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Related Concept Videos

RNA-seq03:21

RNA-seq

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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...
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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.
Applications of ribosome profiling
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3' End Sequencing Library Preparation with A-seq2
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expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform.

Philippa Borrill1, Ricardo Ramirez-Gonzalez1, Cristobal Uauy2

  • 1John Innes Centre, Norwich NR4 7UH, United Kingdom (P.B., C.U.); andGenome Analysis Centre, Norwich NR4 7UH, United Kingdom (R.R.-G.).

Plant Physiology
|February 13, 2016
PubMed
Summary
This summary is machine-generated.

expVIP is a new platform that makes plant RNA-seq data analysis accessible. It simplifies visualizing and integrating gene expression data, even for users with limited bioinformatics skills.

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Area of Science:

  • Plant genomics
  • Bioinformatics
  • Computational biology

Background:

  • Transcriptome sequencing (RNA-seq) studies in plants are often underutilized due to data accessibility and analysis challenges.
  • Disparate transcriptome references and lack of bioinformatics expertise hinder the use of valuable plant gene expression data.

Purpose of the Study:

  • To develop an accessible platform, expVIP, for the analysis and visualization of plant RNA-seq data.
  • To enable researchers with limited bioinformatics skills to easily analyze and integrate gene expression datasets.

Main Methods:

  • Developed expVIP, an expression visualization and integration platform.
  • Utilized a virtual machine for user-friendly analysis of public and user-specified RNA-seq datasets.
  • Created a custom web browser for interactive data visualization, sorting, and filtering.

Main Results:

  • expVIP allows easy analysis and visualization of RNA-seq data through an intuitive interface.
  • The platform supports differential gene expression analysis and is suitable for polyploid crops.
  • A wheat (Triticum aestivum) expression browser was developed as an example of expVIP's application.

Conclusions:

  • The expVIP platform enhances the accessibility and utility of plant RNA-seq data.
  • It facilitates the integration, visualization, and comparison of gene expression data across experiments for various species.
  • expVIP empowers researchers to leverage gene expression data more effectively in crop research and beyond.