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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...
Next-generation Sequencing03:00

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.
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
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The technique helps...
RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific primer.
Since the...

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Related Experiment Video

Updated: May 23, 2026

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing
10:00

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

Published on: May 23, 2018

Highly multiplexed and strand-specific single-cell RNA 5' end sequencing.

Saiful Islam1, Una Kjällquist, Annalena Moliner

  • 1Laboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.

Nature Protocols
|April 7, 2012
PubMed
Summary
This summary is machine-generated.

This study introduces a cost-effective protocol for single-cell gene expression analysis using mRNA 5' end sequencing. The method enables large-scale quantitative analysis and transcription start site characterization in complex tissues.

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Last Updated: May 23, 2026

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Published on: May 23, 2018

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Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
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Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

Area of Science:

  • Molecular Biology
  • Genomics
  • Biotechnology

Background:

  • Single-cell gene expression analysis is crucial for understanding complex biological systems like cancer and stem cell niches.
  • Existing methods can be time-consuming and expensive for large-scale studies.

Purpose of the Study:

  • To present a detailed protocol for quantitative gene expression analysis in single cells.
  • To enable cost-effective and time-efficient large-scale single-cell studies.

Main Methods:

  • A protocol for quantitative gene expression analysis using mRNA 5' end sequencing of 96 single cells.
  • Involves cell lysis, cDNA conversion with template-switching for barcoding, pooling, and 5' end sequencing preparation.
  • Includes fragmentation, adapter ligation, and PCR amplification for sequencing.

Main Results:

  • The early bar-coding strategy significantly reduces cost and time for gene expression analysis.
  • The method is suitable for large-scale quantitative analysis and transcription start site characterization.
  • The protocol is unsuitable for detecting alternatively spliced transcripts.

Conclusions:

  • This protocol offers a powerful, efficient, and scalable approach for single-cell gene expression studies.
  • It facilitates deeper insights into complex tissues by enabling high-throughput analysis.
  • Further optimization may be needed for applications requiring alternative splicing detection.