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Series GSE31859 Query DataSets for GSE31859
Status Public on Sep 06, 2011
Title Expression analysis of OsCc1:AP37 and OsCc1:AP59 transgenic rice plants
Organism Oryza sativa
Experiment type Expression profiling by genome tiling array
Summary For identification of genes up-regulated in OsCc1:AP37, OsCc1:AP59 plants, total RNA (100 μg) was prepared from leaf tissues of 14-d-old transgenic and non-transgenic rice seedlings (Oryza sativa cv Nipponbare) grown under normal growth conditions.
 
Overall design Expression profiling was conducted using a Rice 3’-Tiling Microarray. Information on the microarray can be found at http://www.ggbio.com (GreenGene Biotech). The Rice 3’-Tiling Microarray was designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). Among these, 20,507 genes were from representative RAP1 sequences with cDNA/EST supports and 6,941 genes were predicted without cDNA/EST supports. Ten 60-nt long probes were designed from each gene starting 60 bp ahead the end of stop codon with 10 bp shifts in position so that 10 probes covered 150 bp in the 3' region of the gene. In total, 270,000 probes were designed (average size, 60-nt) to have Tm values of 75 to 85 °C. The microarray was manufactured by NimbleGen Inc. (http://www.nimblegen.com/). Random GC probes (38,000) were used to monitor the hybridization efficiency and fiducial markers at the four corners (225) were included to assist with overlaying the grid on the image. The microarray was used to profile gene expression in OsCc1:AP37, OsCc1:AP59 and Non-transgenic plants. Cy3-labeled target cDNA fragments were synthesized using a Cy3-9mer primer. For normalization, data were processed with cubic alpine normalization using quartiles to adjust signal variation between chips and with Rubust Multi-Chip Analysis using a median polish algorithm implemented in NimbleScan (Workman et al., 2002; Irizarry et al., 2003). To assess the reproducibility of the microarray analysis, we repeated the experiment three times with independently prepared total RNAs.
 
Contributor(s) Oh S, Kim YS, Kwon C, Park HK, Jeong JS, Kim J
Citation(s) 19429605
Submission date Sep 02, 2011
Last update date Mar 23, 2012
Contact name Jin Seo Jeong
E-mail(s) jsjeong74@gmail.com
Organization name Myongji University
Street address San 38-2 Namdong, Cheoin-gu
City Yongin
State/province Gyeonggido
ZIP/Postal code 449-728
Country South Korea
 
Platforms (1)
GPL7344 Rice NimbleGen 390K tiling array (2006-11-14_ggb_rap1_3tile_101706)
Samples (9)
GSM790092 NT_rep1
GSM790093 NT_rep2
GSM790094 NT_rep3
Relations
BioProject PRJNA145097

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE31859_RAW.tar 129.8 Mb (http)(custom) TAR (of PAIR, PROBE)
Processed data included within Sample table
Processed data provided as supplementary file

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