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Related Concept Videos

RNA-seq03:21

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Related Experiment Video

Updated: Apr 30, 2026

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

Canan Külahoglu1, Andrea Bräutigam

  • 1iGrad Plant, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany.

Methods in Molecular Biology (Clifton, N.J.)
|May 6, 2014
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Summary

RNA sequencing (RNA-seq) offers accurate gene expression quantification and detailed transcript information. This workflow guides researchers through RNA-seq experiments, from planning to data analysis.

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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • RNA sequencing (RNA-seq) is the preferred technology for quantifying gene expression.
  • It provides accurate measurements of diurnal gene expression changes, gene discovery, and splice variants.
  • RNA-seq offers absolute expression values and sequence information, surpassing microarrays and qRT-PCR.

Purpose of the Study:

  • To present a comprehensive workflow for RNA sequencing experiments.
  • To guide researchers from experimental planning to biological data extraction.
  • To make RNA-seq accessible to researchers with limited bioinformatics expertise.

Main Methods:

  • Utilizing standard analysis packages like Bowtie2, TopHat, and Cufflinks.
  • Implementing a workflow for RNA-seq experimental planning.
  • Focusing on biological data extraction from RNA-seq experiments.

Main Results:

  • RNA-seq experiments provide sequence information and absolute expression values.
  • The technology allows for quantification of diurnal gene expression changes and splice variants.
  • A standard analysis framework has emerged for RNA-seq data.

Conclusions:

  • RNA-seq is a powerful tool for gene expression analysis.
  • A standardized workflow enhances the accessibility and application of RNA-seq.
  • Careful assessment of RNA integrity and DNA contamination is crucial for reliable results.