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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...

Sanger Sequencing

Sanger 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...

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: Apr 15, 2026

Targeted DNA Methylation Analysis by Next-generation Sequencing

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

RNA Sequencing and Analysis.

Kimberly R Kukurba¹, Stephen B Montgomery²

¹Department of Pathology, Stanford University School of Medicine, Stanford, California 94305; Department of Genetics, Stanford University School of Medicine, Stanford, California 94305;

Cold Spring Harbor Protocols

|April 15, 2015

Summary

This summary is machine-generated.

RNA sequencing (RNA-Seq) offers high-resolution transcriptome analysis, surpassing older methods. This powerful technique quantifies gene expression and reveals novel transcripts and RNA variants.

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Last Updated: Apr 15, 2026

Targeted DNA Methylation Analysis by Next-generation Sequencing

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Published on: February 24, 2015

3' End Sequencing Library Preparation with A-seq2

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

Area of Science:

Molecular Biology
Genomics
Transcriptomics

Background:

RNA sequencing (RNA-Seq) is a high-throughput sequencing technology.
It provides deeper insights into the cell's transcriptome compared to Sanger sequencing and microarrays.
RNA-Seq offers higher coverage and resolution for dynamic transcriptome analysis.

Purpose of the Study:

To introduce RNA sequencing (RNA-Seq) methods.
To discuss the applications, experimental design, and technical challenges of RNA-Seq.
To highlight RNA-Seq's ability to investigate various RNA populations.

Main Methods:

Utilizes high-throughput sequencing capabilities.
Covers sample preparation, library construction, and data analysis.
Applicable to polyadenylated messenger RNA (mRNA), total RNA, pre-mRNA, and noncoding RNA (microRNA, long ncRNA).

Main Results:

Enables quantification of gene expression with high resolution.
Facilitates discovery of novel transcripts.
Identifies alternatively spliced genes and detects allele-specific expression.

Conclusions:

RNA-Seq advances the elucidation of transcriptional functional complexity.
Recent workflow improvements enhance RNA-Seq capabilities.
RNA-Seq is a versatile tool for comprehensive transcriptome analysis.