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Related Concept Videos

RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
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Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
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Related Experiment Video

Updated: May 24, 2026

Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling
07:18

Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling

Published on: May 21, 2020

Transcriptomic analysis of rice (Oryza sativa) developing embryos using the RNA-Seq technique.

Hong Xu1, Yi Gao, Jianbo Wang

  • 1State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.

Plos One
|February 21, 2012
PubMed
Summary

This study profiled rice embryo development using RNA-Seq, identifying stage-specific genes and differentially expressed genes. Key molecular pathways and transcription factors involved in rice embryogenesis were revealed.

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Area of Science:

  • Plant Molecular Biology
  • Developmental Biology
  • Genomics

Background:

  • Rice (Oryza sativa) serves as a model monocot for studying embryogenesis due to its sequenced genome.
  • Understanding the molecular mechanisms of rice embryogenesis is crucial for crop improvement.

Purpose of the Study:

  • To profile the transcriptome of developing rice embryos at three distinct developmental stages.
  • To identify stage-specific genes and differentially expressed genes (DEGs) during rice embryogenesis.
  • To elucidate the molecular and cellular events underlying rice embryo development.

Main Methods:

  • RNA sequencing (RNA-Seq) was employed for transcriptome profiling of rice embryos.
  • Analysis of sequence reads aligned to the rice genome to identify expressed genes.
  • Differential gene expression analysis was performed between developmental stages (3-5, 7, and 14 days after pollination).

Main Results:

  • RNA-Seq generated over 17 million reads, aligning to 27,190 genes.
  • Identified stage-specific genes: 1,131 (3-5 DAP), 1,443 (7 DAP), and 1,223 (14 DAP).
  • Detected 1,011 differentially expressed genes (DEGs) overall, with significant changes between stages (672 between 3-5 and 7 DAP; 504 between 7 and 14 DAP).
  • Genes involved in metabolism, transcriptional regulation, nucleic acid processing, and signal transduction were prominent in early/middle stages.
  • Protein biosynthesis genes peaked in the middle stage, while starch/sucrose metabolism and protein modification genes were high in middle/late stages.
  • Multiple transcription factor families were identified as potentially crucial for various developmental processes.

Conclusions:

  • Transcriptomic changes during rice embryogenesis are substantial.
  • Specific gene sets and transcription factors play critical roles at different developmental stages of rice embryos.
  • These findings enhance the understanding of rice embryogenesis and provide a basis for future research in cereals.