Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Express data from rice endosperm

ABSTRACT: Immatured rice seeds 7-8 days after pollination were used for expression analysis and matured rice leaf was used as control. Targets from biological replicates of both were generated and the expression were determined using Affymetrix Rice Genome arrays. Rice immatured seed after 7-8 days pollination were selected of early development for RNA extraction and hybridization on Affymetrix microarrays. Matured rice leaf was set as control. Each with 3 replicates were analyzed.

ORGANISM(S): Oryza sativa

SUBMITTER: Feng Tan

PROVIDER: E-GEOD-26840 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Comparison of four ChIP-Seq analytical algorithms using rice endosperm H3K27 trimethylation profiling data.

Malone Brandon M BM Tan Feng F Bridges Susan M SM Peng Zhaohua Z

PloS one 20110930 9

Chromatin immunoprecipitation coupled with high throughput DNA Sequencing (ChIP-Seq) has emerged as a powerful tool for genome wide profiling of the binding sites of proteins associated with DNA such as histones and transcription factors. However, no peak calling program has gained consensus acceptance by the scientific community as the preferred tool for ChIP-Seq data analysis. Analyzing the large data sets generated by ChIP-Seq studies remains highly challenging for most molecular biology labo ...[more]

PMID: 21984925

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Project description:Constituting the final growth phase during the lifecycle of maize (Zea Mays L.), leaf senescence plays an important biological role in grain yield in crops. We undertook proteomic and physiological analyses in inbred line Yu816 in order to unravel the underlying mechanisms of leaf senescence induced by preventing pollination. A total of 6,941 proteins were identified by Isobaric tags for Relative and Absolute Quantitation (iTRAQ) analysis. Proteomic analyses between pollinated (POL) and non-pollinated (NONPOL) plants indicated that 973 different proteins accumulated in NONPOL plants. The accumulated proteins were classified into various groups, including response to stimuli, cellular processes, cell death and metabolic processes using functional analysis. Furthermore, in accordance with the changes in these different accumulated proteins, analysis of changes in leaf total soluble sugars and starch content showed that the prevention of pollination can disturb endogenousplant hormone and sugar metabolism and lead to ROS bursts, protein degradation and photosystem breakdown, eventually resulting in leaf senescence. This represents the first attempt at global proteome profiling in response to induced leaf senescence by preventing pollination in maize, and provides a better understanding of the molecular mechanisms involved in induced leaf senescence.Constituting the final growth phase during the lifecycle of maize (Zea Mays L.), leaf senescence plays an important biological role in grain yield in crops. We undertook proteomic and physiological analyses in inbred line Yu816 in order to unravel the underlying mechanisms of leaf senescence induced by preventing pollination. A total of 6,941 proteins were identified by Isobaric tags for Relative and Absolute Quantitation (iTRAQ) analysis. Proteomic analyses between pollinated (POL) and non-pollinated (NONPOL) plants indicated that 973 different proteins accumulated in NONPOL plants. The accumulated proteins were classified into various groups, including response to stimuli, cellular processes, cell death and metabolic processes using functional analysis. Furthermore, in accordance with the changes in these different accumulated proteins, analysis of changes in leaf total soluble sugars and starch content showed that the prevention of pollination can disturb endogenousplant hormone and sugar metabolism and lead to ROS bursts, protein degradation and photosystem breakdown, eventually resulting in leaf senescence. This represents the first attempt at global proteome profiling in response to induced leaf senescence by preventing pollination in maize, and provides a better understanding of the molecular mechanisms involved in induced leaf senescence.

Dataset Information

Express data from rice endosperm

Publications

Comparison of four ChIP-Seq analytical algorithms using rice endosperm H3K27 trimethylation profiling data.

Similar Datasets

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