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Related Concept Videos

RNA-seq03:21

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 Profiling02:24

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...

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Related Experiment Video

Updated: May 15, 2026

VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma
15:07

VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma

Published on: December 28, 2015

High-throughput RNA sequencing in B-cell lymphomas.

Wenming Xiao1, Bao Tran, Louis M Staudt

  • 1Bioinformatics and Molecular Analysis Section, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD, USA.

Methods in Molecular Biology (Clifton, N.J.)
|January 9, 2013
PubMed
Summary
This summary is machine-generated.

High-throughput mRNA sequencing (RNA-seq) provides unbiased analysis of tumor transcription and mutation status. This method uses Illumina sequencing and bioinformatic pipelines for comprehensive transcriptome analysis and mutation discovery.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • High-throughput sequencing technologies enable comprehensive analysis of biological systems.
  • Tumor molecular profiling is crucial for understanding cancer biology and developing targeted therapies.
  • RNA sequencing (RNA-seq) offers a powerful approach for transcriptome-wide analysis.

Purpose of the Study:

  • To describe a protocol for performing RNA sequencing (RNA-seq) using the Illumina platform.
  • To present essential sequencing data quality metrics for RNA-seq experiments.
  • To outline a bioinformatic pipeline for RNA-seq data analysis, including alignment, gene expression, and mutation discovery.

Main Methods:

  • High-throughput mRNA sequencing (RNA-seq) utilizing massively parallel sequencing.
  • Complementary DNA (cDNA) generation and immobilization of amplified DNA fragments.
  • Sequence alignment to a reference genome or transcript database.
  • Bioinformatic pipeline for digital gene expression and mutation discovery.

Main Results:

  • Generation of short sequence reads from millions of amplified DNA fragments.
  • Alignment of resulting sequences to create a comprehensive transcriptome description.
  • Successful application of a bioinformatic pipeline for downstream analysis.

Conclusions:

  • RNA-seq is a versatile method for unbiased analysis of tumor transcription and mutation status.
  • The described protocol and bioinformatic pipeline facilitate robust RNA-seq data analysis.
  • This approach aids in comprehensive characterization of the tumor transcriptome.