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| Status |
Public on Nov 11, 2010 |
| Title |
Rice expression atlas (4): Vegetative tissues |
| Organism |
Oryza sativa |
| Experiment type |
Expression profiling by array
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| Summary |
Gene expression throughout the reproductive process in rice (Oryza sativa) beginning with primordia development through pollination/fertilization to zygote formation was analyzed. We analyzed 25 stages/organs of rice reproductive development including early microsporogenesis stages with 57,381 probe sets, and identified around 26,000 expressed probe sets in each stage. Fine dissection of 25 reproductive stages/organs combined with detailed microarray profiling revealed dramatic, coordinated and finely tuned changes in gene expression. Decrease of expressed genes in the pollen maturation process was observed in a similar way with Arabidopsis and maize. An almost equal number of ab initio predicted genes and cloned genes appeared or disappeared coordinated with developmental stage progression. A large number of organ-/stage-specific genes were identified; notably 2,593 probe sets for developing anther, including 932 probe sets corresponding to ab initio predicted genes. Analysis of cell cycle-related genes revealed that several CDKs, cyclins and components of SCF E3 ubiquitin ligase complexes were expressed specifically in reproductive organs. Cell wall biosynthesis or degradation protein genes and transcription factor genes expressed specifically in reproductive stages were also newly identified. Rice genes homologous to reproduction-related genes in other plants showed expression profiles both consistent and inconsistent with their predicted functions. The rice reproductive expression atlas is likely to be the deepest and most comprehensive dataset available, indispensable for unraveling functions of many specific genes in plant reproductive processes that have not yet been thoroughly analyzed.
Keywords: developmental stage comparison, tissue comparison
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| Overall design |
Regenerating calli on agar plate, young leaves and roots grown in a green house, shoots grown in growth chamber were collected as references of reproductive samples.
Three or four biological replicates at each stage were analyzed with Affymetrix Rice Genome Array, and total number of samples in this series is 25.
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| Contributor(s) |
Fujita M, Horiuchi Y, Ueda Y, Mizuta Y, Kubo T, Yano K, Yamaki S, Tsuda K, Niihama M, Kato H, Kikuchi S, Mochizuki T, Tsutsumi N, Kurata N |
| Citation(s) |
21062870 |
| Submission date |
Jan 06, 2009 |
| Last update date |
Dec 27, 2017 |
| Contact name |
Nori Kurata |
| E-mail(s) |
nkurata@nig.ac.jp
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| Phone |
+81-55-981-6808
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| Organization name |
National Institute of Genetics
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| Lab |
Plant genetics Lab.
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| Street address |
1111 Yata
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| City |
Mishima |
| State/province |
Shizuoka |
| ZIP/Postal code |
411-8540 |
| Country |
Japan |
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| Platforms (1) |
| GPL2025 |
[Rice] Affymetrix Rice Genome Array |
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| Samples (25)
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| GSM357667 |
Regenerating callus 2 days, biological rep1 |
| GSM357668 |
Regenerating callus 2 days, biological rep2 |
| GSM357669 |
Regenerating callus 2 days, biological rep3 |
| GSM357670 |
Regenerating callus 4 days, biological rep1 |
| GSM357671 |
Regenerating callus 4 days, biological rep2 |
| GSM357672 |
Regenerating callus 4 days, biological rep3 |
| GSM357673 |
Regenerating callus 6 days, biological rep1 |
| GSM357674 |
Regenerating callus 6 days, biological rep2 |
| GSM357675 |
Regenerating callus 6 days, biological rep3 |
| GSM357676 |
Regenerating callus 8 days, biological rep1 |
| GSM357677 |
Regenerating callus 8 days, biological rep2 |
| GSM357678 |
Regenerating callus 8 days, biological rep3 |
| GSM357679 |
Root, biological rep1 |
| GSM357680 |
Root, biological rep2 |
| GSM357681 |
Root, biological rep3 |
| GSM357682 |
Shoot, biological rep1 |
| GSM357683 |
Shoot, biological rep2 |
| GSM357684 |
Shoot, biological rep3 |
| GSM357685 |
Young leaf, biological rep1 |
| GSM357686 |
Young leaf, biological rep2 |
| GSM357687 |
Young leaf, biological rep3 |
| GSM357688 |
Young leaf, biological rep4 |
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| This SubSeries is part of SuperSeries: |
| GSE14304 |
Rice expression atlas: Plant reproductive process |
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| Relations |
| BioProject |
PRJNA114551 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE14300_RAW.tar |
105.0 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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