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Updated: Feb 25, 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

High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of

Brian S Gloss^1,2, Bethany Signal^1,2, Seth W Cheetham³

¹Garvan Institute of Medical Research, Sydney, Australia.

Scientific Reports

|July 29, 2017

Summary

Investigating mouse embryonic stem cell differentiation at 6-hour intervals reveals novel short-lived and cycling gene expression patterns. This high-resolution analysis captures dynamic coding and noncoding RNA changes crucial for understanding mammalian development.

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Area of Science:

Molecular Biology
Developmental Biology
Genomics

Background:

Transcriptional response studies often use long intervals, limiting insight into rapid cellular dynamics.
Previous research has largely overlooked the role of long noncoding RNAs (lncRNAs) in developmental transitions.

Purpose of the Study:

To investigate coding and noncoding RNA expression dynamics at high temporal resolution during mouse embryonic stem cell differentiation.
To uncover novel molecular processes, genome organization insights, and regulatory networks involved in differentiation.

Main Methods:

Utilized a 6-hourly time course for analyzing gene expression in differentiating mouse embryonic stem cells.
Evaluated both protein-coding and long noncoding RNA expression profiles.
Analyzed transcription factor network interactions and alternative splicing events.

Main Results:

Revealed a highly resolved differentiation cascade with distinct coding and noncoding transcriptional alterations.
Identified novel, short-lived, and cycling patterns of gene expression.
Dissected temporally ordered gene expression changes, including asynchronous transcription at bidirectional promoters.
Annotated known and novel regulatory lncRNAs and elucidated genome-wide gene co-expression patterns.

Conclusions:

High-resolution temporal analysis is essential for observing complex molecular events in mammalian differentiation.
The study provides new insights into the dynamic interplay of coding and noncoding RNAs, transcription factors, and genome organization during development.