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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.
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Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

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Quantifying entire transcriptomes by aligned RNA-seq data.

Raffaele A Calogero¹, Francesca Zolezzi

¹Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, Torino, 10126, Italy, raffaele.calogero@unito.it.

Methods in Molecular Biology (Clifton, N.J.)

|January 12, 2015

Summary

This summary is machine-generated.

Massive Parallel Sequencing (MPS) offers advanced RNA analysis over microarrays. We detail bioinformatics pipelines for accurate miRNA and mRNA differential expression detection.

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Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Massive Parallel Sequencing (MPS) methods enhance knowledge of both messenger RNAs (mRNAs) and noncoding RNAs compared to conventional microarray technology.
RNA quality and library preparation are primary sources of variability in RNA sequencing (RNA-seq) data.
Bioinformatics pipelines for RNA-seq analysis are complex, with tool choices significantly impacting results.

Purpose of the Study:

To describe standardized bioinformatics pipelines for RNA-seq data analysis.
To focus on the detection of differential expression for both miRNA and mRNA.

Main Methods:

Utilizing Massive Parallel Sequencing (MPS) for comprehensive RNA analysis.
Implementing specific bioinformatics pipelines to process RNA-seq data.
Applying chosen analytical tools at each stage to minimize variability and ensure accurate results.

Main Results:

The described pipelines facilitate the detection of differential gene expression.
The methods are applicable to both miRNA and mRNA analysis.
Standardized pipelines help manage the complexity of RNA-seq data analysis.

Conclusions:

Bioinformatics pipeline selection is critical for reliable RNA-seq results.
The presented pipelines provide a robust framework for miRNA and mRNA differential expression analysis.
Standardization in RNA-seq analysis improves data comparability and knowledge discovery.