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Browse RicePLEX Experiment Data

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Rice expression atlas (3): Early embryogenesis
Nori Kurata, National Institute of Genetics, Plant genetics Lab, Mishima, Japan (nkurata@lab.nig.ac.jp)
Experiment design (27 hybridizations)
organism part name
•embryo sac bottom •embryo sac top
time
•control •1 DAP •2 DAP •3 DAP •4 DAP

This experiment has been imported by PLEXdb from NCBI GEO (GSE14299) Series_summary: Gene expression throughout the reproductive process in ric...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Rice expression atlas (3): Early embryogenesis
Accession No: OS44
Microarray: Rice57k
Visibility: public
Experiment Type:
Experiment Factor(s):
organism part name
•embryo sac bottom   •embryo sac top
time
•control   •1 DAP   •2 DAP   •3 DAP   •4 DAP
Quality Control: biological replicates
Treatment summary:
 organism part name  time  # replicates
 embryo sac bottom  control  3
 embryo sac bottom  1 DAP  3
 embryo sac bottom  2 DAP  3
 embryo sac bottom  3 DAP  3
 embryo sac bottom  4 DAP  3
 embryo sac top  control  3
 embryo sac top  1 DAP  2
 embryo sac top  2 DAP  2
 embryo sac top  3 DAP  2
 embryo sac top  4 DAP  3
Total hybridizations: 27
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE14299)

Series_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, time course

Series_overall_design:
0-4 DAP embryosacs were collected, and dissected into bottom 1/4 part (contains embryo) and remaining top 3/4 part (mainly endosperm).
Two or three biological replicates for each tissue-stage were analyzed with Affymetrix Rice Genome Array, and total number of samples in this series is 27.
Unpollinated embryo and ovary samples were references in this series.

PLEXdb Curator's Note:

OS42 to OS46 are related experiments, OS46 being the super-series both at GEO and at PLEXdb.

OS42: Rice expression atlas (1): Anther development

OS43: Rice expression atlas (2): Pollination - Fertilization.

OS44: Rice expression atlas (3): Early embryogenesis.

OS45: Rice expression atlas (4): Vegetative tissues.

OS46: Rice expression atlas: Plant reproductive process.


Publication: 'Rice expression atlas in reproductive development.', Fujita M, Horiuchi Y, Ueda Y, Mizuta Y, Kubo T, Yano K, Yamaki S, Tsuda K, Nagata T, Niihama M, Kato H, Kikuchi S, Hamada K, Mochizuki T, Ishimizu T, Iwai H, Tsutsumi N, Kurata N.
Plant Cell Physiol 2010 Dec;51(12):2060-81.
pubmed: 21062870
Created: 2011-03-24 12:05:58
Last Update: 2011-03-24 12:45:56
Released: 2011-03-31
GEO Accession GSE14299
Submitter: PLEXdb Curator
Name: Nori Kurata
Institution: National Institute of Genetics, Plant genetics Lab, Mishima, Japan
Head of Laboratory: Nori Kurata
email(s):
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