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Updated: Jun 18, 2026

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

mRNA-sequencing whole transcriptome analysis of a single cell on the SOLiD system.

Kai Q Lao¹, Fuchou Tang, Catalin Barbacioru

¹Applied Biosystems, a division of Life Technologies Corporation, Genetic Analysis Business Unit, Foster City, California 94404, USA. kai.lao@lifetech.com

Journal of Biomolecular Techniques : JBT

|December 2, 2009

Summary

This study introduces a new single-cell gene expression assay using SOLiD sequencing, revealing higher transcriptome complexity and abnormal transposon activity in knockout oocytes. This method enhances gene detection and transcript variant identification.

Keywords:

Ago2 Dicer gene expression

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Last Updated: Jun 18, 2026

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

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Published on: January 10, 2019

Transcriptome Analysis of Single Cells

Transcriptome Analysis of Single Cells

Published on: April 25, 2011

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

Area of Science:

Genomics
Molecular Biology
Developmental Biology

Background:

Understanding gene expression at the single-cell level is crucial for developmental biology.
Existing methods have limitations in detecting the full spectrum of gene expression and transcript variants.

Purpose of the Study:

To develop and validate a novel sequencing-based assay for single-cell gene expression profiling.
To compare the sensitivity and scope of this new assay against traditional cDNA microarray techniques.
To investigate gene expression patterns in early embryonic blastomeres and in oocytes with disrupted RNA interference pathways.

Main Methods:

Development of a modified single-cell whole transcriptome amplification method.
Integration with the SOLiD (Sequencing by Oligonucleotide Ligation and Detection) next-generation sequencing system.
Application of the assay to four-cell stage blastomeres and Dicer/Ago2 knockout oocytes.

Main Results:

The assay demonstrated similar gene expression profiles in four-cell stage blastomeres, correlating with their developmental potential.
Compared to cDNA microarrays, the single-cell cDNA SOLiD sequencing assay detected thousands more genes.
Numerous novel transcript variants were identified, indicating greater transcriptome complexity than previously understood.
Significant upregulation of transposons was observed in Dicer/Ago2 knockout oocytes relative to wild-type controls.

Conclusions:

The developed assay provides unprecedented resolution for single-cell gene expression analysis.
The findings highlight the substantial complexity of the transcriptome and the importance of RNA interference pathways in maintaining genomic stability.
This technique offers a powerful tool for future research in developmental biology and gene regulation.