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Updated: May 18, 2026
10:19
Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project
Published on: April 8, 2017
Transcriptome analysis using next-generation sequencing
Kai-Oliver Mutz1, Alexandra Heilkenbrinker, Maren Lönne
1Leibniz Universität Hannover, Institute for Technical Chemistry, Callinstrasse 5, 30167 Hannover, Germany.
Current Opinion in Biotechnology
|October 2, 2012
Summary
Next-generation sequencing (NGS) offers advanced transcriptome analysis, surpassing microarray limitations. This technology provides extensive possibilities for exploring the modern RNA world in biology and medicine.
Area of Science:
- Molecular Biology
- Genomics
- Biotechnology
Background:
- Modern biological research demands rapid genome and transcriptome analysis for cellular studies.
- Microarray technology and RNA-Seq are current standard methods for transcript analysis.
- Microarrays have limitations in RNA quantity, transcript quantification, and sequence data.
Purpose of the Study:
- To describe next-generation sequencing (NGS) technology.
- To detail the impact of NGS on transcriptome analysis.
- To explain the potential of NGS in exploring the RNA world.
Main Methods:
- Review of next-generation sequencing (NGS) principles.
- Comparative analysis of NGS versus microarray technology.
- Discussion of transcriptome analysis using RNA-Seq.
Main Results:
- RNA-Seq offers superior capabilities over microarrays for transcript quantification and sequence information.
- NGS provides nearly unlimited possibilities for modern bioanalysis.
- NGS significantly advances the investigation of cellular state, physiology, and activity.
Conclusions:
- NGS is a powerful tool for comprehensive transcriptome analysis.
- RNA-Seq revolutionizes biological research by overcoming microarray limitations.
- NGS opens new avenues for understanding the complex RNA world.
Related Concept Videos
03:21RNA-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...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
03:00Next-generation Sequencing
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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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.
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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.
The technique helps...
Applications of ribosome profiling
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02:02Genomics
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
01:57Sanger Sequencing
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...