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Related Concept Videos

RNA-seq03:21

RNA-seq

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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...
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Updated: Aug 9, 2025

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
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Simultaneous Single-Cell Profiling of the Transcriptome and Accessible Chromatin Using SHARE-seq.

Samuel H Kim1,2, Georgi K Marinov3, S Tansu Bagdatli3

  • 1Cancer Biology Program, School of Medicine, Stanford University, Stanford, CA, USA. samhkim@stanford.edu.

Methods in Molecular Biology (Clifton, N.J.)
|February 22, 2023
PubMed
Summary

Single-cell multiomics analyzes multiple cellular features simultaneously. SHARE-seq enables joint measurement of chromatin accessibility and transcriptome for deeper biological insights.

Keywords:
Chromatin accessibilityMultiomicsSplit–poolTranscriptomicsscATAC-seqscRNA-seq

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Area of Science:

  • Single-cell biology
  • Genomics
  • Molecular biology

Background:

  • Single-cell transcriptomic and epigenomic analyses have revolutionized biological process understanding.
  • Advancements focus on enhancing sensitivity and throughput for deeper cellular insights.
  • The next frontier involves multiomic methods for analyzing multiple cellular features concurrently.

Purpose of the Study:

  • To describe SHARE-seq (Simultaneous high-throughput ATAC, and RNA expression with sequencing) for multiomic single-cell analysis.
  • To detail the experimental and analytical considerations for optimizing SHARE-seq results.

Main Methods:

  • SHARE-seq allows simultaneous measurement of chromatin accessibility (ATAC) and transcriptome (RNA) in individual cells.
  • This method integrates epigenomic and transcriptomic profiling at the single-cell level.
  • The chapter discusses both experimental protocols and analytical strategies for SHARE-seq.

Main Results:

  • SHARE-seq provides a powerful approach for multiomic single-cell analysis.
  • Simultaneous measurement of chromatin accessibility and RNA expression offers comprehensive cellular state information.
  • The method facilitates deeper biological insights by linking regulatory elements to gene expression.

Conclusions:

  • SHARE-seq represents a significant advancement in single-cell multiomics.
  • The described methods and considerations enable robust joint profiling of chromatin accessibility and transcriptomes.
  • This approach is crucial for advancing our understanding of cellular heterogeneity and regulatory mechanisms.