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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...
Ribosome Profiling02:24

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.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

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Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
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Uncovering the complexity of transcriptomes with RNA-Seq.

Valerio Costa1, Claudia Angelini, Italia De Feis

  • 1Institute of Genetics and Biophysics A. Buzzati-Traverso, IGB-CNR, Naples, Italy. costav@igb.cnr.it

Journal of Biomedicine & Biotechnology
|July 14, 2010
PubMed
Summary

Next Generation Sequencing (NGS) technologies, like RNA-Seq, offer powerful insights into gene expression and splicing. However, these advanced methods present significant bioinformatics challenges due to massive data output.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Next Generation Sequencing (NGS) has revolutionized genetic studies with massively parallel sequencing.
  • RNA-Seq, a key NGS application, enables detailed transcriptome analysis, surpassing older methods.
  • NGS platforms generate vast datasets, presenting both opportunities and challenges.

Purpose of the Study:

  • To provide a comprehensive survey of RNA-Seq methodology.
  • To highlight the biological and bioinformatics challenges associated with RNA-Seq.
  • To discuss the advancements and complexities introduced by NGS in transcriptomics.

Main Methods:

  • Review of RNA-Seq protocols and applications.
  • Analysis of data generation and processing in transcriptomics.
  • Discussion of bioinformatics tool development for NGS data.

Main Results:

  • RNA-Seq allows accurate determination of gene expression levels, differential splicing, and allele-specific expression.
  • NGS platforms provide unprecedented sensitivity for biological discoveries.
  • The complexity and volume of RNA-Seq data necessitate advanced bioinformatics solutions.

Conclusions:

  • RNA-Seq is a powerful tool for understanding complex biological systems at the transcriptomic level.
  • Addressing the bioinformatics challenges is crucial for fully leveraging NGS capabilities.
  • Continued development of bioinformatics tools is essential for advancing RNA-Seq research.