 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 01, 2011 |
| Title |
Gene expression of two-week old seedlings of OsCc1:OsbHLH148 transgenic rice plants |
| Organism |
Oryza sativa |
| Experiment type |
Expression profiling by genome tiling array
|
| Summary |
To understand downstream genes affected by overexpression of OsbHLH148, the Rice 3’-Tiling Microarray analysis (GreenGene Biotech, Yongin, Korea) was carried out to profile gene expression of OsCc1:OsbHLH148 transgenic plants in comparison with wild-type plants under normal growth conditions. RNA samples from these plants were used to generate cyanine-3 (Cy3)-labeled complementary DNA (cDNA) probes, which were then hybridized to the microarray. Each data set was obtained from two biological repeats with independent transgenic lines.
|
| |
|
| 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:OsbHLH148 transgenic and wild-type rice plants. Cy3-labeled target cDNA fragments were synthesized from two-week old seedlings 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 two times with independent transgenic lines, T-2 and T-9, and analyzed each data set statistically using one-way ANOVA.
|
| Web link |
http://www.ggbio.com
|
| |
|
| Contributor(s) |
Seo J, Choi YD |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Jul 02, 2010 |
| Last update date |
Mar 22, 2012 |
| Contact name |
Ju-Seok Seo |
| E-mail(s) |
tin3725@hanmail.net
|
| Phone |
82-2-880-4659
|
| Organization name |
Seoul National University
|
| Department |
Dept. of Applied Biology & Chemistry
|
| Lab |
Molecular Biology Lab.
|
| Street address |
san 56-1
|
| City |
Seoul |
| ZIP/Postal code |
151-742 |
| Country |
South Korea |
| |
|
| Platforms (1) |
| GPL10634 |
NimbleGen/SNU Rice 3'-tiling 385K array |
|
| Samples (4)
|
|
| Relations |
| BioProject |
PRJNA127995 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE22676_RAW.tar |
44.3 Mb |
(http)(custom) |
TAR (of PAIR) |
| Processed data included within Sample table |
|
|
|
|
 |
Less...
More...