|
| Status |
Public on Dec 25, 2006 |
| Title |
Transcriptome associates with rice organogenesis |
| Organism |
Oryza sativa |
| Experiment type |
Expression profiling by array
|
| Summary |
Most plant cells retain the capacity to differentiate into all the other cell and organ types that constitute a plant. However, genome-wide transcriptional activities underlying the process of cell differentiation are poorly understood, especially in monocot plants. Here we used a rice (Oryza sativa) cell culture system to generate somatic embryos, which were further induced into shoots and roots. The global transcriptional reorganization during the development of somatic embryos, shoots, and roots from cultured cells was studied using a rice whole genome microarray and verified by RNA blotting analysis of representative genes. Overall, only 1-3% of expressed genes were differentially regulated during each organogenesis process at the examined time point. Also metabolic pathways were minimally regulated. Thus the genes that dictating organ formation should be relatively small in number. Comparison of these three transcriptomes revealed little overlap during these three organogenesis processes. These results indicate that each organogenesis involves specific reorganization of genome expression.
Keywords: transcriptome
|
| |
|
| Overall design |
Oryza sativa Genome Oligo Set Version 1.0 was designed by Beijing Genomics Institute (BGI) and contain 60,727 70mer oligos representing both indica and japonica genomes. All oligos were designed from cDNAs, expreseed sequence tag (EST) sequences, predicted genes of BGI rice genome build and other public resources. Mapping to TIGR rice genome pseudommolecues release 2 is based on the BLAST results, if a oligo has greater than 97% identity to a gene sequence from TIGR pseudomolecules, the oligo represents that gene. Rice 30K Operon Version 1.0 -70 mer oligos. The array is in 48 pin conformation. It has 25 columns and 25 rows in each of 4 x 12 subarrays.
|
| |
|
| Contributor(s) |
Su N, He K, Jiao Y, Deng X |
| Citation(s) |
17072560 |
| |
| Submission date |
Dec 17, 2006 |
| Last update date |
Sep 17, 2012 |
| Contact name |
Kun He |
| E-mail(s) |
hek@mail.cbi.pku.edu.cn
|
| Phone |
203-432-8909
|
| Organization name |
Yale University
|
| Department |
Molecular, Cellular & Developmental Biology
|
| Lab |
Denglab
|
| Street address |
165 Prospect
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06520 |
| Country |
USA |
| |
|
| Platforms (2) |
|
| Samples (16)
|
|
| Relations |
| BioProject |
PRJNA98785 |
Less...
More...