880 24922.93667 P
A_55_P2364315 229.8105833 P
A_51_P154780 261.5868167 P

Total number of rows: 39429

Table truncated, full table size 1032 Kbytes.




Supplementary file Size Download File type/resource
GSM898997_252665512576_252665512576_S01_GE1_107_Sep09_1_2.txt.gz 9.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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