GSE14299   Details

GSE Accession GSE14299
Title Rice expression atlas (3): Early embryogenesis
Submission Date 2009-01-06
Last Update Date 2012-09-26
Pubmed ID 21062870
Experiment Type Expression profiling by array
Contributor Masahiro,,Fujita; Youko Horiuchi; Yayoi Ueda; Yoko Mizuta; Takahiko Kubo; Kentaro Yano; Shinichiro Yamaki; Katsutoshi Tsuda; Mitsuru Niihama; Hirotaka Kato; Shunsuke Kikuchi; Takako Mochizuki; Nobuhiro Tsutsumi; Nori Kurata
Contact Name Nori Kurata
Contact E-mail nkurata@lab.nig.ac.jp
Organization Name National Institute of Genetics
Country Japan
Organism Oryza sativa
Organism ID
Organism Synonym red rice;rice
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
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.
Platform ID
Timepoint Count 25
Timepoints gse: [Timepoints, 25]
Disease thrombocytopenia-absent radius syndrome;
congenital disorder;
thrombocytopenia
Disease ID 14699;
759;
1588