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RNA-seq

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 Profiling

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...

Next-generation Sequencing

Next-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.

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Related Experiment Video

Updated: Jun 16, 2026

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

STAR Protocols question-and-answer series: RNA-seq.

Haymanti Bhanot¹

¹STAR Protocols, Cell Press.

|June 13, 2026

Summary

This summary is machine-generated.

RNA sequencing (RNA-seq) offers genome-wide gene expression insights but presents technical challenges. This guide provides expert advice from STAR Protocols authors to address common RNA-seq questions and enhance experimental success.

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

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AQRNA-seq for Quantifying Small RNAs

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Published on: February 2, 2024

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Last Updated: Jun 16, 2026

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

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

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Published on: November 7, 2025

AQRNA-seq for Quantifying Small RNAs

AQRNA-seq for Quantifying Small RNAs

Published on: February 2, 2024

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

RNA sequencing (RNA-seq) is a key technology for genome-wide gene expression analysis.
Recent advancements have improved RNA-seq accuracy and reliability.
Despite progress, RNA-seq experiments and data analysis remain complex and challenging for researchers.

Purpose of the Study:

To provide practical advice and address common questions related to RNA sequencing.
To share insights from experienced STAR Protocols authors and advisory board members.
To help researchers overcome challenges in RNA-seq experimental design and data analysis.

Main Methods:

Expert insights and recommendations from STAR Protocols authors and advisory board members.
Focus on addressing frequently asked questions in RNA sequencing.
Guidance on common challenges encountered in RNA-seq experiments and data analysis.

Main Results:

The article compiles expert advice to demystify RNA sequencing.
It offers solutions and best practices for common RNA-seq challenges.
The content aims to improve the accuracy and reliability of gene expression measurements.

Conclusions:

This resource serves as a valuable guide for researchers conducting RNA sequencing.
It empowers scientists to navigate the complexities of RNA-seq with greater confidence.
The shared expertise aims to enhance the overall quality and reproducibility of RNA-seq studies.