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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.
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Related Experiment Video

Updated: May 19, 2026

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells

Multiplexed Single Cell mRNA Sequencing Analysis of Mouse Embryonic Cells

Published on: January 7, 2020

CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification.

Tamar Hashimshony¹, Florian Wagner, Noa Sher

¹Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.

|September 4, 2012

Summary

This summary is machine-generated.

We developed CEL-Seq, a novel method for single-cell RNA sequencing. This technique offers improved sensitivity and reproducibility for analyzing gene expression in individual cells, crucial for developmental biology research.

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Area of Science:

Molecular Biology
Genomics
Developmental Biology

Background:

High-throughput sequencing offers detailed gene expression analysis but is limited by low RNA input in single cells.
Existing methods face challenges in efficiently analyzing minute RNA quantities from individual cells.

Purpose of the Study:

To develop a novel method, CEL-Seq, for efficient and accurate single-cell RNA sequencing.
To overcome the limitations of small RNA starting amounts in high-throughput sequencing applications.

Main Methods:

CEL-Seq involves barcoding and pooling samples before linear amplification of mRNA via in vitro transcription.
This method utilizes a single round of in vitro transcription for RNA amplification.

Main Results:

CEL-Seq demonstrates superior reproducibility, linearity, and sensitivity compared to PCR-based amplification methods.
Single-cell resolution analysis of early C. elegans embryonic development revealed differential transcript distribution between sister cells at the two-cell stage.
Zygotic expression in somatic cell lineages showed enrichment for transcription factors.

Conclusions:

CEL-Seq provides robust transcriptome quantification, overcoming key limitations in single-cell RNA analysis.
The method is valuable for transcriptomic studies of complex tissues with diverse cell populations.
CEL-Seq enables detailed insights into early embryonic development at the single-cell level.