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Updated: Sep 22, 2025

Transcriptome Analysis of Single Cells
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Single-Cell Analysis of the Transcriptome and Epigenome.

Krystyna Mazan-Mamczarz1, Jisu Ha1, Supriyo De1,2

  • 1Laboratory of Genetics and Genomics, National Institute on Aging (NIA), Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA.

Methods in Molecular Biology (Clifton, N.J.)
|May 23, 2022
PubMed
Summary

Single-cell epigenomics reveals gene regulation insights for organ function. These advanced technologies dissect cellular diversity and genome organization, aiding scientific research.

Keywords:
EpigenomeMultiomicsSingle-cellTranscriptome

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Area of Science:

  • Molecular Biology
  • Genomics
  • Cell Biology

Background:

  • Epigenome regulation is crucial for maintaining organ function in both health and disease.
  • Understanding epigenomic alterations at a single-cell level offers high resolution into cellular heterogeneity and gene expression.

Purpose of the Study:

  • To summarize transformative single-cell epigenomic technologies.
  • To provide insights into gene regulation, transcription factor dynamics, and 3D genome organization.
  • To assist scientists in applying these methods to their research systems.

Main Methods:

  • Review of single-cell epigenomic technologies.
  • Historical perspective of methodological development.
  • Outline of procedures and emphasis on computational tools for data analysis.

Main Results:

  • Single-cell epigenomics provides unprecedented resolution into cellular diversity.
  • These methods deepen the understanding of fundamental gene regulation principles.
  • Analysis reveals insights into transcription factor dynamics and 3D genome organization.

Conclusions:

  • Single-cell epigenomic technologies are powerful tools for dissecting gene regulation.
  • These methods enhance comprehension of cellular heterogeneity and genome architecture.
  • The chapter aims to facilitate the application of these techniques in diverse biological systems.