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Browse RicePLEX Experiment Data

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Rice expression atlas: Plant reproductive process
Nori Kurata, National Institute of Genetics, Plant genetics Lab, Mishima, Japan (nkurata@lab.nig.ac.jp)
Experiment design (98 hybridizations)
tissue type name
•Anther at An1 •Anther at Mei1 •Anther at M1 •Anther at M2 •Anther at M3 •Anther at P1 •Anther at P2 •Anther at P3 •Stigma control •Ovary control •Pollinating stigma •Pollinating ovary •Pollen tube growth •Fertilization •Zygote formation •Embryosac control_bottom •embryosac_bottom 1 DAP •embryosac_bottom 2 DAP •embryosac_bottom 3 DAP •embryosac_bottom 4 DAP •Embryosac control_top •embryosac_top 1 DAP •embryosac_top 2 DAP •embryosac_top 3 DAP •embryosac_top 4 DAP •Growing callus •Regenerating callus 2 days •Regenerating callus 4 days •Regenerating callus 6 days •Regenerating callus 8 days •Root •Shoot •Young leaf

This experiment has been imported by PLEXdb from NCBI GEO (GSE14304) Series_summary: Gene expression throughout the reproductive process in ri...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Rice expression atlas: Plant reproductive process
Accession No: OS46
Microarray: Rice57k
Visibility: public
Experiment Type:
Experiment Factor(s):
tissue type name
•Anther at An1   •Anther at Mei1   •Anther at M1   •Anther at M2   •Anther at M3   •Anther at P1   •Anther at P2   •Anther at P3   •Stigma control   •Ovary control   •Pollinating stigma   •Pollinating ovary   •Pollen tube growth   •Fertilization   •Zygote formation   •Embryosac control_bottom   •embryosac_bottom 1 DAP   •embryosac_bottom 2 DAP   •embryosac_bottom 3 DAP   •embryosac_bottom 4 DAP   •Embryosac control_top   •embryosac_top 1 DAP   •embryosac_top 2 DAP   •embryosac_top 3 DAP   •embryosac_top 4 DAP   •Growing callus   •Regenerating callus 2 days   •Regenerating callus 4 days   •Regenerating callus 6 days   •Regenerating callus 8 days   •Root   •Shoot   •Young leaf
Quality Control: biological replicates
Treatment summary:
 tissue type name  # replicates
 Anther at An1  3
 Anther at Mei1  3
 Anther at M1  4
 Anther at M2  3
 Anther at M3  4
 Anther at P1  3
 Anther at P2  3
 Anther at P3  3
 Stigma control  3
 Ovary control  3
 Pollinating stigma  2
 Pollinating ovary  3
 Pollen tube growth  3
 Fertilization  3
 Zygote formation  3
 Embryosac control_bottom  3
 embryosac_bottom 1 DAP  3
 embryosac_bottom 2 DAP  3
 embryosac_bottom 3 DAP  3
 embryosac_bottom 4 DAP  3
 Embryosac control_top  3
 embryosac_top 1 DAP  2
 embryosac_top 2 DAP  2
 embryosac_top 3 DAP  2
 embryosac_top 4 DAP  3
 Growing callus  3
 Regenerating callus 2 days  3
 Regenerating callus 4 days  3
 Regenerating callus 6 days  3
 Regenerating callus 8 days  3
 Root  3
 Shoot  3
 Young leaf  4
Total hybridizations: 98
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE14304)

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.

This SuperSeries is composed of the following subset Series:
GSE13988: Rice expression atlas (1): Anther development
GSE14298: Rice expression atlas (2): Pollination - Fertilization
GSE14299: Rice expression atlas (3): Early embryogenesis
GSE14300: Rice expression atlas (4): Vegetative tissues
GSE14301: Rice expression atlas (5): Anther development (Agilent data)

Series_overall_design:
Refer to individual 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: 2011-03-25 12:50:58
Last Update: 2011-03-29 13:02:21
Released: 2011-04-06
GEO Accession GSE14304
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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