 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 28, 2016 |
| Title |
Analysis of representative organ specific genes and promoters of rice using 3’ ORF oriented long oligomer microarray |
| Organism |
Oryza sativa |
| Experiment type |
Expression profiling by genome tiling array
|
| Summary |
The profiling was conducted with the Rice 3'-Tiling Microarray designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp).
In this research, an array of 27,448 rice genes was used to elucidate the transcriptome of 7 tissues or organs of Oryza sativa L. cv. Dongjin including calli, regenerating calli, germinating seeds, leaves, roots, and flowers (before and after pollination) using a rice 3′ ORF tilling microarray. The ratio of standard deviation to the mean of microarray intensities was used to distinguish between organ-specific and constitutively expressed genes. Accordingly, the genes are classified into highly variable, variable, and constitutive groups. To isolate the organ-specific promoters, several genes were selected and validated in planta using reporter gene analysis. We found that the Os01g0702500, Os11g0211800, and Os01g0257300 promoters were active in the calli, germinating seeds, and roots, respectively. The Os08g0135500 promoter was shown to drive transgene expression in various organs of the mature flowers, such as the anther, lemma, and palea, whereas the Os03g0369100 promoter was only active in the anther. Lastly, the Os09g0553100 promoter induced high levels of reporter gene expression in all organs. The gene expression data from representative organs could put a frame work for large dataset collections and then subsequent profiling by subdivision of organ/tissues might be more efficient to find appropriate promoters.
|
| |
|
| Overall design |
A total of 14 chips were used for microarray. Total RNAs were extracted from rice 7 tissues or organs of Oryza sativa L. cv. Dongjin including calli, regenerating calli, germinating seeds, leaves, roots, and flowers (before and after pollination. Experiments were duplicated.
|
| |
|
| Contributor(s) |
Chae S, Kim JS, Nahm BH, Kim Y |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Jul 27, 2016 |
| Last update date |
Jul 30, 2016 |
| Contact name |
Yeon-Ki Kim |
| E-mail(s) |
kim750a11@gmail.com
|
| Phone |
82-31-321-6351
|
| Organization name |
GreenGene Biotech Inc.
|
| Department |
GreenGene Biotech Inc.
|
| Lab |
Genomics & Genetics Ins.
|
| Street address |
38-2 Namdong
|
| City |
Yongin |
| State/province |
Kyonggido |
| ZIP/Postal code |
449-728 |
| Country |
South Korea |
| |
|
| Platforms (1) |
| GPL22243 |
NimbleGen Rice 3'-tiling 385K array |
|
| Samples (14)
|
|
| Relations |
| BioProject |
PRJNA335609 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE84903_RAW.tar |
194.5 Mb |
(http)(custom) |
TAR (of PAIR, PROBE) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...